npm - @qe-libs/qeviz - Versions diffs - 0.5.4 → 0.5.6 - Mend

@qe-libs/qeviz 0.5.4 → 0.5.6

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1	- {"version":3,"file":"qeviz.umd.js","sources":["../src/types/DataFrame.ts","../src/objects/Model.ts","../src/utils/debug.ts","../src/elements/QEVisual.ts","../src/objects/Color.ts","../src/objects/Transform.ts","../src/utils/Tools.ts","../src/types/EventBus.ts","../src/objects/Layers.ts","../src/objects/PlottedObject.ts","../src/objects/Extremes.ts","../src/objects/AxisPoint.ts","../src/objects/Graph.ts","../src/elements/DrawableElement.ts","../src/objects/polyfit.ts","../src/objects/Trajectory.ts","../src/objects/Edges.ts","../src/elements/Drawable.ts","../src/objects/Sizing.ts","../src/elements/QELine.ts","../src/elements/QEPoint.ts","../src/elements/QETrajectory.ts","../src/elements/QELayer.ts","../src/elements/QELabel.ts","../src/elements/QEChildElements.ts","../src/elements/QEGraph.ts","../src/index.ts"],"sourcesContent":["export interface DataFrameRowInterface {\n get names(): string[];\n get rowName(): string \| undefined;\n get types(): DataFrameColumnType[];\n get parent(): DataFrame \| undefined;\n}\n\nexport class DataFrameRow extends Array<any> implements DataFrameRowInterface {\n #rowNumber?: number;\n #rowName?: string;\n #names: string[];\n #parent?: DataFrame;\n #classes: string[] \| undefined;\n\n constructor(names: string[], values: any[], rowName?: string, parent?: DataFrame, index?: number) {\n super(...values);\n this.#names = names;\n this.#rowName = rowName;\n this.#parent = parent;\n this.#classes = parent?.classes;\n this.#rowNumber = index;\n }\n\n get parent(): DataFrame \| undefined {\n return this.#parent;\n }\n get names(): string[] {\n return this.#names;\n }\n get rowName(): string \| undefined {\n return this.#rowName;\n }\n get types(): DataFrameColumnType[] {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this row.\");\n return this.#parent.types;\n }\n get classes(): string[] \| undefined {\n return this.#classes;\n }\n\n get rowNumber(): number \| undefined {\n return this.#rowNumber;\n }\n\n col(wh: string \| number): DataFrameColumn \| undefined {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this row.\");\n return this.#parent.col(wh);\n }\n cols(...wh: (string \| number)[]): DataFrame {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this row.\");\n return this.#parent.cols(...wh);\n }\n\n filter(predicate: (value: any, index: number, array: any[]) => boolean): any {\n console.error(\"DataFrameRow does not currently support filtering.\");\n // This method is intentionally left empty to prevent filtering on DataFrameRow.\n }\n}\n\nexport enum DataFrameColumnType {\n Character = 'character',\n Double = 'double',\n Logical = 'logical',\n Integer = 'integer'\n}\n\nexport interface DataFrameColumnInterface {\n get name(): string;\n get type(): DataFrameColumnType;\n get rowNames(): string[] \| undefined;\n}\n\nexport class DataFrameColumn extends Array<any> implements DataFrameColumnInterface {\n #name: string;\n #type: DataFrameColumnType;\n #rowNames: string[] \| undefined;\n #parent?: DataFrame;\n\n constructor(name: string, column: any, rowNames?: string[], parent?: DataFrame) {\n super(column.length);\n for (let i = 0; i < column.length; i++) {\n this[i] = column[i];\n }\n this.#name = name;\n\n if (column.type !== undefined) {\n this.#type = column.type;\n }\n // If undefined, infer type\n else {\n if (column.every((v: any) => typeof v === 'string' \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Character;\n }\n else if (column.every((v: any) => Number.isInteger(v) \|\| v === null \|\| v === undefined)) {\n // If only 1 and 0, consider as logical\n if (column.every((v: any) => v === 0 \|\| v === 1 \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Logical;\n }\n else {\n this.#type = DataFrameColumnType.Integer;\n }\n }\n else if (column.every((v: any) => typeof v === 'number' \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Double;\n }\n else if (column.every((v: any) => typeof v === 'boolean' \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Logical;\n }\n\n // Default to character if mixed types\n else {\n this.#type = DataFrameColumnType.Character;\n }\n }\n this.#parent = parent;\n\n if (rowNames && rowNames.length !== this.length) {\n throw new Error(\"Row names length must match the number of rows in the DataFrameColumn.\");\n }\n if (rowNames && rowNames.length > 0) {\n this.#rowNames = rowNames;\n }\n else {\n this.#rowNames = undefined;\n }\n }\n\n get name(): string {\n return this.#name;\n }\n get type(): DataFrameColumnType {\n return this.#type;\n }\n get rowNames(): string[] \| undefined {\n return this.#rowNames;\n }\n\n\n row(wh: string \| number): DataFrameRow \| undefined {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this column.\");\n return this.#parent.row(wh);\n }\n rows(...wh: (string \| number)[]): DataFrameRow[] {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this column.\");\n return this.#parent.rows(...wh);\n }\n}\n\nexport interface DataFrameInterface {\n // Methods\n getColumnByName(name: string): DataFrameColumn \| undefined;\n getRowByIndex(index: number): any[];\n getRowByName(name: string): any[] \| undefined;\n row(wh: string \| number): any[] \| undefined;\n type(wh: string \| number): DataFrameColumnType \| undefined;\n\n get names(): string[];\n get rowNames(): string[] \| undefined;\n get types(): string[];\n\n // Properties\n nrow: number;\n ncol: number;\n}\n\nexport class DataFrame extends Array<DataFrameColumn> implements DataFrameInterface {\n #names: string[];\n #rowNames: string[] \| undefined;\n #classes: string[] \| undefined;\n\n constructor(names?: string[], colValues?: any[], rowNames?: string[], classes?: string[]) {\n if (!names \|\| !colValues) {\n colValues = [];\n names = [];\n }\n if (colValues.map( (c: any) => c.length ).every( (l: any) => l === names.length )) {\n // Transpose if needed\n const transposed: any[] = [];\n for (let i = 0; i < names.length; i++) {\n const col: any[] = [];\n for (let j = 0; j < colValues.length; j++) {\n col.push(colValues[j][i]);\n }\n transposed.push(col);\n }\n colValues = transposed;\n }\n\n super(colValues.length);\n\n colValues.forEach((col, index) => {\n if (col instanceof DataFrameColumn) {\n // If col is already a DataFrameColumn, just assign it\n this[index] = col as DataFrameColumn;\n } else {\n // Otherwise, create a new DataFrameColumn\n this[index] = new DataFrameColumn(names[index], col, rowNames, this) as DataFrameColumn;\n }\n });\n this.#names = names;\n if (rowNames && this[0] && rowNames.length !== this[0].length) {\n throw new Error(\"Row names length must match the number of rows in the DataFrame.\");\n }\n if (rowNames && rowNames.length > 0) {\n this.#rowNames = rowNames;\n }\n if (classes && classes.length !== this.length) {\n throw new Error(\"Classes length must match the number of columns in the DataFrame.\");\n }\n if (classes && classes.length > 0) {\n this.#classes = classes;\n }\n }\n\n get classes(): string[] \| undefined {\n return this.#classes;\n }\n\n getColumnByName(name: string): DataFrameColumn \| undefined {\n const idx = this.#names.indexOf(name);\n return idx >= 0 ? this[idx] : undefined;\n }\n getRowByIndex(index: number): DataFrameRow {\n if (this && this.length === 0) {\n console.warn(\"DataFrame is empty, cannot get row by index\", index);\n return new DataFrameRow(this.#names, [], undefined, this, index);\n }\n const result_vals: any[] = [];\n for (let col of this) {\n let v = col[index];\n result_vals.push(v);\n }\n return new DataFrameRow(this.#names, result_vals, this.#rowNames ? this.#rowNames[index] : undefined, this, index);\n }\n getRowByName(name: string): DataFrameRow \| undefined {\n if (!this.#rowNames) return undefined;\n\n const index = this.#rowNames.indexOf(name);\n if (index === -1) return undefined;\n return this.getRowByIndex(index);\n }\n\n get types(): DataFrameColumnType[] {\n return this.map(col => col.type);\n }\n type(wh: string \| number): DataFrameColumnType \| undefined {\n if (typeof wh === 'number') {\n return this[wh]?.type;\n }\n else if (typeof wh === 'string') {\n const col = this.getColumnByName(wh);\n return col ? col.type : undefined;\n }\n return undefined;\n }\n\n // row(wh: string \| number): DataFrameRow \| undefined {\n\n row(wh: string \| number): DataFrameRow \| undefined {\n if (typeof wh === 'number') {\n return this.getRowByIndex(wh);\n }\n else if (typeof wh === 'string') {\n return this.getRowByName(wh);\n }\n return undefined;\n }\n // rows(...wh: (string \| number)[]): DataFrame {\n rows(...wh: (string \| number)[]): DataFrameRow[] {\n // Support: rows(\"Data\"), rows(\"Data\", \"Design\"), rows([\"Data\", \"Design\"]), rows()\n let\n selectors: (string \| number)[],\n selectedRows: DataFrameRow[] = [],\n selectedRowNames: string[] \| undefined = []\n ;\n\n // No arguments: return all rows\n if (wh.length === 0) {\n if (!this[0] \|\| this.length === 0) {\n return [];\n }\n const numRows = this[0].length;\n selectedRows = Array.from({ length: numRows }, (_, i) => this.getRowByIndex(i));\n selectedRowNames = this.#rowNames;\n }\n\n else {\n // Single array argument\n if (wh.length === 1 && Array.isArray(wh[0])) {\n selectors = wh[0] as (string \| number)[];\n }\n else {\n // Rest arguments\n selectors = wh;\n }\n\n selectedRows = selectors.map((item, i: number) => {\n let r = this.row(item);\n if (this.#rowNames && r) {\n selectedRowNames?.push(this.#rowNames[i]);\n }\n return r;\n }).filter((row): row is DataFrameRow => row !== undefined);\n }\n\n // Build columns from selected rows\n // const\n // colNames = this.#names,\n // columns = colNames.map((name, colIdx) => selectedRows.map(row => row[colIdx])),\n // colObjs = colNames.map((name, idx) => new DataFrameColumn(name, { values: columns[idx], type: this[idx].type }, selectedRowNames, this))\n // ;\n\n // return new DataFrame(\n // colNames,\n // colObjs,\n // selectedRowNames\n // );\n\n return selectedRows;\n }\n\n col(wh: string \| number): DataFrameColumn \| undefined {\n if (typeof wh === 'number') {\n return this[wh];\n } else if (typeof wh === 'string') {\n return this.getColumnByName(wh);\n }\n return undefined;\n }\n\n cols(...wh: (string \| number)[]): DataFrame {\n // Support: cols(\"Data\"), cols(\"Data\", \"Design\"), cols([\"Data\", \"Design\"]), cols()\n let\n selectors: (string \| number)[],\n selectedCols: DataFrameColumn[],\n selectedNames: string[] = []\n ;\n\n // No arguments: return all columns\n if (wh.length === 0) {\n selectedCols = this.slice();\n selectedNames = this.#names;\n }\n else {\n // Single array argument\n if (wh.length === 1 && Array.isArray(wh[0])) {\n selectors = wh[0] as (string \| number)[];\n }\n // Rest arguments\n else {\n selectors = wh;\n }\n\n selectedCols = selectors.map((item) => this.col(item)).filter((col): col is DataFrameColumn => col !== undefined);\n selectedNames = selectedCols.map(col => col.name);\n }\n\n return new DataFrame(selectedNames, selectedCols, this.#rowNames);\n }\n\n subset(rows?: (string \| number)[], cols?: (string \| number)[]): DataFrame {\n const selectedCols: DataFrameColumn[] = (cols && cols.length > 0)\n ? this.cols(...cols)\n : this.slice();\n\n return new DataFrame(\n selectedCols.map(col => col.name),\n selectedCols.map(col => col.values),\n this.#rowNames\n );\n }\n\n get names(): string[] {\n return this.#names;\n }\n\n get rowNames(): string[] \| undefined {\n return this.#rowNames;\n }\n\n get nrow(): number {\n return this[0] ? this[0].length : 0;\n }\n\n get ncol(): number {\n return this.length;\n }\n}\n","import { DataFrame, DataFrameRow } from \"../types/DataFrame\";\n\n/** Internal key union for Model.setByKey /\nexport type ModelKey =\n \| \"updated\" \| \"points\" \| \"nodes\" \| \"edges\"\n \| \"dimensions\" \| \"confidence\" \| \"outlier\" \| \"groups\" \| \"trajectories\" \| \"networks\" \| \"pointsets\";\n\n/* Internal shape of the Model class — used by setByKey /\nexport interface ModelSpec {\n updated?: number;\n points: DataFrame;\n nodes: DataFrame;\n edges: DataFrame;\n dimensions: (string \| number)[];\n confidence?: DataFrame;\n outlier?: DataFrame;\n groups?: DataFrame;\n trajectories?: DataFrame;\n networks?: DataFrame;\n pointsets?: DataFrame;\n}\n\nexport class Model implements ModelSpec {\n private _updated: number \| undefined;\n private _points: DataFrame;\n private _nodes: DataFrame;\n private _edges: DataFrame;\n private _dimensions: (string \| number)[];\n private _params: any;\n private _confidence: DataFrame \| undefined;\n private _outlier: DataFrame \| undefined;\n private _groups: DataFrame \| undefined;\n private _trajectories: DataFrame \| undefined;\n private _networks: DataFrame \| undefined;\n private _pointsets: DataFrame \| undefined;\n\n // Resolved column names — set by QEVisual.setModelData() via auto-detection\n // or caller-supplied overrides. Renderers read these instead of hardcoding.\n /* ID column in the points and edges frames /\n unit_id_col: string = 'id';\n /* ID column in the nodes frame /\n node_id_col: string = 'id';\n /* Group column in the points frame (null = no grouping) /\n group_col: string \| null = null;\n /* Directed network mode — true renders arrowheads; false (default) undirected /\n directed: boolean = false;\n /* Group palette override (ModelData.palette); empty = qeviz default. /\n palette: string[] = [];\n\n constructor(o: Partial<ModelSpec> = {}) {\n this._points = o.points ?? new DataFrame();\n this._nodes = o.nodes ?? new DataFrame();\n this._edges = o.edges ?? new DataFrame();\n this._dimensions = o.dimensions ?? [];\n this._confidence = undefined;\n this._outlier = undefined;\n this._groups = undefined;\n }\n\n get updated(): number \| undefined { return this._updated; }\n set updated(v: number \| undefined) { this._updated = v; }\n\n get points(): DataFrame { return this._points; }\n set points(v: DataFrame) { this._points = v; }\n\n get nodes(): DataFrame { return this._nodes; }\n set nodes(v: DataFrame) { this._nodes = v; }\n\n get edges(): DataFrame { return this._edges; }\n set edges(v: DataFrame) { this._edges = v; }\n\n get confidence(): DataFrame \| undefined { return this._confidence; }\n set confidence(v: DataFrame \| undefined) { this._confidence = v; }\n\n get outlier(): DataFrame \| undefined { return this._outlier; }\n set outlier(v: DataFrame \| undefined) { this._outlier = v; }\n\n get groups(): DataFrame \| undefined { return this._groups; }\n set groups(v: DataFrame \| undefined) { this._groups = v; }\n\n get trajectories(): DataFrame \| undefined { return this._trajectories; }\n set trajectories(v: DataFrame \| undefined) { this._trajectories = v; }\n\n /* Explicit networks (one row per named layer, edge columns as in `edges`),\n * drawn by <qe-edges network=\"name\">. /\n get networks(): DataFrame \| undefined { return this._networks; }\n set networks(v: DataFrame \| undefined) { this._networks = v; }\n\n /* Explicit point sets (rows: set, id, x, y, group?, color?, shape?, label?),\n * drawn by <qe-points set=\"name\">. /\n get pointsets(): DataFrame \| undefined { return this._pointsets; }\n set pointsets(v: DataFrame \| undefined) { this._pointsets = v; }\n\n get dimensions(): (string \| number)[] { return this._dimensions; }\n set dimensions(v: (string \| number)[]) { this._dimensions = v; }\n\n get params(): any { return this._params; }\n set params(v: any) { this._params = v; }\n\n point(id: string): DataFrameRow \| undefined {\n return this._points.row(id);\n }\n\n setByKey<K extends keyof ModelSpec>(key: K, value: ModelSpec[K]): void {\n (this as any)[key] = value;\n }\n}\n\nexport default Model;\n","export const DEBUG: boolean = (globalThis as any).__QEVIZ_DEBUG__ === true;\n\nexport function dbg(...args: any[]): void {\n if (DEBUG) console.log(...args);\n}\n","import { Label, Point } from \"../objects/PlottedObject\";\nimport { Edge } from \"../objects/Edges\";\nimport Model, { ModelKey } from \"../objects/Model\";\nimport { DataFrame } from \"../types/DataFrame.js\";\nimport { dbg } from \"../utils/debug.js\";\nimport { ModelData } from \"../types/ModelData.js\";\n\nexport const vizENA = {\n get: (n: number) => {\n const elements = [...(document as any).querySelectorAll(\"qe-graph\")];\n if (typeof n === \"number\" && n >= 0) {\n return elements[n];\n }\n return elements;\n },\n}\n\nexport class QEVisualElement extends HTMLElement {\n static tagName = 'qe-visual';\n\n static get observedAttributes() {\n return ['updated'];\n }\n\n static styles = `\n :host { display: block; width: 100%; }\n :host(.hidden) { display: none !important; }\n / The output wrapper and the slotted graph fill the host so the plot\n stretches to its container instead of collapsing to intrinsic size. /\n div { display: block; width: 100%; height: 100%; }\n ::slotted(qe-graph) { display: block; width: 100%; height: 100%; }\n `;\n\n protected _outputElement!: HTMLElement;\n protected _isVisible: boolean = true;\n protected output: string = '';\n\n private _model: Model;\n /* Public accessor so ena-graph (and external code) can read the model. /\n get model(): Model {\n return this._model;\n }\n\n private _updated: string = '';\n get updated(): string {\n return this._updated;\n }\n set updated(val: string) {\n this._updated = val;\n this.setAttribute('updated', val);\n // Notify via CustomEvent instead of directly coupling to StateManager.\n // RQEVisualElement (and any other arbor consumer) listens for this and\n // forwards to globalStateManager.\n this.dispatchEvent(new CustomEvent('model-updated', {\n detail: this._model,\n bubbles: true,\n composed: true,\n }));\n }\n\n private _active_points: Point[] = [];\n private _points: Map<any, Point> = new Map();\n get points(): Map<any, Point> {\n return this._points;\n }\n set points(pts: Map<any, Point> \| Point[]) {\n this._points.clear();\n if (pts instanceof Map) {\n this._points = pts;\n } else if (Array.isArray(pts)) {\n pts.forEach(p => this._points.set(p.ID, p));\n }\n }\n get active_points(): Point[] {\n return Array.from(this._active_points.values());\n }\n\n private _edges: Map<any, Edge> = new Map();\n get edges(): Map<any, Edge> {\n return this._edges;\n }\n set edges(edges: Map<any, Edge> \| Edge[]) {\n this._edges.clear();\n if (edges instanceof Map) {\n this._edges = edges;\n } else if (Array.isArray(edges)) {\n this._edges = new Map();\n edges.forEach(e => this._edges.set(e.ID, e));\n }\n }\n\n private _labels: Map<any, Label> = new Map();\n get labels(): Map<any, Label> {\n return this._labels;\n }\n\n constructor() {\n super();\n\n this._model = new Model();\n\n const shadow = this.attachShadow({ mode: 'open' });\n\n const style = document.createElement('style');\n style.textContent = QEVisualElement.styles;\n shadow.appendChild(style);\n\n this._outputElement = document.createElement('div');\n shadow.appendChild(this._outputElement);\n }\n\n connectedCallback(): void {\n dbg(\"QEVisualElement connected\");\n this.render();\n }\n\n /\n Accept pre-fetched ENA model data and update the visualization.\n * Call this directly when data is available from any source —\n * rENA R package, Python package, or static JSON.\n /\n setModelData(data: ModelData): void {\n const frameKeys: ModelKey[] = ['nodes', 'edges', 'points', 'groups', 'confidence', 'outlier', 'trajectories', 'networks', 'pointsets'] as ModelKey[];\n\n // ── Step 1: ingest all frames into DataFrames ──────────────────────────\n frameKeys.forEach((name) => {\n const raw = (data as any)[name];\n if (!raw?.data?.length) return;\n\n const\n rows: any[] = raw.data,\n types: any = raw.types \|\| {},\n colNames: string[] = Object.keys(rows[0]),\n colValues: any[][] = rows.map((v: any) => Object.values(v)),\n classes: string[] = colNames.map(col => (types[col] ?? 'character') as string);\n\n // Determine which column is the row-identifier (stored as DataFrame.rowName).\n // The caller can supply overrides; otherwise we auto-detect.\n let idCol: string \| undefined;\n if (name === 'networks') {\n idCol = 'name'; // one row per explicit network layer\n } else if (name === 'pointsets') {\n idCol = 'id'; // point id within its set\n } else if (name === 'nodes') {\n idCol = data.node_id_col\n ?? colNames.find(c => (types[c] ?? 'character') === 'character');\n } else if (name === 'edges' \|\| name === 'points' \|\| name === 'trajectories') {\n idCol = data.id_col\n ?? colNames.find(c => (types[c] ?? 'character') === 'character');\n } else {\n // groups / confidence / outlier: first character column is the group id\n idCol = data.group_col\n ?? colNames.find(c => (types[c] ?? 'character') === 'character');\n }\n\n const removalCol = idCol ? colNames.indexOf(idCol) : 0;\n const rowNames = colValues.map((v: any) => String(v[removalCol]));\n this._model.setByKey(name, new DataFrame(colNames, colValues, rowNames, classes));\n });\n\n // ── Step 2: ingest scalar fields ─────────────────────────────────────\n if (data.updated !== undefined) this._model.setByKey('updated', data.updated);\n if (data.directed !== undefined) this._model.directed = data.directed;\n if (Array.isArray((data as any).palette)) this._model.palette = (data as any).palette.map(String);\n\n // ── Step 3: resolve and store column names on the model ───────────────\n // These are read by QEGraph at render time instead of hardcoded strings.\n\n // node id col — first character column in nodes, or override\n const nodesDF = this._model.nodes;\n this._model.node_id_col = data.node_id_col\n ?? nodesDF?.names?.find(n => nodesDF.col(n)?.type === 'character')\n ?? 'id';\n\n // unit id col — first character column in points, or override\n const pointsDF = this._model.points;\n this._model.unit_id_col = data.id_col\n ?? pointsDF?.names?.find(n => pointsDF.col(n)?.type === 'character')\n ?? 'id';\n\n // group col — caller override, or first non-unit-id character col in points\n const unitId = this._model.unit_id_col;\n this._model.group_col = data.group_col\n ?? pointsDF?.names?.find(n => n !== unitId && pointsDF.col(n)?.type === 'character')\n ?? null;\n\n // ── Step 4: auto-detect dimension (x/y) columns from nodes ───────────\n // Numeric columns that aren't the node id. Caller can override via\n // x_col / y_col but those are passed in ModelData for the renderer to use\n // directly; here we just set model.dimensions as the default.\n if (nodesDF?.names?.length) {\n const nodeId = this._model.node_id_col;\n const xColOvr = data.x_col;\n const yColOvr = data.y_col;\n if (xColOvr && yColOvr) {\n this._model.dimensions = [xColOvr, yColOvr];\n } else {\n const numCols = nodesDF.names.filter(n => {\n if (n === nodeId) return false;\n const col = nodesDF.col(n);\n return col && col.type !== 'character' && col.type !== 'logical';\n });\n if (numCols.length >= 2) {\n this._model.dimensions = [xColOvr ?? numCols[0], yColOvr ?? numCols[1]];\n }\n }\n }\n\n this.updated = this._model.updated !== undefined ? String(this._model.updated) : String(Date.now());\n dbg(\"Model updated via setModelData:\", this.updated);\n this.render();\n }\n\n /\n Base implementation is a no-op. Subclasses (e.g. RQEVisualElement) override\n * this to fetch data from a backend and call setModelData().\n /\n async calculate(): Promise<void> {}\n\n render(): void {\n if (!this._isVisible) {\n this.classList.add('hidden');\n } else {\n this.classList.remove('hidden');\n }\n\n if (this._model?.updated !== undefined && this._model.updated !== null) {\n this._outputElement.innerHTML = `${this.output}<slot></slot>`;\n } else {\n this._outputElement.innerHTML = \"Define the model on the left.\";\n }\n }\n}\ncustomElements.define(QEVisualElement.tagName, QEVisualElement);\n\nexport default QEVisualElement;\n","export class Color {\n base: string;\n\n constructor(base: Color \| string) {\n this.base = typeof base === \"string\" ? base : base.base;\n\n // Return a Proxy to allow 0-based indexing for r, g, b\n return new Proxy(this, {\n get(target, prop) {\n if (typeof prop === \"string\" && /^[0-2]$/.test(prop)) {\n const { r, g, b } = Color.parseColor(target.base);\n return [r, g, b][Number(prop)];\n }\n return (target as any)[prop];\n }\n });\n }\n\n toString(): string {\n return this.base;\n }\n\n setBase(base: string): void {\n this.base = base;\n }\n\n static parseColor(color: string): { r: number; g: number; b: number } {\n // Parse hex color (e.g., \"#RRGGBB\")\n if (color.startsWith(\"#\")) {\n const bigint = parseInt(color.slice(1), 16);\n return {\n r: (bigint >> 16) & 255,\n g: (bigint >> 8) & 255,\n b: bigint & 255,\n };\n }\n throw new Error(\"Unsupported color format\");\n }\n\n static rgb(r: number, g: number, b: number): string {\n return `rgb(${r}, ${g}, ${b})`;\n }\n}\n\nexport class WeightedColor extends Color {\n weight: number;\n /* Optional alpha; defaults to `weight` (saturation and alpha together). /\n alpha: number \| undefined;\n\n constructor(base: Color \| string, weight: number, alpha?: number) {\n super(base);\n this.weight = weight;\n this.alpha = alpha;\n }\n\n // Parse hex → HSV (h in [0, 360), s/v in [0, 1]).\n static toHSV(hex: string): { h: number; s: number; v: number } {\n const { r, g, b } = Color.parseColor(hex);\n const rn = r / 255, gn = g / 255, bn = b / 255;\n const max = Math.max(rn, gn, bn), min = Math.min(rn, gn, bn);\n const d = max - min;\n const v = max;\n const s = max === 0 ? 0 : d / max;\n let h = 0;\n if (d > 0) {\n switch (max) {\n case rn: h = ((gn - bn) / d + (gn < bn ? 6 : 0)) / 6; break;\n case gn: h = ((bn - rn) / d + 2) / 6; break;\n default: h = ((rn - gn) / d + 4) / 6;\n }\n }\n return { h: h 360, s, v };\n }\n\n // Convert HSV + alpha → rgba() CSS string.\n static hsvToRgba(h: number, s: number, v: number, a: number): string {\n const c = v * s;\n const x = c * (1 - Math.abs((h / 60) % 2 - 1));\n const m = v - c;\n let r = 0, g = 0, b = 0;\n if (h < 60) { r = c; g = x; b = 0; }\n else if (h < 120) { r = x; g = c; b = 0; }\n else if (h < 180) { r = 0; g = c; b = x; }\n else if (h < 240) { r = 0; g = x; b = c; }\n else if (h < 300) { r = x; g = 0; b = c; }\n else { r = c; g = 0; b = x; }\n return `rgba(${Math.round((r + m) * 255)},${Math.round((g + m) * 255)},${Math.round((b + m) * 255)},${a.toFixed(4)})`;\n }\n\n // Returns rgba(...) matching rENA's edge-color convention (ena.plot.network):\n // • hue and value (brightness) are preserved from the base color\n // • HSV saturation is set to \|weight\| directly (0 = grey, 1 = fully vivid)\n // • alpha is also set to \|weight\|\n //\n // rENA converts the input color to HSV, replaces the S component with the\n // normalized edge weight, and additionally sets plotly element opacity to the\n // same value. Working in HSV (not HSL) is essential: palette colors like\n // #EE6677 have HSL lightness ≈ 67%, so 100% HSL saturation still looks\n // washed-out, whereas HSV value ≈ 0.93 gives the expected vivid output.\n toString(): string {\n const { h, v } = WeightedColor.toHSV(this.base);\n const w = Math.min(1, Math.abs(this.weight));\n const a = this.alpha === undefined ? w : Math.min(1, Math.max(0, this.alpha));\n return WeightedColor.hsvToRgba(h, w, v, a);\n }\n}","export class Transform {\n private _values: number[] = [1, 0, 0, 1, 0, 0];\n private _keys: string[] = [\"a\", \"b\", \"c\", \"d\", \"e\", \"f\"];\n\n get values() {\n return this._values;\n }\n set values(vals: number[]) {\n if (vals && vals.length === 6) {\n this._values = vals;\n }\n }\n get keys() {\n return this._keys;\n }\n set keys(vals: string[]) {\n if (vals && vals.length === 6) {\n this._keys = vals;\n }\n }\n\n constructor(vals: number[] \| null = null) {\n if (vals) {\n this.values = vals;\n }\n }\n\n toString() {\n let matrix_str = this.keys.map((k, i) => this.values[i]).join(\" \")\n ;\n\n return `matrix(${matrix_str})`;\n }\n\n toMatrix() {\n return Object.fromEntries(this._keys.map((k, i) => [k, this._values[i]]));\n }\n\n toArray() {\n return this._values;\n }\n\n set(wh: string, val: number) {\n if (val !== 0.0075 && val !== 0) {\n this._values[this._keys.findIndex(k => k === wh)] = val;\n }\n }\n get(wh: string) {\n return this._values[this._keys.findIndex(k => k === wh)];\n }\n\n scale(a: number, d: number = a) {\n this.a = a;\n this.d = d;\n }\n\n zoom(z: number) {\n this.a = z;\n this.d = z;\n }\n\n pan(x: number, y: number) {\n this.e = this.e + x;\n this.f = this.f + y;\n }\n\n set a(x: number) { this.set(\"a\", x); }\n set b(x: number) { this.set(\"b\", x); }\n set c(x: number) { this.set(\"c\", x); }\n set d(x: number) { this.set(\"d\", x); }\n set e(x: number) { this.set(\"e\", x); }\n set f(x: number) { this.set(\"f\", x); }\n\n get a() { return this.get(\"a\"); }\n get b() { return this.get(\"b\"); }\n get c() { return this.get(\"c\"); }\n get d() { return this.get(\"d\"); }\n get e() { return this.get(\"e\"); }\n get f() { return this.get(\"f\"); }\n}","// const __ = {\n// matrix_string: (matrix) => {\n// let matrix_str = ['a','b','c','d','e','f'].map( l => matrix[l] ).join(\" \")\n// return `matrix(${matrix_str})`\n// },\n// isArray: (obj) => {\n// return typeof Array.isArray === \"function\" ? Array.isArray(obj) :\n// (obj && typeof obj === \"object\" && obj.constructor.name === \"Array\");\n// },\n// recurse: (obj, opt, iterator) => {\n// function recurse(obj, i, parent = null) {\n// if (__.isArray(obj)) {\n// for (const [i, o] of obj.entries()) {\n// recurse(o, i, parent);\n// }\n// } else {\n// iterator(obj, i, parent);\n// if (obj && __.isArray(obj[opt.children])) {\n// for (const [i, o] of obj[opt.children].entries()) {\n// recurse(o, i, obj);\n// }\n// }\n// }\n// }\n\n// recurse(obj);\n// },\n// geom: {\n// point: {\n// // source https://github.com/HarryStevens/geometric/\n// translate: (point, angle, distance) => {\n// const r = __.geom.angle.torad(angle);\n// return [point[0] + distance * Math.cos(r), point[1] + distance * Math.sin(r)];\n// },\n\n// // source https://github.com/HarryStevens/geometric/\n// rotate: (point, angle, origin) => {\n\n// // See: https://en.wikipedia.org/wiki/Cartesian_coordinate_system#Rotation\n// function rotate(point, angle){\n// return [\n// (point[0] * Math.cos(angle)) - point[1] * Math.sin(angle),\n// (point[0] * Math.sin(angle)) + point[1] * Math.cos(angle)\n// ];\n// }\n\n// const r = __.geom.angle.torad(angle);\n\n// if (!origin \|\| (origin[0] === 0 && origin[1] === 0)){\n// return rotate(point, r);\n// }\n// else {\n// // See: https://math.stackexchange.com/questions/1964905/rotation-around-non-zero-point\n// const p0 = point.map((c, i) => c - origin[i]);\n// const rotated = rotate(p0, r);\n// return rotated.map((c, i) => c + origin[i]);\n// }\n// }\n// },\n// line: {\n// slope: (p1, p2) => {\n// let\n// m = (p2[1] - p1[1])/(p2[0] - p1[0]),\n// n = p1[0] - m * p1[0]\n// ;\n// return m;\n// },\n// intercept: (p1, p2) => {\n// let\n// m = __.geom.line.slope(p1, p2),\n// n = p1[1] - m * p1[0]\n// ;\n// return n;\n// },\n// slope_intercept: (p1, p2) => {\n// return {\n// slope: __.geom.line.slope(p1, p2),\n// intercept: __.geom.line.intercept(p1, p2)\n// };\n// },\n// midpoint: (p1, p2, w = 0.5) => {\n// if(Array.isArray(p1[0])) {\n// p2 = (p1[1]);\n// p1 = (p1[0]);\n// }\n// return [0, 1].map( i => (parseFloat(p1[i]) + parseFloat(p2[i])) * w );\n// },\n// length: (p1, p2) => {\n// if(Array.isArray(p1[0])) {\n// p2 = p1[1];\n// p1 = p1[0];\n// }\n// return Math.sqrt([0, 1].map( i => Math.pow(p2[i] - p1[i], 2) ).reduce( (a,b) => a + b, 0))\n// },\n// interpolate: (line) => {\n// // source https://github.com/HarryStevens/geometric/\n// return t =>\n// t === 0 ?\n// line[0] :\n// t === 1 ?\n// line[1] :\n// __.geom.point.translate(line[0], __.geom.angle.line(line), __.geom.line.length(line) * t)\n// ;\n// },\n// point_along: (line, distance = 0) => {\n// let\n// len = __.geom.line.length(line),\n// ratio = distance / len,\n// Xt = ((1 - ratio) * line[0][0] + (ratio * line[1][0])),\n// Yt = ((1 - ratio) * line[0][1] + (ratio * line[1][1]))\n// ;\n// return [Xt, Yt];\n// },\n// rotate: (line, by = [0, 0]) => {\n// let\n// translated = [line[1][0] - by[0], line[1][1] - by[1]],\n// rotated = [-(translated[1]), translated[0]],\n// rotated_reflection = [-(rotated[0]), -(rotated[1])],\n// untranslated = [rotated[0] + by[0], rotated[1] + by[1]],\n// untranslated2 = [rotated_reflection[0] + by[0], rotated_reflection[1] + by[1]]\n// ;\n// return [untranslated, untranslated2];\n// },\n// rotate2: (line, fixed, angle = 90) => {\n// let\n// line_si = __.geom.line.slope_intercept(line[0], line[1]),\n// P = [0, line_si.intercept],\n// Q = [1, line_si.slope + line_si.intercept]\n// ;\n// line = [P, Q];\n\n// let\n// xx = [line[0][0], line[1][0]],\n// yy = [line[0][1], line[1][1]],\n// x_fixed = fixed[0],\n// y_fixed = fixed[1],\n// angle_rad = -2 * Math.PI * angle/360,\n// xx_new = xx.map( (x, i) => (x - x_fixed) * Math.cos(angle_rad) - (yy[i] - y_fixed) * Math.sin(angle_rad) + x_fixed ),\n// yy_new = yy.map( (y, i) => (xx[i] - x_fixed) * Math.sin(angle_rad) - (y - y_fixed) * Math.cos(angle_rad) + y_fixed ),\n// object_new = [\n// [xx_new[0], yy_new[0]],\n// [xx_new[1], yy_new[1]]\n// ]\n// ;\n\n// return(object_new);\n// },\n// intersection: (lineA, lineB) => {\n// const\n// [[x1, y1], [x2, y2]] = lineA,\n// [[x3, y3], [x4, y4]] = lineB,\n// D = ( (x1 - x2) * (y3 - y4) ) - ( (y1 - y2) * (x3 - x4) ),\n// num1 = ( ((x1 * y2) - (y1 * x2)) * (x3 - x4) ) -\n// ( (x1 - x2) * ((x3 * y4) - (y3 * x4)) ),\n// num2 = ( ((x1 * y2) - (y1 * x2)) * (y3 - y4) ) -\n// ( (y1 - y2) * ((x3 * y4) - (y3 * x4)) )\n// ;\n// return [num1 / D, num2 / D];\n// },\n// intersect_circle(line, circle_xy, circle_r) {\n// let { slope: m, intercept: n } = __.geom.line.slope_intercept(line[0], line[1]);\n// let\n// a = 1 + Math.pow(m,2),\n// b = 2 * m * n - 2 * circle_xy[1] * m - 2 * circle_xy[0],\n// c = Math.pow(circle_xy[0], 2) + Math.pow(n, 2) + Math.pow(circle_xy[1], 2) - 2 * circle_xy[1] * n - Math.pow(circle_r, 2),\n// int\n// ;\n// if (Math.sqrt( Math.pow(b, 2) - (4 * a * c)) >= 0) {\n// let\n// x1 = (-b + Math.sqrt( Math.pow(b, 2) - (4 * a * c)))/(2 * a),\n// x2 = (-b - Math.sqrt( Math.pow(b, 2) - (4 * a * c)))/(2 * a),\n// y1 = m * x1 + n,\n// y2 = m * x2 + n\n// ;\n// int = [[x1, y1], [x2, y2]];\n// }\n// else {\n// int = \"The line and the circumference do not intersect\"\n// }\n// return(int)\n// }\n// },\n// angle: {\n// torad: (a) => a / 180 * Math.PI,\n// todeg: (a) => a * 180 / Math.PI,\n// line: (line) => {\n// // source https://github.com/HarryStevens/geometric/\n// return __.geom.angle.todeg(\n// Math.atan2(line[1][1] - line[0][1], line[1][0] - line[0][0])\n// );\n// }\n// }\n// },\n// object: {\n// proxy(obj, handler, deep = false) {\n// if(deep === false) {\n// return new Proxy(obj, handler);\n// }\n// else {\n// if (typeof obj !== 'object' \|\| obj === null) {\n// return obj;\n// }\n\n// for (const key in obj) {\n// if (obj.hasOwnProperty(key)) {\n// obj[key] = __.object.proxy(obj[key], handler, deep);\n// }\n// }\n\n// return new Proxy(obj, handler);\n// }\n// },\n// handler: {\n// set: function(target, property, value) {\n// target[property] = value;\n// window.dispatchEvent(__.event(\"settingUpdate\", this, { target, property, value }))\n\n// return true;\n// },\n// get: function(target, property) {\n// return target[property];\n// }\n// },\n// get: (obj, key) => {\n// const parts = key.split(\".\");\n// let current = obj;\n// for (const part of parts) {\n// if (current && typeof current === \"object\" && current.hasOwnProperty(part)) {\n// current = current[part];\n// }\n// else {\n// return undefined;\n// }\n// }\n// return current;\n// },\n// set: (obj, key, value) => {\n// const parts = key.split(\".\");\n// let current = obj,\n// i\n// ;\n\n// for (i = 0; i < parts.length - 1; i++) {\n// const part = parts[i];\n// if (current && typeof current === \"object\") {\n// if (!current.hasOwnProperty(part)) {\n// current[part] = {};\n// }\n// current = current[part];\n// }\n// else {\n// return false;\n// }\n// }\n\n// if (current && typeof current === \"object\") {\n// current[parts[i]] = value;\n// return true;\n// }\n// else {\n// return false;\n// }\n// }\n// },\n// array: {\n// unique: (x) => [...new Set(x)],\n// divide: (a, b) => {\n// let ret;\n\n// if(Array.isArray(a)) {\n// if(Array.isArray(b)) {\n// if(a.length === b.length) {\n// ret = a.map( (a_,i) => a_ / b[i] )\n// }\n// else {\n// console.error(\"If both are arrays, they must be equal length.\")\n// }\n// }\n// else {\n// ret = a.map( a_ => a_ / b );\n// }\n// }\n// else {\n// ret = a / b;\n// }\n\n// return(ret);\n// },\n// multiply: (a, b) => {\n// let ret;\n\n// if(Array.isArray(a)) {\n// if(Array.isArray(b)) {\n// if(a.length === b.length) {\n// ret = a.map( (a_,i) => a_ * b[i] )\n// }\n// else {\n// console.error(\"If both are arrays, they must be equal length.\")\n// }\n// }\n// else {\n// ret = a.map( a_ => a_ * b );\n// }\n// }\n// else {\n// ret = a * b;\n// }\n\n// return(ret);\n// },\n// subtract: (a, b) => {\n// let ret;\n\n// if(Array.isArray(a)) {\n// if(Array.isArray(b)) {\n// if(a.length === b.length) {\n// ret = a.map( (a_,i) => a_ - b[i] )\n// }\n// else {\n// console.error(\"If both are arrays, they must be equal length.\")\n// }\n// }\n// else {\n// ret = a.map( a_ => a_ - b );\n// }\n// }\n// else {\n// ret = a - b;\n// }\n\n// return(ret);\n// },\n// shift: () => {\n// return Array.from(a, (b, i) => a[i + 1]);\n// }\n// },\n// math: {\n// sum: (a) => a.reduce( (a,b) => a + b, 0),\n// mean: (a) => __.math.sum(a) / a.length,\n// round: (a, b) => {\n// const factor = Math.pow(10, b);\n// return Math.round(a * factor) / factor;\n// }\n// },\n// event: (nm, elm, data) => {\n// return new CustomEvent(nm, {\n// bubbles: true,\n// cancelable: true,\n// detail: {\n// element: elm,\n// data: data \|\| (elm ? elm.__data__ : undefined)\n// }\n// })\n// },\n// hash: {\n// parts: () => location.hash.replace(/#/,'').split(/\\//).filter(a => a).map(a => a.split(/:/)),\n// exists: (x) => __.hash.parts().flat().findIndex(a => a === x) >= 0\n// },\n// url: {\n// parse: (l = window.location) => {\n// },\n// query: {\n// parse: (l = window.location.search) =>\n// Object.fromEntries(l.replace(/^\\?/,'').split(/&/).map( i => i.split(/=/) ))\n// ,\n// keys: (l = window.location.search) =>\n// l.replace(/^\\?/,'').split(/&/).map( i => i.split(/=/)[0] )\n// ,\n// has: (k, l = window.location.search) =>\n// __.url.query.keys(l).findIndex(i => i == k) >= 0\n// }\n// }\n// };\n\nexport namespace Tools {\n export namespace Matrix {\n export function matrixString(matrix: Record<string, number>): string {\n const matrixStr = ['a', 'b', 'c', 'd', 'e', 'f'].map(l => matrix[l]).join(' ');\n return `matrix(${matrixStr})`;\n }\n }\n\n export namespace Geometry {\n export namespace Point {\n export function translate(point: [number, number], angle: number, distance: number): [number, number] {\n const r = Angle.toRad(angle);\n return [point[0] + distance * Math.cos(r), point[1] + distance * Math.sin(r)];\n }\n\n export function rotate(point: [number, number], angle: number, origin?: [number, number]): [number, number] {\n const r = Angle.toRad(angle);\n\n function rotatePoint(p: [number, number], a: number): [number, number] {\n return [\n p[0] * Math.cos(a) - p[1] * Math.sin(a),\n p[0] * Math.sin(a) + p[1] * Math.cos(a),\n ];\n }\n\n if (!origin \|\| (origin[0] === 0 && origin[1] === 0)) {\n return rotatePoint(point, r);\n } else {\n const p0 = point.map((c, i) => c - origin[i]) as [number, number];\n const rotated = rotatePoint(p0, r);\n return rotated.map((c, i) => c + origin[i]) as [number, number];\n }\n }\n }\n\n export namespace Line {\n export function slope(p1: [number, number], p2: [number, number]): number {\n return (p2[1] - p1[1]) / (p2[0] - p1[0]);\n }\n export function intercept(p1: [number, number], p2: [number, number]): number {\n const m = slope(p1, p2);\n return p1[1] - m * p1[0];\n }\n export function slopeIntercept(p1: [number, number], p2: [number, number]): { slope: number; intercept: number } {\n return {\n slope: slope(p1, p2),\n intercept: intercept(p1, p2),\n };\n }\n export function point_along(line: [[number, number], [number, number]], distance: number = 0): [number, number] {\n const ratio = distance;\n const Xt = ((1 - ratio) * line[0][0] + (ratio * line[1][0]));\n const Yt = ((1 - ratio) * line[0][1] + (ratio * line[1][1]));\n return [Xt, Yt];\n }\n export function midpoint(p1: [number, number], p2: [number, number], w = 0.5): [number, number] {\n if (Array.isArray(p1[0])) {\n p2 = (p1[1] as any);\n p1 = (p1[0] as any);\n }\n\n return [0, 1].map(i => (parseFloat(p1[i] as any) + parseFloat(p2[i] as any)) * w) as [number, number];\n }\n export function length(\n p1: [number, number] \| [[number, number], [number, number]],\n p2?: [number, number]\n ): number {\n if (Array.isArray((p1 as any)[0])) {\n p2 = (p1 as [[number, number], [number, number]])[1];\n p1 = (p1 as [[number, number], [number, number]])[0];\n }\n return Math.sqrt(\n [0, 1].map(i => Math.pow((p2 as [number, number])[i] - (p1 as [number, number])[i], 2)).reduce((a, b) => a + b, 0)\n );\n }\n export function rotate(\n line: [[number, number], [number, number]],\n by: [number, number] = [0, 0]\n ): [[number, number], [number, number]] {\n const translated: [number, number] = [\n line[1][0] - by[0],\n line[1][1] - by[1]\n ];\n const rotated: [number, number] = [\n -translated[1],\n translated[0]\n ];\n const rotated_reflection: [number, number] = [\n -rotated[0],\n -rotated[1]\n ];\n const untranslated: [number, number] = [\n rotated[0] + by[0],\n rotated[1] + by[1]\n ];\n const untranslated2: [number, number] = [\n rotated_reflection[0] + by[0],\n rotated_reflection[1] + by[1]\n ];\n return [untranslated, untranslated2];\n }\n export function rotate2(\n line: [[number, number], [number, number]],\n fixed: [number, number],\n angle: number = 90\n ): [[number, number], [number, number]] {\n // Calculate slope and intercept\n const m = Tools.Geometry.Line.slope(line[0], line[1]);\n const n = Tools.Geometry.Line.intercept(line[0], line[1]);\n const P: [number, number] = [0, n];\n const Q: [number, number] = [1, m + n];\n line = [P, Q];\n\n const xx = [line[0][0], line[1][0]];\n const yy = [line[0][1], line[1][1]];\n const x_fixed = fixed[0];\n const y_fixed = fixed[1];\n const angle_rad = -2 * Math.PI * angle / 360;\n const xx_new = xx.map((x, i) =>\n (x - x_fixed) * Math.cos(angle_rad) - (yy[i] - y_fixed) * Math.sin(angle_rad) + x_fixed\n );\n const yy_new = yy.map((y, i) =>\n (xx[i] - x_fixed) * Math.sin(angle_rad) - (y - y_fixed) * Math.cos(angle_rad) + y_fixed\n );\n const object_new: [[number, number], [number, number]] = [\n [xx_new[0], yy_new[0]],\n [xx_new[1], yy_new[1]]\n ];\n\n return object_new;\n }\n export function intersection(\n lineA: [[number, number], [number, number]],\n lineB: [[number, number], [number, number]]\n ): [number, number] {\n const\n [[x1, y1], [x2, y2]] = lineA,\n [[x3, y3], [x4, y4]] = lineB,\n D = ((x1 - x2) * (y3 - y4)) - ((y1 - y2) * (x3 - x4)),\n num1 = (((x1 * y2) - (y1 * x2)) * (x3 - x4)) -\n ((x1 - x2) * ((x3 * y4) - (y3 * x4))),\n num2 = (((x1 * y2) - (y1 * x2)) * (y3 - y4)) -\n ((y1 - y2) * ((x3 * y4) - (y3 * x4)));\n return [num1 / D, num2 / D];\n }\n export function intersect_circle(line: [[number, number], [number, number]], circle_xy: [number, number], circle_r: number): [[number, number], [number, number]] {\n let { slope: m, intercept: n } = Tools.Geometry.Line.slopeIntercept(line[0], line[1]);\n let\n a = 1 + Math.pow(m, 2),\n b = 2 * m * n - 2 * circle_xy[1] * m - 2 * circle_xy[0],\n c = Math.pow(circle_xy[0], 2) + Math.pow(n, 2) + Math.pow(circle_xy[1], 2) - 2 * circle_xy[1] * n - Math.pow(circle_r, 2),\n int: [[number, number], [number, number]] = [[Infinity, Infinity], [Infinity, Infinity]]\n ;\n\n if (Math.sqrt(Math.pow(b, 2) - (4 * a * c)) >= 0) {\n let\n x1 = (-b + Math.sqrt(Math.pow(b, 2) - (4 * a * c))) / (2 * a),\n x2 = (-b - Math.sqrt(Math.pow(b, 2) - (4 * a * c))) / (2 * a),\n y1 = m * x1 + n,\n y2 = m * x2 + n\n ;\n int = [[x1, y1], [x2, y2]];\n }\n else {\n console.error(\"The line and the circumference do not intersect\");\n }\n\n return (int)\n }\n export function interpolate(line: [[number, number], [number, number]]): (t: number) => [number, number] {\n // source https://github.com/HarryStevens/geometric/\n return t =>\n t === 0 ?\n line[0] :\n t === 1 ?\n line[1] :\n Tools.Geometry.Point.translate(line[0], Tools.Geometry.Angle.line(line), Tools.Geometry.Line.length(line) * t)\n ;\n }\n }\n\n export namespace Angle {\n export function toRad(angle: number): number {\n return (angle / 180) * Math.PI;\n }\n\n export function toDeg(angle: number): number {\n return (angle * 180) / Math.PI;\n }\n // source https://github.com/HarryStevens/geometric/\n export function line(line: [[number, number], [number, number]]): number {\n if (line.length !== 2 \|\| !Array.isArray(line[0]) \|\| !Array.isArray(line[1]) \|\| line[0].length !== 2 \|\| line[1].length !== 2) {\n throw new Error('Invalid line format. Expected [[x1, y1], [x2, y2]].');\n }\n //console.log(\"line: \", line)\n return Tools.Geometry.Angle.toDeg(\n Math.atan2(line[1][1] - line[0][1], line[1][0] - line[0][0])\n );\n }\n }\n }\n\n export namespace ArrayTools {\n export function unique<T>(arr: T[]): T[] {\n return [...new Set(arr)];\n }\n\n export function divide(a: number \| number[], b: number \| number[]): number \| number[] {\n if (Array.isArray(a)) {\n if (Array.isArray(b)) {\n if (a.length !== b.length) throw new Error('Arrays must be of equal length');\n return a.map((val, i) => val / b[i]);\n }\n return a.map(val => val / (b as number));\n }\n return (a as number) / (b as number);\n }\n\n export function isArray(obj: any): boolean {\n return typeof Array.isArray === \"function\" ? Array.isArray(obj) :\n (obj && typeof obj === \"object\" && obj.constructor.name === \"Array\");\n }\n }\n\n export namespace Mathematics {\n export function sum(arr: number[]): number {\n return arr.reduce((a, b) => a + b, 0);\n }\n\n export function mean(arr: number[]): number {\n return sum(arr) / arr.length;\n }\n\n export function round(value: number, decimals: number): number {\n const factor = Math.pow(10, decimals);\n return Math.round(value * factor) / factor;\n }\n }\n\n export namespace Events {\n export function createEvent(name: string, element?: HTMLElement, data?: any): CustomEvent {\n return new CustomEvent(name, {\n bubbles: true,\n cancelable: true,\n detail: {\n element,\n data: data \|\| (element ? (element as any).__data__ : undefined),\n },\n });\n }\n }\n\n export namespace Hash {\n export function parts(): string[][] {\n return location.hash\n .replace(/#/, '')\n .split(/\\//)\n .filter(a => a)\n .map(a => a.split(/:/));\n }\n\n export function exists(key: string): boolean {\n return parts().flat().findIndex(a => a === key) >= 0;\n }\n }\n\n\n export namespace Objects {\n export function proxy<T extends object>(obj: T, handler: ProxyHandler<any>, deep = false): T {\n if (!deep) {\n return new Proxy(obj, handler);\n } else {\n if (typeof obj !== 'object' \|\| obj === null) {\n return obj;\n }\n\n for (const key in obj) {\n if (Object.prototype.hasOwnProperty.call(obj, key)) {\n (obj as any)[key] = proxy((obj as any)[key], handler, deep);\n }\n }\n\n return new Proxy(obj, handler);\n }\n }\n\n export const handler: ProxyHandler<any> = {\n set(target, property, value) {\n target[property] = value;\n window.dispatchEvent(\n Tools.Events.createEvent(\"settingUpdate\", window as any, { target, property, value })\n );\n return true;\n },\n get(target, property) {\n return target[property];\n }\n };\n\n export function get(obj: any, key: string): any {\n const parts = key.split(\".\");\n let current = obj;\n for (const part of parts) {\n if (current && typeof current === \"object\" && Object.prototype.hasOwnProperty.call(current, part)) {\n current = current[part];\n } else {\n return undefined;\n }\n }\n return current;\n }\n\n export function set(obj: any, key: string, value: any): boolean {\n const parts = key.split(\".\");\n let current = obj;\n let i: number;\n\n for (i = 0; i < parts.length - 1; i++) {\n const part = parts[i];\n if (current && typeof current === \"object\") {\n if (!Object.prototype.hasOwnProperty.call(current, part)) {\n current[part] = {};\n }\n current = current[part];\n } else {\n return false;\n }\n }\n\n if (current && typeof current === \"object\") {\n current[parts[i]] = value;\n return true;\n } else {\n return false;\n }\n }\n }\n\n export namespace URL {\n export function parse(location: Location = window.location): Record<string, string> {\n return Object.fromEntries(new URLSearchParams(location.search));\n }\n\n export namespace Query {\n export function parse(location: string = window.location.search): Record<string, string> {\n return Object.fromEntries(\n location.replace(/^\\?/, '').split(/&/).map(i => i.split(/=/))\n );\n }\n\n export function keys(location: string = window.location.search): string[] {\n return location.replace(/^\\?/, '').split(/&/).map(i => i.split(/=/)[0]);\n }\n\n export function has(key: string, location: string = window.location.search): boolean {\n return keys(location).findIndex(i => i === key) >= 0;\n }\n }\n }\n}\n\n","export type EventBusListener = (details: { key: string, newValue: any, oldValue: any }) => any;\n\n/*\n Minimal local pub/sub used by vizena Graph and Layer objects.\n * Has the same API surface as arbor's StateManager but carries no R/arbor deps.\n /\nexport class EventBus {\n private _state: Map<string, any> = new Map();\n private listeners: Map<string, Map<string, Set<EventBusListener>>> = new Map();\n\n get state(): Map<string, any> {\n return this._state;\n }\n\n hasVariable(key: string): boolean {\n return this._state.has(key);\n }\n\n getVariable(key: string): any {\n return this._state.get(key);\n }\n\n setVariable(key: string, value: any, options?: { lazy?: boolean }): void {\n const oldValue = this._state.get(key);\n this._state.set(key, value);\n if (!options?.lazy) {\n this.notifyListeners(key, value, oldValue);\n }\n }\n\n addListener(key: string, type: string, listener: EventBusListener): void {\n if (!this.listeners.has(key)) this.listeners.set(key, new Map());\n const typeMap = this.listeners.get(key)!;\n if (!typeMap.has(type)) typeMap.set(type, new Set());\n typeMap.get(type)!.add(listener);\n }\n\n removeListener(key: string, type: string, listener: EventBusListener): void {\n this.listeners.get(key)?.get(type)?.delete(listener);\n }\n\n getListeners(key: string, type: string): EventBusListener[] {\n return Array.from(this.listeners.get(key)?.get(type) ?? []);\n }\n\n notifyListeners(key: string, newValue: any, oldValue: any): void {\n const typeMap = this.listeners.get(key);\n if (!typeMap) return;\n for (const set of typeMap.values()) {\n set.forEach((listener) => {\n if (typeof listener === 'function') {\n listener({ key, newValue, oldValue });\n } else if (typeof (listener as any).calculate === 'function') {\n (listener as any).calculate.call(listener, { key, newValue, oldValue });\n }\n });\n }\n }\n}\n","import { Transform } from \"./Transform.js\";\nimport { Tools } from \"../utils/Tools.js\";\nconst { ArrayTools } = Tools;\nimport { Graph } from \"./Graph.js\";\nimport { PlottedObject } from \"./PlottedObject.js\";\nimport { EventBus as StateManager } from \"../types/EventBus.js\";\n\nexport type LayerLike = {\n name?: string;\n layers?: LayerArray;\n [key: string]: any;\n};\n\nexport class LayerArray extends Array<LayerLike> {\n constructor(...args: any[]) {\n super(...args);\n }\n\n search(key: string, name: string): LayerLike \| undefined {\n let found: LayerLike \| undefined;\n\n function fn(a: LayerLike): LayerLike \| undefined {\n return a.name === name ? a : undefined;\n }\n\n function recurse(obj: any, i?: number, parent: any = null): LayerLike \| undefined {\n if (ArrayTools.isArray(obj)) {\n for (const [i, o] of obj.entries()) {\n found = recurse(o, i, parent);\n if (found) {\n return found;\n }\n }\n } else {\n found = fn(obj);\n if (!found) {\n if (obj && ArrayTools.isArray(obj[key])) {\n for (const [i, o] of obj[key].entries()) {\n found = recurse(o, i, obj);\n if (found) {\n return found;\n }\n }\n }\n } else {\n return found;\n }\n }\n return found;\n }\n\n return recurse(this);\n }\n\n flatten(): LayerLike[] {\n return this.reduce<LayerLike[]>((a, l: LayerLike) => {\n a.push(l);\n if (l.layers && Array.isArray(l.layers)) {\n a.push(...l.layers);\n }\n return a;\n }, []);\n }\n \n recurse(\n key: string,\n callback: (layer: LayerLike, parent?: LayerLike \| null, depth?: number) => any, \n parent: LayerLike \| null = null, \n depth: number = 0\n ): any {\n let results: any[] = new LayerArray();\n for (const layer of this) {\n let result = callback(layer, parent, depth);\n \n if (layer[key] && Array.isArray(layer[key])) {\n let r = new LayerArray(...layer[key]).recurse(key, callback, layer, depth + 1);\n if (r !== undefined) {\n results.push(...r);\n }\n }\n\n results.push(result);\n }\n console.log(\"Recurse results: \", results);\n return results;\n }\n}\n\nexport class Layer {\n __state__: StateManager = new StateManager();\n\n name: string;\n ID: string;\n scale_x: number = 1;\n scale_y: number = 1;\n tabindex?: number;\n _transform: Transform;\n scale_objects: boolean = true;\n layers: LayerArray = new LayerArray();\n objects: Map<string, PlottedObject> = new Map();\n parent?: Layer \| Graph;\n visible: boolean = true;\n\n constructor(ID: string, o: any, parent?: Graph \| Layer) {\n this.ID = ID;\n this.name = o.name \|\| `layer-${ID}`;\n this.tabindex = o.tabindex;\n this.parent = parent;\n this._transform = new Transform();\n\n parent?.__state__.addListener(\"graph_updated\", \"live\", ({ key, newValue, oldValue }) => {\n // console.log(`Graph updated, updating layer: ${this.name}`);\n });\n \n parent?.__state__.addListener(`graph_updated_${this.name}`, \"live\", ({ key, newValue, oldValue }) => {\n // console.log(`Graph updated, updating layer: ${this.name}, Key: ${key}`, \"New Value: \", newValue, \"Old Value: \", oldValue);\n this.objects = newValue;\n this.__state__.setVariable(`layer_updated`, this );\n });\n }\n\n get transform(): Transform {\n return this._transform;\n }\n set transform(t: Transform) {\n this._transform = t;\n }\n}","import { Transform } from './Transform';\nimport { Color } from './Color';\nimport { Edge } from './Edges';\nimport { DataFrameRow } from '../types/DataFrame';\n\nexport type DimensionType = DimensionVector \| DataFrameRow \| number[];\n\nexport interface DimensionVectorInterface extends Array<number> {\n\n [index: number]: number;\n flipped: boolean;\n flip(): DimensionVector;\n get names(): string[];\n get(wh: string \| number): number \| undefined;\n}\nexport class DimensionVector extends Array<number> implements DimensionVectorInterface {\n #flipped: boolean = false;\n #names: string[] \| undefined;\n\n constructor(...args: number[]) {\n super(arguments.length);\n for (let i = 0; i < args.length; i++) {\n this[i] = args[i];\n }\n this.#flipped = false;\n }\n\n static fromArray(arr: DataFrameRow): DimensionVector {\n const vec = new DimensionVector();\n arr.forEach((v, i) => {\n vec.push(v);\n });\n vec.#names = arr.names;\n\n return vec;\n }\n\n flip(): DimensionVector {\n this.#flipped = !this.#flipped;\n for (let i = 0; i < this.length; i++) {\n this[i] = -this[i];\n }\n return this;\n }\n\n get(wh: string \| number): number \| undefined {\n if (typeof wh === 'number') {\n return this[wh];\n } else if (this.#names && this.#names.includes(wh)) {\n return this[this.#names.indexOf(wh)];\n } else {\n return undefined;\n }\n }\n\n get flipped(): boolean {\n return this.#flipped;\n }\n\n get names(): string[] {\n if (this.#names) {\n return this.#names;\n } else {\n return this.map((_, i) => `V${i + 1}`);\n }\n }\n}\n\nexport interface PlottedObjectOptions {\n ID: string;\n dimensions?: DimensionVector;\n x?: number \| number[];\n y?: number \| number[];\n size: number \| 0;\n color: Color;\n highlight: Color \| null;\n shape?: any;\n active: boolean;\n meta: any;\n\n [key: string]: any;\n}\n\nexport class PlottedObject implements PlottedObjectOptions {\n private readonly _original: PlottedObjectOptions;\n private readonly _dimensions: DimensionVector;\n\n ID: string;\n scale_x: number = 1;\n scale_y: number = 1;\n scale_size: number = 0.05;\n active: boolean = false;\n visible: boolean = false;\n highlighting: boolean = false;\n meta: any = {};\n \n _transform: Transform;\n _x: any = 0;\n _y: any = 0;\n _color: Color;\n _highlight: Color;\n _highlight_default: Color = new Color('#000000');\n _size: number = 0;\n\n shape?: any;\n\n // graph: Graph;\n parent: any;\n\n get dimensions(): DimensionVector {\n return this._dimensions;\n }\n\n get color(): Color {\n return (\n // This was expecting hightight to be an object with a color property\n // but now it is just a Color object, so we can simplify this.\n (this.highlighting && this._highlight) ? this._highlight : this._color\n );\n }\n set color(c: Color) {\n this._color = c;\n }\n get highlight(): Color {\n return this._highlight \|\| this._highlight_default;\n }\n set highlight(h: Color) {\n this._highlight = h;\n }\n\n get size(): number {\n return this._size;\n }\n set size(s: number) {\n this._size = s;\n }\n\n get original(): PlottedObjectOptions {\n return this._original;\n }\n\n get x() {\n return this._x; // this.graph.x_mirror();\n }\n get y() {\n return this._y; // * this.graph.y_mirror();\n }\n set x(x_: any) { this._x = x_; }\n set y(y_: any) { this._y = y_; }\n dimension(wh: string \| number): number \| undefined {\n return this._dimensions.get(wh);\n }\n\n get transform() { return this._transform; }\n set transform(t: any) { this._transform = t; }\n\n constructor(dimensions: DimensionType, o: PlottedObjectOptions) {\n this.ID = o.ID;\n // this.graph = graph;\n this._transform = new Transform();\n\n // If dimensions is already a DimensionVector, use it directly\n if (dimensions instanceof DimensionVector) {\n this._dimensions = dimensions;\n }\n else if (dimensions instanceof DataFrameRow) {\n // If dimensions is a DataFrameRow, convert it to a DimensionVector\n this._dimensions = DimensionVector.fromArray(dimensions);\n }\n\n // If dimensions is an array, convert it to a DimensionVector\n else if (Array.isArray(dimensions)) {\n this._dimensions = new DimensionVector(...dimensions);\n }\n\n // Else is a warning and fallback to a default DimensionVector\n else {\n console.warn(\"Invalid dimensions provided, using default DimensionVector(0, 0)\");\n this._dimensions = new DimensionVector(0, 0);\n }\n\n // make a copy of the object to avoid mutating the original\n let data: PlottedObjectOptions = { ...o };\n\n // keep the original data for reference\n this._original = { ...data };\n\n this.ID = data.ID;\n this.x = data.x \|\| this._dimensions[0];\n this.y = data.y \|\| this._dimensions[1];\n this._size = data.size \|\| 1;\n this._color = data.color \|\| new Color('#000000');\n this.active = data.active \|\| false;\n this.shape = data.shape \|\| null;\n this.meta = data.meta \|\| {};\n\n this._highlight = this._highlight_default;\n if (data.highlight) {\n this._highlight = data.highlight;\n }\n // else if (graph && graph.options && graph.options[this.constructor.name.toUpperCase()]) {\n // this._highlight = graph.options[this.constructor.name.toUpperCase()].highlight;\n // }\n }\n}\n\nexport interface LineOptions extends PlottedObjectOptions {\n x1: number \| string;\n y1: number \| string;\n x2: number \| string;\n y2: number \| string;\n width?: number;\n color: Color;\n shape: string \| null;\n [key: string]: any;\n}\n\nexport class Line extends PlottedObject {\n from: Point;\n to: Point;\n width?: number;\n _color!: Color;\n shape!: string;\n\n // constructor(x: LineOptions) {\n // super([], x);\n // // const data = Object.assign({}, x);\n // const { x1, y1, x2, y2, width, color, shape } = x;\n\n // // console.log(\"Line constructor data:\", data);\n // // console.warn(\" this was using `meta` but it is deprecated now - should be using `original` instead\");\n // // this.meta = Object.keys(data)\n // // .filter(k => ['ID', 'x1', 'y1', 'x2', 'y2', 'size', 'color'].indexOf(k) < 0)\n // // .reduce((n: any, k: string) => { n[k] = data[k]; return n; }, {});\n\n // this.x1 = parseFloat(x1 as string);\n // this.y1 = parseFloat(y1 as string);\n // this.x2 = parseFloat(x2 as string);\n // this.y2 = parseFloat(y2 as string);\n // this.width = width;\n // this._color = color \|\| new Color('#000000');\n // this.shape = shape \|\| 'line';\n // }\n\n constructor(data: DataFrameRow \| any, from: Point, to: Point) {\n // let\n // // dimensions: DimensionType = data.classes.map( (c: string, i: number) => c === \"ena.co.occurrence\" ? data[i] : -1).filter(a => a !== -1),\n // // meta: any = data.classes.map( (c: string, i: number) => c === \"ena.metadata\" ? [data.names[i], data[i]] : null).filter(a => a !== null).reduce((n: any, c: any) => { n[c[0]] = c[1]; return n; }, {}),\n // // ID: string = data.rowName \|\| `point-${Math.random().toString(36).substring(2, 9)}`\n // ;\n\n super([], {} as any);\n\n this.from = from;\n this.to = to;\n }\n\n get line(): [[number, number], [number, number]] {\n return [[this.from.x, this.from.y], [this.to.x, this.to.y]];\n }\n get midpoint(): [number, number] {\n return [\n (this.from.x + this.to.x) / 2,\n (this.from.y + this.to.y) / 2\n ];\n }\n get length(): number {\n return Math.sqrt(\n Math.pow(this.to.x - this.from.x, 2) +\n Math.pow(this.to.y - this.from.y, 2)\n );\n }\n get color(): Color { return this._color; }\n set color(c: Color) { this._color = c; }\n}\n\nexport interface PointOptions extends PlottedObjectOptions {\n shape?: string;\n label?: string;\n [key: string]: any;\n}\n\nexport class Point extends PlottedObject {\n static SHAPES = { CIRCLE: 'circle', SQUARE: 'rect' };\n\n private _label: Label \| undefined;\n edges: Map<any, Edge> = new Map();\n shape: string = Point.SHAPES.CIRCLE;\n\n // constructor(dimensions: DimensionType, o: PointOptions) { //, graph?: any) {\n // super(dimensions, o);\n // this.active = o.active \|\| false;\n // this.visible = o.visible \|\| false;\n // this.size = o.size \|\| 1;\n // this.color = o.color \|\| new Color('#000000');\n // this.shape = o.shape ? o.shape : \"circle\";\n // this.scale_size = 2;\n // this._x = dimensions[0];\n // this._y = dimensions[1];\n // this.label = new Label(this.ID, this);\n // }\n constructor(data: DataFrameRow \| any) {\n let\n dimensions: DimensionType \| undefined, // = data.classes.map( (c, i) => (c === \"ena.co.occurrence\" \|\| c === \"ena.dimension\") ? data[i] : -1).filter(a => a !== -1),\n meta: any, // = data.classes.map( (c, i) => c === \"ena.metadata\" ? [data.names[i], data[i]] : null).filter(a => a !== null).reduce((n: any, c: any) => { n[c[0]] = c[1]; return n; }, {}),\n ID: string // = data.rowName \|\| `point-${Math.random().toString(36).substring(2, 9)}`\n ;\n\n if(data) {\n if(data instanceof DataFrameRow) {\n dimensions = data.classes?.map( (c, i) => (c === \"ena.co.occurrence\" \|\| c === \"ena.dimension\") ? data[i] : -1).filter(a => a !== -1);\n meta = data.classes?.map( (c, i) => c === \"ena.metadata\" ? [data.names[i], data[i]] : null).filter(a => a !== null).reduce((n: any, c: any) => { n[c[0]] = c[1]; return n; }, {});\n ID = data.rowName \|\| `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n else if(typeof data === \"object\") {\n dimensions = data.dimensions \|\| [];\n meta = data.meta \|\| {};\n ID = data.ID \|\| `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n else {\n console.warn(\"Invalid data provided for Point, using default values\");\n dimensions = [];\n meta = {};\n ID = `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n }\n else {\n dimensions = [];\n meta = {};\n ID = `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n\n super(dimensions ?? [], { meta, ID } as any);\n }\n\n set label(l: Label \| undefined) {\n this._label = l;\n }\n get label(): Label \| undefined {\n return this._label;\n }\n get x(): number {\n // const dims = this.graph.options.GRAPH.dimensions;\n // const _ = this.meta[dims[0]];\n // const mult = 1;\n // return parseFloat(_) * mult;\n return this._x;\n }\n get y(): number {\n // const dims = this.graph.options.GRAPH.dimensions;\n // const _ = this.meta[dims[1]];\n // const mult = 1;\n // return parseFloat(_) * mult;\n return this._y;\n }\n set x(x_: number) { this._x = parseFloat(x_ as any); }\n set y(y_: number) { this._y = parseFloat(y_ as any); }\n}\n\nexport class ConfidenceInterval extends PlottedObject {\n width?: number;\n z: number = 1.959964;\n // meta: any;\n\n private _mean: any;\n\n constructor(mean: any) {\n super(mean.dimensions, mean);\n this.ID = \"mean_ci_\" + mean.ID;\n this._mean = mean;\n }\n\n get line(): [[number, number], [number, number]] {\n // x1, y1, x2, y2 should be defined on mean or this\n return [\n [this._mean.x1, this._mean.y1],\n [this._mean.x2, this._mean.y2]\n ];\n }\n get variance(): [number, number] {\n const points = [...this._mean.points.values()];\n return [\n points.length > 1 ? points.map(p => Math.pow(p.x - this._mean.x, 2)).reduce((a, b) => a + b, 0) / (points.length - 1) : 0,\n points.length > 1 ? points.map(p => Math.pow(p.y - this._mean.y, 2)).reduce((a, b) => a + b, 0) / (points.length - 1) : 0\n ];\n }\n get std(): [number, number] {\n return this.variance.map(Math.sqrt) as [number, number];\n }\n get value(): [number, number] {\n const pointsSize = this._mean.points.size;\n return this.std.map(s => this.z * (s / Math.sqrt(pointsSize))) as [number, number];\n }\n get length(): number {\n const [a, b] = this.line;\n return Math.sqrt(Math.pow(b[0] - a[0], 2) + Math.pow(b[1] - a[1], 2));\n }\n\n get path(): string {\n const x_ = this._mean.x;\n const y_ = this._mean.y;\n const v = this.value;\n const x = v[0];\n const y = v[1];\n const xl = x_ - x;\n const xr = x_ + x;\n const yt = y_ - y;\n const yb = y_ + y;\n return `M${xl},${yt} ${xr},${yt} ${xr},${yb} ${xl},${yb}z`;\n }\n}\n\nexport class Label extends PlottedObject {\n object: PlottedObject;\n _visible: boolean = false;\n text: string;\n offset: number = 0;\n dragging?: boolean;\n\n constructor(txt: string, object: PlottedObject) {\n // super(object.ID);\n super(object.dimensions, object);\n this.text = txt;\n this.ID = object.ID;\n this.object = object;\n this.x = this.dimensions[0]; //object.x;\n this.y = this.dimensions[1]; //object.y;\n this.offset = object.size \|\| 0;\n this.size = this.offset / 4;\n this.visible = false;\n\n this._transform.set(\"e\", 1); // this.object.size * this.graph.SIZE_EFFECT * 2);\n this._transform.set(\"f\", 1); // this.object.size * this.graph.SIZE_EFFECT * 2);\n }\n\n get x(): number {\n return parseFloat(this._x);\n }\n get y(): number {\n return parseFloat(this._y);\n }\n set x(x_: number) { this._x = x_; }\n set y(y_: number) { this._y = y_; }\n\n get transform(): Transform {\n console.warn(\"transform is disabled - need updated reference for the graph options\")\n // if (\n // !this.dragging &&\n // this.graph.options[this.object.constructor.name.toUpperCase()].labelposition === Label.POSITION.OBJECT\n // ) {\n // const s = this.object.size;\n // const effect = 1; // this.graph.object.SIZE_EFFECT\n // this._transform.set(\"e\", s * effect / 2 / this._transform.a);\n // this._transform.set(\"f\", s * effect / 2 / this._transform.a);\n // } else if (\n // !this.dragging &&\n // this.graph.options[this.object.constructor.name.toUpperCase()].labelposition === Label.POSITION.STATIC\n // ) {\n // const eVal = this.graph.extremes[this.graph.options.LABEL.position[1] as keyof typeof this.graph.extremes];\n // const fVal = this.graph.extremes[this.graph.options.LABEL.position[0] as keyof typeof this.graph.extremes];\n // this._transform.set(\"e\", typeof eVal === \"number\" ? eVal : 0);\n // this._transform.set(\"f\", typeof fVal === \"number\" ? fVal : 0);\n // }\n return this._transform;\n }\n set transform(t: Transform) { this._transform = t; }\n\n static DISPLAY_TYPES = { OFF: 0, AUTO: 1, CLICK: 2, ON: 3 };\n static HIGHLIGHT = { OFF: 0, ON: 2 };\n static POSITION = { OBJECT: 1, STATIC: 2, CONTAINER: 3, CUSTOM: 4 };\n}\n","\nclass Extremes {\n x_max: number;\n y_max: number;\n // _point_max?: Point;\n // _node_max?: Point;\n\n /** Centre of the view; (0, 0) — the ENA origin — unless centred on the content /\n cx: number;\n cy: number;\n\n constructor(x: number, y: number, cx: number = 0, cy: number = 0) { //, n?: Point, p?: Point) {\n this.x_max = x;\n this.y_max = y;\n this.cx = cx;\n this.cy = cy;\n // this._point_max = p;\n // this._node_max = n;\n }\n as_viewBox(p: number = 1.2): string {\n let x = this.x_max p;\n let y = this.y_max * p;\n return (`${this.cx - x} ${this.cy - y} ${x * 2} ${y * 2}`);\n }\n\n // get point_max(): Point {\n // return this._point_max \|\| { x: 1, y: 1 };\n // }\n // get node_max(): Point {\n // return this._node_max \|\| { x: 1, y: 1 };\n // }\n\n get height(): number {\n return this.y_max * 2;\n } \n get width(): number {\n return this.x_max * 2;\n }\n get top(): number {\n return this.y_max * -1;\n }\n get bottom(): number {\n return this.y_max;\n }\n get left(): number {\n return this.x_max * -1;\n }\n get right(): number {\n return this.x_max;\n }\n}\n\nexport { Extremes };","import { DimensionVector, PlottedObject } from \"./PlottedObject\";\n\nexport class AxisPoint extends PlottedObject {\n\n constructor(dimensions: DimensionVector, o: any) {\n super(dimensions, o);\n\n this.visible = true;\n\n this.size = o.size;\n }\n\n set size(s: number) {\n this._size = s;\n }\n get size(): number {\n return this._size;\n }\n\n get x(): number {\n return this._x;\n }\n get y(): number {\n return this._y;\n }\n set x(x_: number) { this._x = x_; }\n set y(y_: number) { this._y = y_; }\n\n get transform() {\n return this._transform;\n }\n}","import { Color } from \"./Color\";\nimport { Layer, LayerArray, LayerLike } from \"./Layers\";\nimport { DimensionVector, Label, Line, Point } from \"./PlottedObject\";\nimport { Transform } from \"./Transform\";\nimport { Extremes } from \"./Extremes\";\nimport { Node } from \"./Points\";\nimport { Edge } from \"./Edges\";\nimport { AxisPoint } from \"./AxisPoint\";\nimport { DataFrame, DataFrameRow } from \"../types/DataFrame\";\nimport { EventBus as StateManager } from \"../types/EventBus\";\n\nexport let DefaultGraphOptions = {\n GRAPH: {\n ratio: 1,\n x_max: 1,\n y_max: 1,\n selector: \"body\",\n width: 1,\n height: 1,\n axes: true,\n SIZE_EFFECT: 1,\n dimensions: [ 0, 1 ]\n },\n NODE: {\n size: 1,\n highlight: {\n color: 'yellow',\n labels: Label.DISPLAY_TYPES.ON,\n },\n labels: Label.DISPLAY_TYPES.ON,\n labelposition: Label.POSITION.OBJECT\n },\n POINT: {\n active: 2,\n size: 0.05,\n color: \"#000\",\n shape: Point.SHAPES.CIRCLE,\n labels: Label.DISPLAY_TYPES.AUTO,\n labelposition: Label.POSITION.OBJECT\n },\n MEAN: {\n shape: Point.SHAPES.SQUARE,\n labels: Label.DISPLAY_TYPES.AUTO,\n },\n LABEL: {\n highlight: Label.HIGHLIGHT.OFF,\n position: ['top', 'left'],\n container: \"#label-container\"\n },\n EDGE: {\n multiplier: 1\n }\n};\n\nexport class Graph {\n __state__: StateManager = new StateManager();\n\n name: string = \"unnamed-graph\";\n origin: AxisPoint \| undefined = undefined;\n\n options: typeof DefaultGraphOptions;\n\n points: Map<string, Point \| AxisPoint> = new Map();\n nodes: Map<string, Node> = new Map();\n edges: Map<string, Edge> = new Map();\n trajectories: Map<string, any> = new Map();\n labels: Map<string, Label> = new Map();\n transform: Transform = new Transform();\n\n scale_x: number = 1;\n scale_y: number = 1;\n\n _extremes!: Extremes;\n SIZE_EFFECT: number = 1;\n _mirror_y: boolean = true;\n _mirror_x: boolean = false;\n\n layers: LayerArray;\n _layers: LayerArray = new LayerArray(\n { name: \"graph\", tabindex: 0, layers: [\n { \n name: \"axes\",\n layers: [\n { \n name: \"axis_lines\", tabindex: 0, layers: [], \n objects: [\n\n ]\n },\n { \n name: \"axis_labels\", tabindex: 0, layers: [], objects: []\n },\n {\n name: \"axis_points\", \n tabindex: 0, \n layers: [], \n objects: [\n this.origin\n ]\n }\n ]\n },\n\n {\n name: \"network\",\n layers: [\n { name: \"edges\", layers: [], tabindex: 0 },\n { name: \"nodes\", layers: [], tabindex: 0 },\n { name: \"edgenodes\", layers: [], tabindex: 0 },\n ]\n },\n { name: \"trajectories\", layers: [], tabindex: 0 },\n { name: \"points\", layers: [], tabindex: 0 },\n\n { name: \"labels\", layers: [], tabindex: 0 },\n ] },\n );\n\n constructor(\n options: typeof DefaultGraphOptions = { ...DefaultGraphOptions }\n ) {\n this.options = options;\n \n this.origin = new AxisPoint(\n new DimensionVector(0, 0),\n {\n ID: \"origin\",\n x: 0, y: 0,\n size: 0,\n meta: {},\n graph: this,\n color: new Color(\"#FFFFFF\"),\n highlight: new Color(\"#FFFFFF\"),\n active: false\n }\n );\n\n let layer_id = 1;\n function buildLayerTree(layerData: any, parent: Layer \| null, graph: Graph): Layer {\n const new_layer = new Layer(`${layer_id}`, layerData, graph);\n layer_id += 1;\n new_layer.parent = parent \|\| undefined;\n if (layerData.layers && Array.isArray(layerData.layers)) {\n new_layer.layers = new LayerArray(...layerData.layers.map((child: any) => buildLayerTree(child, new_layer, graph)));\n }\n return new_layer;\n }\n\n this.layers = new LayerArray(...this._layers.map((l: any) => buildLayerTree(l, null, this)));\n\n let axisPointLayer: LayerLike \| undefined = this.layers.search(\"layers\", \"axis_points\");\n if (axisPointLayer) {\n axisPointLayer.objects.set(this.origin.ID, this.origin);\n }\n \n let axisLineLayer: LayerLike \| undefined = this.layers.search(\"layers\", \"axis_lines\");\n if (axisLineLayer) {\n let extremes = this.extremes \|\| new Extremes(1, 1);\n let axis_x = new Line(\n {}, \n new Point({ ID: \"axis-x-start\", dimensions: [-extremes.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] }), \n new Point({ ID: \"axis-x-end\", dimensions: [extremes.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] })\n );\n axis_x.ID = \"axis-x\";\n axisLineLayer.objects.set(axis_x.ID, axis_x);\n let axis_y = new Line(\n {}, \n new Point({ ID: \"axis-y-start\", dimensions: [0, -extremes.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] }),\n new Point({ ID: \"axis-y-end\", dimensions: [0, extremes.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] })\n );\n axis_y.ID = \"axis-y\";\n axisLineLayer.objects.set(axis_y.ID, axis_y);\n console.log(\"Added axis lines to layer: \", axisLineLayer);\n }\n\n // Define extremes based on options\n this.extremes = new Extremes(options.GRAPH.x_max, options.GRAPH.y_max);\n }\n\n set extremes(e: Extremes) {\n this._extremes = e;\n }\n get extremes(): Extremes {\n return this._extremes;\n }\n get mirror_x(): boolean {\n return this._mirror_x;\n }\n set mirror_x(m: boolean) {\n this._mirror_x = m;\n }\n get mirror_y(): boolean {\n return this._mirror_y;\n }\n set mirror_y(m: boolean) {\n this._mirror_y = m;\n }\n\n x_mirror(): number {\n return (this.mirror_x ? -1 : 1);\n }\n y_mirror(): number {\n return (this.mirror_y ? -1 : 1);\n }\n\n add_point(p: DataFrameRow) {\n const point: Point = new Point(p);\n this.points.set(point.ID, point);\n\n // if (g_.options.POINT && g_.options.POINT.label) {\n // p.label = new Label(p.meta[g_.options.POINT.label], p, g_);\n // g_.labels.set(p.label.ID, p.label);\n // }\n // g_.points.set(p.ID, p);\n // const pointsLayer = g_.layers.search(\"layers\", \"points\");\n // if (pointsLayer) {\n // pointsLayer.objects.push(p);\n // }\n // g_.update_extremes();\n }\n add_points(ps: DataFrame) {\n let g_ = this;\n ps.rows().forEach((p: DataFrameRow) => {\n g_.add_point(p);\n });\n }\n\n add_nodes(ns: any[]) {\n let\n g_ = this\n ;\n\n ns.forEach((new_node) => {\n // if (g_.options.NODE && g_.options.NODE.label) {\n // new_node.label = new Label(new_node.meta[g_.options.NODE.label], new_node, g_);\n new_node.label = new Label(new_node.ID, new_node);\n g_.labels.set(new_node.label.ID, new_node.label);\n // }\n g_.nodes.set(new_node.ID, new_node);\n const nodesLayer = g_.layers.search(\"layers\", \"nodes\");\n if (nodesLayer) {\n nodesLayer.objects.push(new_node);\n }\n });\n g_.update_extremes();\n }\n add_edge(e: any, from?: any, to?: any) {\n let g_ = this;\n g_.edges.set(e.ID, e);\n\n this.add_nodes([from \|\| e.from, to \|\| e.to]);\n\n return (e);\n }\n add_edges(es: any[]) {\n let added = es.map(e => this.add_edge(e));\n const edgesLayer = this.layers.search(\"layers\", \"edges\");\n if (edgesLayer) {\n edgesLayer.objects.push(...added);\n }\n return (added);\n }\n\n /*\n The visible extent: 1.3 × the farthest point or node. Centred on the\n * origin (the ENA convention: (0, 0) is the mean of the points), or with\n * `centerContent`, on the middle of the points' and nodes' bounding box, so\n * a network that sits off to one side of the origin fills the plot.\n /\n update_extremes(centerContent: boolean = false) {\n // let\n // dim1 = this.options.GRAPH.dimensions[0],\n // dim2 = this.options.GRAPH.dimensions[1],\n // // Get all points and nodes to calculate extremes\n // all_points = [...this.points.values(), ...this.nodes.values()].flat(),\n // x_max = Math.max(...all_points.map((p: PlottedObject) => Math.abs(p.dimension(dim1) \|\| 0))),\n // y_max = Math.max(...all_points.map((p: PlottedObject) => Math.abs(p.dimension(dim2) \|\| 0))),\n // max = Math.max(x_max, y_max)\n // ;\n // this.extremes = new Extremes(Math.ceil(max), Math.ceil(max), { x: 1, y: 1 }, { x: 1, y: 1 });\n\n const search_layers = [\n this.layers.search(\"layers\", \"points\"),\n this.layers.search(\"layers\", \"nodes\")\n ].filter((l): l is LayerLike => l !== undefined);\n if (search_layers.length === 0) {\n this.extremes = new Extremes(1, 1);\n }\n else {\n // Bound = largest \|x\|/\|y\| across points and nodes, plus a modest margin\n // for peripheral node labels. The previous Math.ceil() snapped this up to\n // the next integer, which — for ENA's small coordinate ranges (≈1–2) —\n // left the network floating in a lot of dead space. Keep the raw value so\n // the drawing fills the canvas.\n let minX = Infinity, maxX = -Infinity, minY = Infinity, maxY = -Infinity;\n search_layers.forEach(l => l.objects.forEach((o: any) => {\n if (Number.isFinite(o.x)) { minX = Math.min(minX, o.x); maxX = Math.max(maxX, o.x); }\n if (Number.isFinite(o.y)) { minY = Math.min(minY, o.y); maxY = Math.max(maxY, o.y); }\n }));\n const found = Number.isFinite(minX) && Number.isFinite(minY);\n const cx = centerContent && found ? (minX + maxX) / 2 : 0;\n const cy = centerContent && found ? (minY + maxY) / 2 : 0;\n const content_max = found\n ? Math.max(Math.abs(minX - cx), Math.abs(maxX - cx), Math.abs(minY - cy), Math.abs(maxY - cy))\n : 0;\n const found_max = (content_max > 0 ? content_max : 1) 1.3;\n this.extremes = new Extremes(found_max, found_max, cx, cy);\n }\n }\n\n /** Farthest node from (cx, cy), on either axis /\n nodeExtentFrom(cx: number, cy: number): number {\n const nodes = this.layers.search(\"layers\", \"nodes\");\n let max = 0;\n nodes?.objects.forEach((o: any) => {\n if (Number.isFinite(o.x) && Number.isFinite(o.y)) max = Math.max(max, Math.abs(o.x - cx), Math.abs(o.y - cy));\n });\n return max;\n }\n\n base_point_size(scale = 8): number {\n let minDim = Math.min(this.extremes.x_max, this.extremes.y_max);\n let n = this.points.size + this.nodes.size;\n return Math.min(1, minDim / (Math.sqrt(n) scale));\n }\n}\n","import { Graph } from \"../objects/Graph\";\nimport { Layer } from \"../objects/Layers\";\nimport { PlottedObject } from \"../objects/PlottedObject\";\n\nexport abstract class DrawableElement extends HTMLElement {\n \n static style: string = `\n :host {\n max-width: 100%;\n display: block;\n }\n .wrapper {\n height: 100%;\n display: flex;\n justify-content: center;\n }\n `;\n\n element: Element \| null = null;\n object: PlottedObject \| Graph \| Layer \| null = null;\n\n get wrapper() {\n const\n element = this,\n shadow = element.shadowRoot,\n wrapper = shadow?.querySelector(\".wrapper\")\n ;\n return wrapper;\n }\n\n constructor() {\n super();\n\n const\n element = this,\n shadow = element.attachShadow({ mode: 'open' }),\n style = document.createElement('style'),\n wrapper = document.createElement('div')\n ;\n\n style.textContent = (this.constructor as any).style;\n shadow.appendChild(style);\n\n wrapper.setAttribute('class', 'wrapper');\n shadow.appendChild(wrapper);\n }\n}","// Pure, DOM-free polynomial trajectory fitting.\n//\n// Ported from `ena.plot.trajectory()` in the ETM Explorer (RescuShell) R kit:\n// - near-origin filtering of the fit set (points at the cumulative origin are\n// drawn but excluded from the fit),\n// - `loocv_2d` degree selection (joint 2D leave-one-out CV via the hat-matrix\n// shortcut), with a `fixed` escape hatch,\n// - least-squares polynomial fit solved by QR for numerical parity with R's\n// `lm(y ~ poly(t, deg))`.\n//\n// Leverages and residuals depend only on the column space of the design, so a\n// raw monomial basis solved by QR reproduces R's selected degree and fitted\n// curve to floating-point tolerance despite R using orthogonal `poly()`.\n\n/** Near-origin tolerance; hardcoded to match the R kit's `zero_eps` default. /\nexport const TRAJECTORY_ZERO_EPS = 1e-8;\n\nexport interface XY {\n x: number;\n y: number;\n}\n\nexport type DegreeSelection = 'loocv_2d' \| 'fixed';\n\nexport interface TrajectoryFit {\n degree: number;\n coeffsX: number[];\n coeffsY: number[];\n}\n\n/* Drop near-origin points (both coords within eps of 0) from the fit set. /\nexport function nearOriginFilter(pts: XY[], eps: number = TRAJECTORY_ZERO_EPS): XY[] {\n return pts.filter(p => Math.abs(p.x) > eps \|\| Math.abs(p.y) > eps);\n}\n\n/* Evenly spaced parameter t in [0,1] by index — matches R's seq(0,1,length.out=n). /\nfunction normalizedT(n: number): number[] {\n if (n <= 0) return [];\n if (n === 1) return [0];\n const t = new Array(n);\n for (let i = 0; i < n; i++) t[i] = i / (n - 1);\n return t;\n}\n\n/* Vandermonde design [1, t, t^2, ..., t^deg], n×(deg+1). /\nfunction design(t: number[], degree: number): number[][] {\n return t.map(ti => {\n const row = new Array(degree + 1);\n let p = 1;\n for (let k = 0; k <= degree; k++) {\n row[k] = p;\n p = ti;\n }\n return row;\n });\n}\n\n/*\n Modified Gram-Schmidt QR. `A` is n×m (n >= m). Returns Q (n×m, orthonormal\n * columns) and R (m×m upper triangular). More stable than raw normal equations,\n * matching what R's `lm` does internally.\n /\nfunction qr(A: number[][]): { Q: number[][]; R: number[][] } {\n const n = A.length;\n const m = A[0].length;\n const Q = A.map(row => row.slice());\n const R = Array.from({ length: m }, () => new Array(m).fill(0));\n for (let j = 0; j < m; j++) {\n let norm = 0;\n for (let i = 0; i < n; i++) norm += Q[i][j] Q[i][j];\n norm = Math.sqrt(norm);\n R[j][j] = norm;\n if (norm > 1e-300) {\n for (let i = 0; i < n; i++) Q[i][j] /= norm;\n }\n for (let k = j + 1; k < m; k++) {\n let dot = 0;\n for (let i = 0; i < n; i++) dot += Q[i][j] * Q[i][k];\n R[j][k] = dot;\n for (let i = 0; i < n; i++) Q[i][k] -= dot * Q[i][j];\n }\n }\n return { Q, R };\n}\n\n/** Qᵀy (length m). /\nfunction qtY(Q: number[][], y: number[]): number[] {\n const n = Q.length;\n const m = Q[0].length;\n const out = new Array(m).fill(0);\n for (let j = 0; j < m; j++) {\n let s = 0;\n for (let i = 0; i < n; i++) s += Q[i][j] y[i];\n out[j] = s;\n }\n return out;\n}\n\n/** Back-substitution for R c = b, R upper triangular m×m. /\nfunction backSolve(R: number[][], b: number[]): number[] {\n const m = b.length;\n const c = new Array(m).fill(0);\n for (let i = m - 1; i >= 0; i--) {\n let s = b[i];\n for (let j = i + 1; j < m; j++) s -= R[i][j] c[j];\n c[i] = Math.abs(R[i][i]) > 1e-12 ? s / R[i][i] : 0;\n }\n return c;\n}\n\n/** Leverages h_ii = sum_j Q[i][j]^2 (diagonal of the hat matrix). /\nfunction leverages(Q: number[][]): number[] {\n return Q.map(row => {\n let s = 0;\n for (let j = 0; j < row.length; j++) s += row[j] row[j];\n return s;\n });\n}\n\n/** Least-squares monomial coefficients for y ~ poly(t, degree). /\nfunction fitCoeffs(t: number[], y: number[], degree: number): number[] {\n const X = design(t, degree);\n const { Q, R } = qr(X);\n return backSolve(R, qtY(Q, y));\n}\n\n/* Evaluate a monomial polynomial (ascending coeffs) at t. /\nexport function evalPoly(coeffs: number[], t: number): number {\n let v = 0;\n let p = 1;\n for (let k = 0; k < coeffs.length; k++) {\n v += coeffs[k] p;\n p = t;\n }\n return v;\n}\n\n/\n Joint 2D leave-one-out CV PRESS for a candidate degree. x(t) and y(t) share\n * one design (hence one hat matrix), so LOO residuals are e_i / (1 - h_ii).\n * Returns Infinity for a degenerate (saturated) fit so it is never selected.\n /\nfunction loocv2d(t: number[], x: number[], y: number[], degree: number): number {\n const X = design(t, degree);\n const { Q, R } = qr(X);\n const h = leverages(Q);\n const cx = backSolve(R, qtY(Q, x));\n const cy = backSolve(R, qtY(Q, y));\n let press = 0;\n for (let i = 0; i < t.length; i++) {\n const denom = 1 - h[i];\n if (denom <= 0) return Infinity;\n const ex = x[i] - evalPoly(cx, t[i]);\n const ey = y[i] - evalPoly(cy, t[i]);\n press += (ex / denom) * 2 + (ey / denom) 2;\n }\n return press;\n}\n\n/\n * Select a degree in 1..min(maxDegree, n-1). For `loocv_2d`, minimises the joint\n * 2D LOOCV PRESS; ties resolve to the smallest degree (matching R's which.min).\n * For `fixed`, or when there are too few points to run CV, returns the cap.\n /\nexport function selectDegree(fitPts: XY[], maxDegree: number, mode: DegreeSelection): number {\n const n = fitPts.length;\n const cap = Math.min(Math.max(1, Math.floor(maxDegree)), Math.max(1, n - 1));\n if (mode === 'fixed' \|\| n < 3) return cap;\n const t = normalizedT(n);\n const x = fitPts.map(p => p.x);\n const y = fitPts.map(p => p.y);\n let best = 1;\n let bestVal = Infinity;\n for (let deg = 1; deg <= cap; deg++) {\n const v = loocv2d(t, x, y, deg);\n if (v < bestVal) {\n bestVal = v;\n best = deg;\n }\n }\n return best;\n}\n\n/\n Fit a trajectory polynomial. The near-origin filter is applied to both the\n * per-frame points and the (optional) full-trajectory `selectionSet`. The degree\n * is chosen on `selectionSet` when given — so it stays constant as a playhead\n * scrubs a growing prefix — then clamped to what the current frame can support,\n * and the coefficients are re-fit on the current frame's points.\n \n Returns null when fewer than three non-origin points are available (matching\n * the R kit's n_fit < 3 guard); callers should fall back to raw steps.\n /\nexport function fitTrajectory(\n activePts: XY[],\n opts: { maxDegree: number; degreeSelection: DegreeSelection; selectionSet?: XY[] \| null }\n): TrajectoryFit \| null {\n const fitPts = nearOriginFilter(activePts);\n if (fitPts.length < 3) return null;\n\n const selBasis = opts.selectionSet ? nearOriginFilter(opts.selectionSet) : fitPts;\n const basis = selBasis.length >= 3 ? selBasis : fitPts;\n let degree = selectDegree(basis, opts.maxDegree, opts.degreeSelection);\n\n // A growing playhead prefix may hold fewer points than the held degree needs.\n degree = Math.min(degree, Math.max(1, fitPts.length - 1));\n\n const t = normalizedT(fitPts.length);\n const coeffsX = fitCoeffs(t, fitPts.map(p => p.x), degree);\n const coeffsY = fitCoeffs(t, fitPts.map(p => p.y), degree);\n return { degree, coeffsX, coeffsY };\n}\n\n/* Sample the fitted curve at steps+1 evenly spaced points over t in [0,1]. /\nexport function sampleCurve(fit: TrajectoryFit, steps = 100): XY[] {\n const out: XY[] = [];\n for (let s = 0; s <= steps; s++) {\n const t = s / steps;\n out.push({ x: evalPoly(fit.coeffsX, t), y: evalPoly(fit.coeffsY, t) });\n }\n return out;\n}\n","import { PlottedObject, PlottedObjectOptions, Point } from './PlottedObject';\nimport { Color } from './Color';\nimport { DegreeSelection, fitTrajectory, sampleCurve } from './polyfit';\n\nexport interface TrajectoryOptions {\n ID?: string;\n unitId?: string;\n points?: Point[] \| { x: number; y: number; time?: number; label?: string }[];\n color?: Color \| string;\n smooth?: 'none' \| 'poly' \| 'spline';\n maxDegree?: number;\n degreeSelection?: DegreeSelection;\n polyCoeffsX?: number[];\n polyCoeffsY?: number[];\n currentTime?: number;\n showPoints?: boolean;\n showTips?: boolean;\n lineStyle?: 'uniform' \| 'tapered';\n strokeWidth?: number;\n strokeWidthRange?: [number, number];\n opacityRange?: [number, number];\n size?: number;\n active?: boolean;\n meta?: any;\n [key: string]: any;\n}\n\nconst TRAJECTORY_CURVE_STEPS = 100;\n\nexport class Trajectory extends PlottedObject {\n readonly _typeName: string = 'Trajectory';\n trajPoints: Point[] = [];\n smooth: 'none' \| 'poly' \| 'spline' = 'none';\n maxDegree: number = 3;\n degreeSelection: DegreeSelection = 'loocv_2d';\n /* Degree chosen at the most recent fit; -1 until a poly curve is built. /\n selectedDegree: number = -1;\n polyCoeffsX: number[] = [];\n polyCoeffsY: number[] = [];\n currentTime: number = Infinity;\n showPoints: boolean = true;\n showTips: boolean = true;\n lineStyle: 'uniform' \| 'tapered' = 'uniform';\n strokeWidth: number = 2;\n strokeWidthRange: [number, number] = [1, 6];\n opacityRange: [number, number] = [0.3, 1];\n\n constructor(options: TrajectoryOptions = {}) {\n const defaultColor = options.color instanceof Color ? options.color : new Color(typeof options.color === 'string' ? options.color : '#000000');\n super([], {\n ID: options.ID \|\| `traj-${Math.random().toString(36).substring(2, 9)}`,\n size: options.size \|\| 1,\n color: defaultColor,\n highlight: null,\n active: options.active \|\| false,\n meta: options.meta \|\| {},\n ...options\n } as PlottedObjectOptions);\n\n this.smooth = options.smooth \|\| 'none';\n this.maxDegree = options.maxDegree !== undefined ? options.maxDegree : 3;\n this.degreeSelection = options.degreeSelection \|\| 'loocv_2d';\n this.polyCoeffsX = options.polyCoeffsX \|\| [];\n this.polyCoeffsY = options.polyCoeffsY \|\| [];\n this.currentTime = options.currentTime !== undefined ? options.currentTime : Infinity;\n this.showPoints = options.showPoints !== undefined ? options.showPoints : true;\n this.showTips = options.showTips !== undefined ? options.showTips : true;\n this.lineStyle = options.lineStyle \|\| 'uniform';\n this.strokeWidth = options.strokeWidth \|\| 2;\n this.strokeWidthRange = options.strokeWidthRange \|\| [1, 6];\n this.opacityRange = options.opacityRange \|\| [0.3, 1];\n\n if (options.points && Array.isArray(options.points)) {\n this.trajPoints = options.points.map(p => {\n if (p instanceof Point) return p;\n const pt = new Point({ dimensions: [p.x, p.y], meta: { time: p.time, label: p.label } });\n pt.x = p.x;\n pt.y = p.y;\n return pt;\n });\n }\n }\n\n get activePoints(): Point[] {\n if (this.currentTime === Infinity) {\n return this.trajPoints;\n }\n return this.trajPoints.filter(p => {\n const t = (p.meta && typeof p.meta.time === 'number') ? p.meta.time : 0;\n return t <= this.currentTime;\n });\n }\n\n get path(): string {\n return this.pathPoints.reduce((acc, pt, idx) => {\n return idx === 0 ? `M${pt.x},${pt.y}` : `${acc} L${pt.x},${pt.y}`;\n }, '');\n }\n\n get pathPoints(): Array<{ x: number; y: number }> {\n const pts = this.activePoints;\n if (pts.length < 2) return [];\n\n if (this.smooth === 'poly') {\n // Precomputed coefficients override the fit (caller-supplied curve).\n if (this.polyCoeffsX.length > 0 && this.polyCoeffsY.length > 0) {\n return sampleCurve(\n { degree: this.polyCoeffsX.length - 1, coeffsX: this.polyCoeffsX, coeffsY: this.polyCoeffsY },\n TRAJECTORY_CURVE_STEPS\n );\n }\n\n // Select the degree on the full trajectory so it stays constant while a\n // playhead scrubs a growing prefix; fit coefficients on the visible frame.\n const fit = fitTrajectory(\n pts.map(p => ({ x: p.x, y: p.y })),\n {\n maxDegree: this.maxDegree,\n degreeSelection: this.degreeSelection,\n selectionSet: this.trajPoints.map(p => ({ x: p.x, y: p.y }))\n }\n );\n if (fit) {\n this.selectedDegree = fit.degree;\n return sampleCurve(fit, TRAJECTORY_CURVE_STEPS);\n }\n // Too few non-origin points to fit — fall back to raw steps below.\n }\n\n return pts.map(pt => ({ x: pt.x, y: pt.y }));\n }\n}\n","import { PlottedObject, Line, PlottedObjectOptions } from './PlottedObject.js';\nimport { Node } from './Points.js';\nimport { Color, WeightedColor } from './Color.js';\nimport { Tools } from '../utils/Tools.js';\nimport { DataFrameRow } from '../types/DataFrame.js';\n\n// Placeholder for zoom level, should be defined in the context of the application\nconst zoom_level = 1;\n\nexport class Edge extends Line {\n declare from: Node;\n declare to: Node;\n _totalweight: number = 0;\n _weight: number;\n declare _color: WeightedColor;\n\n constructor(data: DataFrameRow \| any, from: Node, to: Node, weight: number = 0) {\n super(data, from, to);\n this._weight = weight;\n }\n\n get base_color(): Color { return this._color };\n get color(): WeightedColor {\n const base = this._color \|\| new Color(\"#000000\");\n return new WeightedColor(base, Math.abs(this.weight));\n }\n set color(c: Color) { this._color = c as any; }\n\n base_weight() { return this._weight };\n get weight() {\n // let w = Array.isArray(this.#weight) ? this.#weight.reduce( (a, b) => a - b, 0) : this.#weight;\n let w = Array.isArray(this._weight) ? (this._weight[0] - this._weight[1]) : this._weight;\n return w; // this.graph.options.EDGE.multiplier\n }\n set weight(w) {\n this._weight = w;\n }\n\n get totalweight(): number {\n return this.weight;\n }\n set totalweight(w: number) {\n this._totalweight = w;\n }\n}\n\nexport class SubtractedEdges extends Edge {\n edge_one: Edge;\n edge_two: Edge;\n\n #weight: number;\n #color: WeightedColor;\n\n constructor(e1: Edge, e2: Edge) {\n super(e1, e1.from, e1.to);\n\n this.edge_one = e1;\n this.edge_two = e2;\n\n this.#weight = this.edge_one.weight - this.edge_two.weight;\n\n let\n color_type_fn: new (color: Color \| string, weight: number) => WeightedColor = this.edge_one.color.constructor as any,\n color: string = this.edge_one.color.base\n ;\n if (this.weight > 0) {\n color = this.edge_one.color.base;\n }\n else {\n color = this.edge_two.color.base;\n }\n\n this.#color = new color_type_fn(color, this.#weight);\n }\n\n get weight() {\n return this.#weight;\n }\n set weight(w) {\n this.#weight = w;\n }\n\n get color() {\n return this.#color;\n }\n set color(c) {\n this.#color = c;\n }\n}\n\nexport class MeanEdge extends Edge {\n edges: Set<Edge> = new Set<Edge>();\n\n constructor(o: any) {\n super(o, o.from, o.to);\n\n this.visible = true;\n // this.meta = o.meta \|\| { ID: this.ID };\n }\n\n // get weight() { return __.math.mean([...this.edges.values()].map( e => e.weight )) * this.graph.options.EDGE.multiplier; }\n get weight() {\n let wt = Tools.Mathematics.mean([...this.edges.values()].map((e: Edge) => e.weight)) * 1;\n return wt;\n }\n set weight(w) { this._weight = w; }\n\n get path() {\n return `M${this.from.x} ${this.from.y} L${this.to.x} ${this.to.y}z`;\n }\n\n get totalweight() {\n return Array.from(this.edges).reduce((acc, edge) => acc + edge.totalweight, 0);\n }\n}\n\nexport class EdgeArrow extends PlottedObject {\n #edge;\n\n constructor(edge: PlottedObjectOptions) {\n super(edge.dimensions \|\| [], edge);\n this.#edge = edge;\n }\n\n get edge() {\n return this.#edge;\n }\n\n get path(): string {\n /*\n \n * mid_int0 nock_int0\n * --------------------------------- <- edge of arrow from midpoint to base_pt0\n * / /\n * / /\n * / /\n * / /\n * / /\n * / /\n * <-- edge node head--> * * * <-- nock ---> edge midpoint this way ---->\n * \\ ^-mid \|\n * \\ \| \\ \|\n * \\ \| \\ \| <---- showing line from nock to edge used to find\n * \\ \| \\ \| intersection with edge\n * \\\| \\\|\n * --------------------------------- <- edge of arrow from midpoint to base_pt1\n * mid_int1---^ ^----nock_int1\n \n /\n // Pure vector geometry on the tapered edge: T = target (wide end, base\n // points B0/B1), A = apex. The chevron sits 20% of the way from T toward\n // A, but its length follows the triangle's local width (≈ a constant\n // shape) rather than a fixed share of the edge length — on long, thin\n // edges the old fractional sizing stretched it into a sliver. (The old\n // slope-intercept intersections also misbehaved on near-vertical edges.)\n const _this = this.#edge;\n const T: [number, number] = [_this.to.x, _this.to.y];\n const A: [number, number] = _this.from_point;\n const [B0, B1] = _this.base_pts as [[number, number], [number, number]];\n const L = Math.hypot(A[0] - T[0], A[1] - T[1]);\n const W = Math.hypot(B0[0] - B1[0], B0[1] - B1[1]);\n if (!(L > 0) \|\| !(W > 0)) return '';\n const u = [(A[0] - T[0]) / L, (A[1] - T[1]) / L]; // along the edge, T → A\n const b = Math.hypot(B0[0] - T[0], B0[1] - T[1]);\n const v = [(B0[0] - T[0]) / b, (B0[1] - T[1]) / b]; // across, toward B0\n const halfW = (d: number) => (W / 2) * Math.max(0, 1 - d / L);\n const at = (d: number, s: number) => `${T[0] + u[0] * d + v[0] * s} ${T[1] + u[1] * d + v[1] * s}`;\n\n const dh = 0.2 * L; // head\n const c = Math.min(0.15 * L, 0.8 * 2 * halfW(dh)); // length ≈ local width\n const dm = dh + c / 2, dn = dh + c; // notch, back\n const p = `M${at(dh, 0)} L${at(dm, halfW(dm))} L${at(dn, halfW(dn))} ` +\n `L${at(dm, 0)} L${at(dn, -halfW(dn))} L${at(dm, -halfW(dm))}z`;\n return p;\n }\n}\n\nexport enum EdgeDirection {\n FROM = 'from',\n TO = 'to'\n}\n\nexport class TaperedEdge extends Edge {\n // base_pts = [];\n _path: string = '';\n // Arrowheads are off by default — the tapered triangle shape already\n // communicates direction. Enabling #with_arrow currently throws because\n // EdgeArrow.constructor passes the edge as the lone super() arg.\n #with_arrow = false;\n #arrow;\n\n _directions: EdgeDirection[] = [EdgeDirection.FROM, EdgeDirection.TO];\n towards: EdgeDirection = EdgeDirection.TO;\n\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n\n if (this.#with_arrow === true) {\n this.#arrow = new EdgeArrow(this);\n }\n }\n\n get path(): string {\n return `M${this.from.x} ${this.from.y} L${this.base_pts[0].join(' ')} L${this.base_pts[1].join(' ')}z`;\n }\n static calculate_base_points(edg: TaperedEdge): [[number, number], [number, number]] {\n // Find the two endpoints of the tapered edge based on its `towards` direction.\n const top: EdgeDirection = edg.towards;\n const base: EdgeDirection = edg._directions.find(d => d !== edg.towards) as EdgeDirection;\n\n const bx = edg[base].x, by = edg[base].y;\n const tx = edg[top].x, ty = edg[top].y;\n const dx = tx - bx, dy = ty - by;\n const L = Math.hypot(dx, dy);\n\n // Degenerate: zero-length edge or unset weight — collapse to a point at `top`.\n const wt = (edg.weight ?? 0) * zoom_level;\n if (L === 0 \|\| !isFinite(wt) \|\| wt === 0) {\n return [[tx, ty], [tx, ty]];\n }\n\n // Unit perpendicular to the edge direction; offset both sides by wt/2.\n // Pure vector math here avoids the slope-intercept form used by\n // Tools.Geometry, which produces NaN for vertical edges and ill-conditioned\n // values for horizontal ones.\n const px = -dy / L, py = dx / L;\n const halfW = wt / 2;\n return [\n [tx + px * halfW, ty + py * halfW],\n [tx - px * halfW, ty - py * halfW],\n ];\n }\n get base_pts() {\n return TaperedEdge.calculate_base_points(this);\n }\n get arrow() {\n return this.#arrow;\n }\n get with_arrow() {\n return this.#with_arrow;\n }\n get from_point() {\n return [this.from.x, this.from.y];\n }\n}\n\nexport class TaperedMidpointEdge extends TaperedEdge {\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n }\n\n get path(): string {\n return `M${this.midpoint[0]} ${this.midpoint[1]} L${this.base_pts[0].join(' ')} L${this.base_pts[1].join(' ')}z`;\n }\n get from_point(): [number, number] {\n return this.midpoint;\n }\n}\n\nexport class TaperedWeightedMidpointEdge extends TaperedEdge {\n // Preserve the original data weight so that QELine.update()'s\n // `edge.weight = sw * 4` (which sets _weight for display sizing) doesn't\n // corrupt the midpoint calculation.\n private _dataWeight: number = 0;\n\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n this._totalweight = data.totalweight ?? 0;\n this._dataWeight = data.weight ?? this._weight;\n }\n\n get weighted_midpoint(): [number, number] {\n return Tools.Geometry.Line.interpolate(this.line)(1 - (this._dataWeight / this._totalweight));\n }\n\n get base_pts(): [[number, number], [number, number]] {\n return TaperedEdge.calculate_base_points(this);\n }\n\n static build_path(edg: TaperedWeightedMidpointEdge \| MeanTaperedWeightedMidpointEdge): string {\n if (edg._totalweight > 0) {\n let p = `M${edg.weighted_midpoint[0]} ${edg.weighted_midpoint[1]} L${edg.base_pts[0].join(' ')} L${edg.base_pts[1].join(' ')}z`;\n\n return p\n }\n else {\n console.error(\"TaperedWeightedMidpointEdge: No totalweight, returning empty path\");\n return '';\n }\n }\n get path(): string {\n return TaperedWeightedMidpointEdge.build_path(this);\n }\n\n get from_point() {\n return this.weighted_midpoint;\n }\n}\n\nexport class MeanNodeEdge extends MeanEdge {\n constructor(o: any) {\n super(o);\n }\n get path() {\n return NodeEdge.build_path(this.weight, [...this.edges.values()][0].to)\n }\n get weight() {\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.weight)) * 1;\n }\n set weight(w) { this._weight = w; }\n}\n\nexport class MeanTaperedEdge extends MeanEdge {\n #with_arrow = true;\n #arrow;\n\n constructor(o: PlottedObjectOptions) {\n super(o);\n\n if (this.#with_arrow === true) {\n this.#arrow = new EdgeArrow(this);\n }\n }\n\n get with_arrow() {\n return this.#with_arrow;\n }\n get arrow() {\n return this.#arrow;\n }\n get from_point() {\n return [this.from.x, this.from.y];\n }\n}\n\nexport class MeanTaperedMidpointEdge extends MeanTaperedEdge {\n constructor(o: PlottedObjectOptions) {\n super(o);\n }\n\n get base_pts(): [[number, number], [number, number]] {\n const\n top = EdgeDirection.TO,\n base = EdgeDirection.FROM\n ;\n\n let\n edge_line: [[number, number], [number, number]] = [[this[base].x, this[base].y], [this[top].x, this[top].y]],\n perp_line = Tools.Geometry.Line.rotate2(edge_line, edge_line[1], 90),\n ints = Tools.Geometry.Line.intersect_circle(perp_line, edge_line[1], this.weight / 2)\n ;\n\n return ints;\n }\n get path(): string {\n return `M${this.midpoint[0]} ${this.midpoint[1]} L${this.base_pts[0].join(' ')} L${this.base_pts[1].join(' ')}z`;\n }\n get weight(): number {\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.weight)) * 1;\n }\n set weight(w) { this._weight = w; }\n}\n\nexport class MeanTaperedWeightedMidpointEdge extends MeanTaperedEdge {\n constructor(o: PlottedObjectOptions) {\n super(o);\n }\n\n get totalweight(): number {\n // debugger;\n // console.error(\"THIS NEEDS THE MEAN WEIGHT OF ITS COUNTERPART (FROM -> TO -- TO --> FROM)\")\n // or does the mean of the edges.totalweight equal to the same?\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.totalweight));\n }\n\n get weighted_midpoint() {\n // console.log(\"Weighted: \", this.weight, this.totalweight)\n return Tools.Geometry.Line.interpolate(this.line)(1 - (this.weight / this.totalweight))\n }\n\n get base_pts() {\n const\n top = EdgeDirection.TO, //this.#directions[this.#directions.findIndex( d => d === this.towards )],\n base = EdgeDirection.FROM //this.#directions[this.#directions.findIndex( d => d !== this.towards )]\n ;\n\n let\n edge_line: [[number, number], [number, number]] = [[this[base].x, this[base].y], [this[top].x, this[top].y]],\n perp_line = Tools.Geometry.Line.rotate2(edge_line, edge_line[1], 90),\n ints = Tools.Geometry.Line.intersect_circle(perp_line, edge_line[1], this.weight / 2)\n ;\n\n return ints;\n }\n\n get path() {\n let p = TaperedWeightedMidpointEdge.build_path(this)\n // console.log(\"Static p: \", p);\n return p;\n }\n get weight() {\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.weight)) * 1;\n }\n set weight(w) { this._weight = w; }\n}\n\nexport class NodeEdge extends Edge {\n\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n }\n\n static build_path(weight: number, to: Node) {\n let\n R = weight / 2,\n CX = to.x - R,\n R2 = R * 2,\n p = `M ${CX}, ${to.y} a ${R},${R} 0 1,0 ${R2},0 a ${R},${R} 0 1,0 -${R2},0`\n ;\n\n return p;\n }\n\n get path() {\n let wt = this.weight * zoom_level; //this.graph.get_graphs()[0].object.SIZE_EFFECT;\n return NodeEdge.build_path(wt, this.to);\n }\n}\n","import { PlottedObject } from \"../objects/PlottedObject\";\nimport { QEArray, } from \"./QELayer\";\nimport { QEGraphElement } from \"./QEGraph\";\n\nexport abstract class Drawable {\n abstract create(): SVGElement;\n \n svg_element: SVGElement;\n\n constructor(\n public __data__: PlottedObject, \n public parent: SVGElement, \n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray()\n ) {\n this.svg_element = this.create();\n }\n\n get_size() {\n return this.__data__.size;\n }\n\n draw() {\n this.parent?.appendChild(this.svg_element);\n }\n\n update(elem: SVGElement, animate = true) {\n // this.update(elem);\n }\n\n animateSVGAttribute(elem: SVGElement, attr: string, to: number) {\n const from = parseFloat(elem.getAttribute(attr) \|\| '0');\n if (from === to) return;\n\n const duration = 5000;\n const start = performance.now();\n function animate(now: number) {\n const t = Math.min(1, (now - start) / duration);\n const value = from + (to - from) * t;\n elem.setAttribute(attr, value.toString());\n if (t < 1) requestAnimationFrame(animate);\n else elem.setAttribute(attr, to.toString());\n }\n requestAnimationFrame(animate);\n }\n}\n","// Shared mark-size and colour rules, sizes in units of the coordinate extent.\n//\n// Width follows webENA: absolute, raw weight × a constant (`edge-width`, as a\n// fraction of the plot width), so equal weights draw equally wide in graphs of\n// the same size. That one width-per-weight drives undirected strokes, the\n// wide ends of directed edges, self-connection dots, and code nodes (whose\n// diameter is the sum of their edges' widths).\n//\n// Colour follows webENA's ramps (saturation 0.25–1, opacity 0.3–1), but the\n// rescaling range is taken across the whole model rather than per network.\n\n/** Default `<qe-graph edge-width>`: the width of an edge of weight 1 as a\n * fraction of the plot width. Width is absolute — raw weight × this — as in\n * webENA, so equal weights get equal widths in graphs of the same size. /\nexport const DEFAULT_EDGE_WIDTH = 0.04;\n\n/* webENA's colour ramps: non-zero weights are rescaled linearly from the\n * reference [min, max] onto these saturation and opacity ranges. /\nexport const SATURATION_RANGE: [number, number] = [0.25, 1];\nexport const OPACITY_RANGE: [number, number] = [0.3, 1];\n\n/* Linear map of \|w\| from [lo, hi] onto `range`; 0 stays 0 (not drawn). /\nexport function rampFor(w: number, lo: number, hi: number, range: [number, number]): number {\n const a = Math.abs(w);\n if (!(a > 0)) return 0;\n if (!(hi > lo)) return range[1];\n const t = Math.min(1, Math.max(0, (a - lo) / (hi - lo)));\n return range[0] + t (range[1] - range[0]);\n}\n\n/** Edge stroke width for edges drawn outside the network rule (fallback). /\nexport const EDGE_WIDTH_PER_EXTENT = 0.011;\n\n/* On-screen width (CSS px) of the outline drawn around directed (tapered)\n * edges so long, thin triangles stay legible along their whole length. /\nexport const TAPERED_OUTLINE_PX = 0.75;\n\n/* Direction chevrons on directed edges: RGB multiplier applied to the\n * (opaque, white-flattened) edge colour, and the white halo's on-screen\n * width in CSS px. /\nexport const CHEVRON_DARKEN = 0.8;\nexport const CHEVRON_HALO_PX = 0.75;\n\n/* Point radius per unit of `size` (QEPoint). /\nexport const POINT_RADIUS_PER_EXTENT = 0.006;\n\n/* `size` for a code node with no drawn edges: a tiny dot that still marks\n * where the code sits (hide it with <qe-nodes unconnected=\"hide\">). /\nexport const UNCONNECTED_NODE_SIZE = 0.6;\n\n/* Width per unit of weight in extent units (plot width = 2 × extent). /\nexport function widthPerWeight(edgeWidth: number): number {\n return 2 edgeWidth;\n}\n\n/** QEPoint `size` for a node whose diameter equals the summed widths of its\n * edges, `weightSum × widthFrac` (both in extent units). /\nexport function nodeSizeForEdges(weightSum: number, widthFrac: number): number {\n return (weightSum widthFrac) / (2 * POINT_RADIUS_PER_EXTENT);\n}\n","import { Line } from \"../objects/PlottedObject\";\nimport { NodeEdge, TaperedEdge, EdgeArrow } from \"../objects/Edges\";\nimport { Color, WeightedColor } from \"../objects/Color\";\nimport { Drawable } from \"./Drawable\";\nimport { QEArray, QEElement } from \"./QELayer\";\nimport { QEGraphElement } from \"./QEGraph\";\nimport { CHEVRON_DARKEN, CHEVRON_HALO_PX, EDGE_WIDTH_PER_EXTENT, TAPERED_OUTLINE_PX } from \"../objects/Sizing\";\n\n/** Composite an rgba() colour over white, returning an opaque rgb(). /\nfunction flattenOnWhite(col: string): string {\n const m = /rgba?\$([^)]+)\$/.exec(col);\n if (!m) return col;\n const [r, g, b, a = 1] = m[1].split(',').map(Number);\n const f = (c: number) => Math.round(255 + (c - 255) a);\n return `rgb(${f(r)},${f(g)},${f(b)})`;\n}\n\n/** Scale an rgba()/rgb() colour's RGB channels by `k` (alpha unchanged). /\nfunction darkenRgba(col: string, k: number): string {\n const m = /rgba?\$([^)]+)\$/.exec(col);\n if (!m) return col;\n const [r, g, b, a = 1] = m[1].split(',').map(Number);\n return `rgba(${Math.round(r k)},${Math.round(g * k)},${Math.round(b * k)},${a})`;\n}\n\nexport class QELine extends Drawable implements QEElement {\n __name__: string = \"unnamed-line\";\n // Optional second element for the direction-indicator chevron on directed edges.\n private _arrow_el: SVGPathElement \| null = null;\n // Invisible wide companion line giving thin undirected edges a clickable/\n // hoverable hit target for the qe-edge-* interaction events.\n private _hit_el: SVGLineElement \| null = null;\n\n /** Stamp edge identity onto an element so <qe-graph> delegation can resolve\n * qe-edge-* events. No-op for non-edges (e.g. axis lines). /\n private _stampEdge(el: SVGElement): void {\n const meta = (this.__data__ as any).meta ?? {};\n if (!meta.isMeanEdge) return;\n el.setAttribute('data-edge-source', String(meta.source ?? ''));\n el.setAttribute('data-edge-target', String(meta.target ?? ''));\n el.setAttribute('data-edge-weight', String(meta.weight ?? 0));\n el.setAttribute('data-edge-directed', meta.isDirected ? 'true' : 'false');\n if (meta.isSelf) el.setAttribute('data-edge-self', 'true');\n if (meta.group != null) el.setAttribute('data-edge-group', String(meta.group));\n if (meta.unit != null) el.setAttribute('data-edge-unit', String(meta.unit));\n }\n\n constructor(\n public __data__: Line,\n public parent: SVGElement,\n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray(),\n ) {\n super(__data__, parent, graph, __children__);\n\n this.svg_element = this.create();\n }\n\n create() {\n if (this.__data__ instanceof NodeEdge) {\n // Self-connection: filled circle inside the node, sized by weight.\n const path = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n path.setAttribute('fill', this.__data__.color.toString());\n path.setAttribute('stroke', 'none');\n this.svg_element = path;\n return path;\n }\n\n if (this.__data__ instanceof TaperedEdge) {\n // Directed edges render as filled triangles via TaperedEdge.path.\n // A second SVG path is reserved for the direction-indicator chevron;\n // it is populated lazily in update() once meta.isDirected is known.\n const path = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n path.setAttribute('fill', this.__data__.color.toString());\n path.setAttribute('stroke', 'none');\n this.svg_element = path;\n return path;\n }\n\n const line = document.createElementNS('http://www.w3.org/2000/svg', 'line');\n line.setAttribute('x1', this.__data__.from.x.toString());\n line.setAttribute('y1', this.__data__.from.y.toString());\n line.setAttribute('x2', this.__data__.to.x.toString());\n line.setAttribute('y2', this.__data__.to.y.toString());\n line.setAttribute('stroke-width', this.get_size().toString());\n line.setAttribute('stroke', this.__data__.color.toString());\n\n this.svg_element = line;\n return line;\n }\n\n update() {\n if (!this.svg_element) {\n this.create();\n }\n if (!this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n\n const extent = (this.graph.__data__ as any).extremes?.x_max ?? 1;\n const meta = (this.__data__ as any).meta ?? {};\n\n if (meta.isMeanEdge) {\n this._stampEdge(this.svg_element);\n const weight = typeof meta.weight === 'number' ? meta.weight : 0;\n const maxW = typeof meta.maxWeight === 'number' ? meta.maxWeight : 1;\n const opacity = typeof meta.opacity === 'number' ? meta.opacity : Math.min(1, weight / (maxW \|\| 1));\n // Target ≈ multiplier×5 in plotly-px to match rENA (ena.plot.network\n // default: multiplier=5, width = raw_weight × 5). For a ±2.66-extent\n // coordinate space rendered at ~460px, 1 data-unit ≈ 86px, so\n // rENA's max stroke (0.47 × 5 ≈ 2.4px) ≈ 0.028 data units.\n // Factor 0.011 × extent(2.66) × 1.0 ≈ 0.029 → ~2.5px at 86px/unit.\n // Width = weight × the plot's shared width-per-weight (objects/Sizing.ts);\n // the fallback keeps edges visible if an edge arrives without one.\n const ext = extent > 0 ? extent : 1;\n const sw = typeof meta.widthFrac === 'number'\n ? ext meta.widthFrac * weight\n : ext * EDGE_WIDTH_PER_EXTENT * (weight / (maxW \|\| 1));\n\n // Build a WeightedColor from the stored base color + normalized weight so\n // that toString() produces hsla(h, sw%, l%, w) — matching the Web ENA\n // convention of scaling both saturation and alpha together with weight.\n const baseColor = (this.__data__ as any)._color \|\| new Color('#000000');\n // Saturation and opacity come from the graph's colour ramps\n // (<qe-edges color-scale>); older edges carry only opacity.\n const saturation = typeof meta.saturation === 'number' ? meta.saturation : opacity;\n const edgeColor = new WeightedColor(baseColor, saturation, opacity).toString();\n\n if (this.__data__ instanceof NodeEdge) {\n // Diameter = the self weight's width (same width-per-weight as edges\n // and nodes), matching ona. The node's diameter includes this self\n // weight, so the dot always fits inside it. Computed here because the\n // live extent is not known when the edge objects are built.\n (this.__data__ as NodeEdge).weight = sw;\n (this.svg_element as SVGPathElement).setAttribute('d', (this.__data__ as NodeEdge).path);\n this.svg_element.setAttribute('fill', edgeColor);\n this.svg_element.setAttribute('stroke', 'none');\n } else if (this.__data__ instanceof TaperedEdge) {\n // TaperedEdge.path uses .weight as the total base width (the wide end,\n // at the target node); node sizes sum these base widths.\n (this.__data__ as TaperedEdge).weight = sw;\n (this.svg_element as SVGPathElement).setAttribute('d', (this.__data__ as TaperedEdge).path);\n this.svg_element.setAttribute('fill', edgeColor);\n // Hairline outline (constant on-screen width, same weighted colour as\n // the fill). A long, thin triangle tapers below a pixel for most of its\n // length; the outline keeps the whole connection legible without\n // changing its width or colour encoding (ona draws a similar halo).\n this.svg_element.setAttribute('stroke', edgeColor);\n this.svg_element.setAttribute('stroke-width', String(TAPERED_OUTLINE_PX));\n this.svg_element.setAttribute('vector-effect', 'non-scaling-stroke');\n this.svg_element.setAttribute('stroke-linejoin', 'round');\n\n // ── Direction-indicator chevron ──────────────────────────────────────\n // For directed mean edges, overlay an EdgeArrow chevron filled with a\n // more-opaque/saturated version of the edge colour. Rendered over the\n // semi-transparent triangle body, the fully-opaque fill reads as a\n // visibly darker notch that indicates the direction without introducing\n // a foreign colour.\n if (meta.isDirected) {\n try {\n const arrow = new EdgeArrow(this.__data__ as any);\n const arrowPath = arrow.path;\n // Discard degenerate paths that contain NaN or Infinity (geometry\n // collapsed — zero-length edge, parallel lines, etc.).\n if (arrowPath && !arrowPath.includes('NaN') && !arrowPath.includes('Infinity')) {\n if (!this._arrow_el) {\n this._arrow_el = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n this._arrow_el.setAttribute('stroke', 'none');\n }\n if (!this._arrow_el.parentElement) {\n this.parent.appendChild(this._arrow_el);\n }\n this._arrow_el.setAttribute('d', arrowPath);\n // As ona draws arrows: the edge's weighted colour flattened onto\n // white (\"fake alpha\", so it is opaque and weak edges still get\n // lighter chevrons), then darkened — plus ona's optional white\n // halo, at a constant on-screen width, so it stands out from the\n // triangle it sits on.\n this._arrow_el.setAttribute('fill', darkenRgba(flattenOnWhite(edgeColor), CHEVRON_DARKEN));\n this._arrow_el.setAttribute('stroke', '#ffffff');\n this._arrow_el.setAttribute('stroke-width', String(CHEVRON_HALO_PX));\n this._arrow_el.setAttribute('vector-effect', 'non-scaling-stroke');\n this._arrow_el.setAttribute('stroke-linejoin', 'round');\n }\n } catch (_) {\n // EdgeArrow geometry degenerates for very short or zero-weight edges —\n // silently skip rather than crashing the render loop.\n }\n }\n } else {\n // Regular undirected edge\n const x1 = this.__data__.from.x, y1 = this.__data__.from.y;\n const x2 = this.__data__.to.x, y2 = this.__data__.to.y;\n (this.svg_element as SVGLineElement).setAttribute('x1', x1.toString());\n (this.svg_element as SVGLineElement).setAttribute('y1', y1.toString());\n (this.svg_element as SVGLineElement).setAttribute('x2', x2.toString());\n (this.svg_element as SVGLineElement).setAttribute('y2', y2.toString());\n this.svg_element.setAttribute('stroke-width', sw.toString());\n this.svg_element.setAttribute('stroke', edgeColor);\n this.svg_element.setAttribute('pointer-events', 'stroke');\n this.svg_element.removeAttribute('marker-end');\n\n // Transparent wide hit target so thin edges are clickable/hoverable.\n // Sized to a comfortable minimum regardless of the visible stroke width.\n if (!this._hit_el) {\n this._hit_el = document.createElementNS('http://www.w3.org/2000/svg', 'line');\n this._hit_el.setAttribute('stroke', 'transparent');\n this._hit_el.setAttribute('stroke-linecap', 'round');\n this._hit_el.setAttribute('pointer-events', 'stroke');\n }\n if (!this._hit_el.parentElement) this.parent.appendChild(this._hit_el);\n this._hit_el.setAttribute('x1', x1.toString());\n this._hit_el.setAttribute('y1', y1.toString());\n this._hit_el.setAttribute('x2', x2.toString());\n this._hit_el.setAttribute('y2', y2.toString());\n this._hit_el.setAttribute('stroke-width', Math.max(sw, extent 0.03).toString());\n this._stampEdge(this._hit_el);\n }\n } else {\n // Thin axis lines: ~0.4% of coordinate extent\n (this.svg_element as SVGLineElement).setAttribute('x1', this.__data__.from.x.toString());\n (this.svg_element as SVGLineElement).setAttribute('y1', this.__data__.from.y.toString());\n (this.svg_element as SVGLineElement).setAttribute('x2', this.__data__.to.x.toString());\n (this.svg_element as SVGLineElement).setAttribute('y2', this.__data__.to.y.toString());\n const sw = (extent > 0 ? extent : 1) * 0.004 * this.get_size();\n this.svg_element.setAttribute('stroke-width', sw.toString());\n this.svg_element.setAttribute('stroke-opacity', '1');\n this.svg_element.setAttribute('stroke', this.__data__.color.toString());\n }\n }\n\n draw() {\n if (this._hit_el) this.parent?.appendChild(this._hit_el);\n this.parent?.appendChild(this.svg_element);\n if (this._arrow_el) {\n this.parent?.appendChild(this._arrow_el);\n }\n }\n}\n","import { PlottedObject } from \"../objects/PlottedObject\";\nimport { Drawable } from \"./Drawable\";\nimport { QEArray, QEElement } from \"./QELayer\";\nimport { QEGraphElement } from \"./QEGraph\";\nimport { POINT_RADIUS_PER_EXTENT } from \"../objects/Sizing\";\n\nexport class QEPoint extends Drawable implements QEElement {\n __name__: string = \"unnamed-point\";\n\n constructor(\n public __data__: PlottedObject,\n public parent: SVGElement,\n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray(),\n ) {\n super(__data__, parent, graph, __children__);\n\n this.svg_element = this.create();\n }\n\n get x() {\n return this.__data__.dimensions[this.graph.__data__.options.GRAPH.dimensions[0]];\n }\n get y() {\n return this.__data__.dimensions[this.graph.__data__.options.GRAPH.dimensions[1]];\n }\n\n get isSquare(): boolean {\n return (this.__data__ as any).shape === 'rect';\n }\n\n /** \"circle\" (default) \| \"rect\" \| \"triangle\" \| \"diamond\". /\n get shapeKind(): 'circle' \| 'rect' \| 'triangle' \| 'diamond' {\n const s = (this.__data__ as any).shape;\n return s === 'rect' \|\| s === 'square' ? 'rect'\n : s === 'triangle' \|\| s === 'diamond' ? s : 'circle';\n }\n\n /* SVG tag for the current shape. /\n private get tag(): string {\n const k = this.shapeKind;\n return k === 'circle' ? 'circle' : k === 'rect' ? 'rect' : 'path';\n }\n\n /* Position / size the element for its shape (r = half-size). /\n private setGeometry(el: SVGElement, r: number): void {\n const x = this.x, y = this.y;\n switch (this.shapeKind) {\n case 'rect':\n el.setAttribute('x', (x - r).toString()); el.setAttribute('y', (y - r).toString());\n el.setAttribute('width', (r 2).toString()); el.setAttribute('height', (r * 2).toString());\n break;\n case 'triangle': {\n // Equilateral, pointing up (SVG y-down), centred on the point.\n const h = r * 1.15;\n el.setAttribute('d', `M${x} ${y - h} L${x + h * 0.866} ${y + h * 0.5} L${x - h * 0.866} ${y + h * 0.5}Z`);\n break;\n }\n case 'diamond':\n el.setAttribute('d', `M${x} ${y - r * 1.2} L${x + r} ${y} L${x} ${y + r * 1.2} L${x - r} ${y}Z`);\n break;\n default:\n el.setAttribute('cx', x.toString()); el.setAttribute('cy', y.toString());\n el.setAttribute('r', r.toString());\n }\n }\n\n /** Half-side length for squares / radius for circles, in SVG user units.\n * Factor 0.006 keeps code-node diameters in the same visual range as rENA\n * (≈ 1–2 % of the coordinate half-extent for a typical ENA network).\n /\n computeRadius(): number {\n const r = this.baseRadius();\n // Optional ceiling (user units): group means are capped to their CI box so\n // a tight interval is never hidden under the marker.\n const cap = (this.__data__ as any).meta?.maxRadius;\n return typeof cap === 'number' && cap > 0 ? Math.min(r, cap) : r;\n }\n\n private baseRadius(): number {\n const extent = (this.graph.__data__.extremes.x_max) \|\| 1;\n const sizeScale = (this.__data__ as any).meta?.sizeScale ?? 1;\n // Fixed-on-screen mode (webENA size decoupling): keep a constant pixel size\n // regardless of data extent / container size / wheel-zoom, by converting a\n // target px into user units via the current px-per-unit and zoom. Otherwise\n // size scales with the coordinate space (default — nodes/edges do the same).\n if ((this.__data__ as any).meta?.fixedSize) {\n const rect = (this.graph.svg_element as SVGSVGElement)?.getBoundingClientRect?.();\n const zoom = (this.graph as any).zoom_level \|\| 1;\n const pxPerUnit = rect && rect.width > 0 ? rect.width / (2 extent) : 1;\n const targetPx = this.__data__.size * 2 * sizeScale; // size 2.5 → 5px radius\n return (targetPx / pxPerUnit) / zoom;\n }\n return extent * POINT_RADIUS_PER_EXTENT * this.__data__.size * sizeScale;\n }\n\n /** Optional halo stroke (e.g. white outline on unit points to separate\n * overlapping dots in dense clusters). Width scales with the dot so it holds\n * up at any zoom. No-op unless the object requests it via meta.stroke. /\n private applyStroke(el: SVGElement): void {\n const stroke = (this.__data__ as any).meta?.stroke;\n if (!stroke) return;\n el.setAttribute('stroke', stroke);\n el.setAttribute('stroke-width', (this.computeRadius() 0.22).toString());\n }\n\n create() {\n const el = document.createElementNS('http://www.w3.org/2000/svg', this.tag) as SVGElement;\n\n el.setAttribute('data-point-id', this.__data__.ID);\n // Identity for <qe-graph> delegation → qe-node-* interaction events.\n const meta = (this.__data__ as any).meta ?? {};\n if (meta.kind) el.setAttribute('data-kind', meta.kind);\n if (meta.name != null) el.setAttribute('data-name', String(meta.name));\n if (meta.group != null) el.setAttribute('data-group', String(meta.group));\n if (meta.unit != null) el.setAttribute('data-unit', String(meta.unit));\n el.setAttribute('fill', this.__data__.color.toString());\n this.applyStroke(el);\n\n this.setGeometry(el, this.computeRadius());\n\n this.svg_element = el;\n\n el.addEventListener('click', () => {\n // Note: do NOT stopPropagation — the click must bubble to <qe-graph>'s\n // delegation so it can emit the public qe-node-click event.\n this.__data__.active = !this.__data__.active;\n this.update();\n\n const pointEvent = new CustomEvent('point-clicked', {\n detail: { pointData: this.__data__ },\n bubbles: true, composed: true\n });\n this.svg_element.dispatchEvent(pointEvent);\n });\n\n el.addEventListener('mouseover', () => {\n // Do not stopPropagation — the parent SVG uses mouseover delegation\n // to show AUTO-mode labels. The fill is already set; this handler is\n // retained as a hook for future hover-highlight logic.\n });\n\n return el;\n }\n\n update() {\n if (!this.svg_element) {\n (this.parent as any).__data__.__children__.push(this.create());\n }\n if (!this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n\n this.svg_element.setAttribute('fill', this.__data__.color.toString());\n this.applyStroke(this.svg_element);\n this.setGeometry(this.svg_element, this.computeRadius());\n }\n\n draw() {\n this.parent?.appendChild(this.svg_element);\n }\n}\n","import { Trajectory } from '../objects/Trajectory';\nimport { Drawable } from './Drawable';\nimport { QEArray, QEElement } from './QELayer';\nimport { QEGraphElement } from './QEGraph';\n\nexport class QETrajectory extends Drawable implements QEElement {\n __name__: string = 'trajectory';\n private _path_el: SVGPathElement \| null = null;\n private _segments_group: SVGGElement \| null = null;\n private _tip_el: SVGCircleElement \| null = null;\n private _points_group: SVGGElement \| null = null;\n\n constructor(\n public __data__: Trajectory,\n public parent: SVGElement,\n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray()\n ) {\n super(__data__, parent, graph, __children__);\n this.svg_element = this.create();\n }\n\n // Trajectory styling is specified in display pixels, while SVG paths use\n // graph coordinates. Convert at render time so marks stay legible at any scale.\n private graphUnitsForPixels(pixels: number): number {\n const extent = this.graph.__data__.extremes.x_max \|\| 1;\n const width = this.graph.svg_element?.getBoundingClientRect().width \|\| 0;\n return width > 0 ? pixels * (2 * extent / width) : pixels * extent * 0.006;\n }\n\n create() {\n const group = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n group.setAttribute('class', 'qe-trajectory-group');\n\n const path = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n path.setAttribute('fill', 'none');\n path.setAttribute('stroke', this.__data__.color.toString());\n path.setAttribute('stroke-width', this.graphUnitsForPixels(this.__data__.strokeWidth).toString());\n group.appendChild(path);\n this._path_el = path;\n\n const segmentsGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n segmentsGroup.setAttribute('class', 'qe-trajectory-segments');\n group.appendChild(segmentsGroup);\n this._segments_group = segmentsGroup;\n\n const pointsGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n pointsGroup.setAttribute('class', 'qe-trajectory-points');\n group.appendChild(pointsGroup);\n this._points_group = pointsGroup;\n\n if (this.__data__.showTips) {\n const tip = document.createElementNS('http://www.w3.org/2000/svg', 'circle');\n tip.setAttribute('fill', this.__data__.color.toString());\n tip.setAttribute('r', this.graphUnitsForPixels(4).toString());\n tip.setAttribute('stroke', '#ffffff');\n tip.setAttribute('stroke-width', this.graphUnitsForPixels(1.5).toString());\n group.appendChild(tip);\n this._tip_el = tip;\n }\n\n this.svg_element = group;\n return group;\n }\n\n update() {\n if (!this.svg_element) {\n this.create();\n }\n if (!this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n\n const dStr = this.__data__.path;\n if (this._path_el) {\n this._path_el.setAttribute('d', dStr);\n this._path_el.setAttribute('stroke', this.__data__.color.toString());\n this._path_el.setAttribute('stroke-width', this.graphUnitsForPixels(this.__data__.strokeWidth).toString());\n this._path_el.style.display = this.__data__.lineStyle === 'tapered' ? 'none' : 'block';\n }\n\n if (this._segments_group) {\n this._segments_group.innerHTML = '';\n if (this.__data__.lineStyle === 'tapered') {\n const pathPts = this.__data__.pathPoints;\n const nSegments = pathPts.length - 1;\n const [minWidth, maxWidth] = this.__data__.strokeWidthRange;\n const [minOpacity, maxOpacity] = this.__data__.opacityRange;\n\n for (let i = 0; i < nSegments; i++) {\n const start = pathPts[i];\n const end = pathPts[i + 1];\n const progress = nSegments <= 1 ? 1 : i / (nSegments - 1);\n const width = minWidth + (maxWidth - minWidth) * progress;\n const opacity = minOpacity + (maxOpacity - minOpacity) * progress;\n const segment = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n\n segment.setAttribute('d', `M${start.x},${start.y} L${end.x},${end.y}`);\n segment.setAttribute('fill', 'none');\n segment.setAttribute('stroke', this.__data__.color.toString());\n segment.setAttribute('stroke-linecap', 'round');\n segment.setAttribute('stroke-linejoin', 'round');\n segment.setAttribute('stroke-width', this.graphUnitsForPixels(width).toString());\n segment.setAttribute('opacity', opacity.toString());\n this._segments_group.appendChild(segment);\n }\n this._segments_group.style.display = 'block';\n } else {\n this._segments_group.style.display = 'none';\n }\n }\n\n const pts = this.__data__.activePoints;\n\n if (this._points_group) {\n if (this.__data__.showPoints && pts.length > 0) {\n this._points_group.innerHTML = '';\n pts.forEach(pt => {\n const dot = document.createElementNS('http://www.w3.org/2000/svg', 'circle');\n dot.setAttribute('cx', pt.x.toString());\n dot.setAttribute('cy', pt.y.toString());\n dot.setAttribute('r', this.graphUnitsForPixels(2.5).toString());\n dot.setAttribute('fill', this.__data__.color.toString());\n dot.setAttribute('opacity', '0.7');\n this._points_group?.appendChild(dot);\n });\n this._points_group.style.display = 'block';\n } else {\n this._points_group.style.display = 'none';\n }\n }\n\n if (this._tip_el && this.__data__.showTips) {\n if (pts.length > 0) {\n const lastPt = pts[pts.length - 1];\n this._tip_el.setAttribute('cx', lastPt.x.toString());\n this._tip_el.setAttribute('cy', lastPt.y.toString());\n this._tip_el.setAttribute('fill', this.__data__.color.toString());\n this._tip_el.setAttribute('r', this.graphUnitsForPixels(4).toString());\n this._tip_el.setAttribute('stroke-width', this.graphUnitsForPixels(1.5).toString());\n this._tip_el.style.display = 'block';\n } else {\n this._tip_el.style.display = 'none';\n }\n }\n }\n\n draw() {\n if (this.svg_element && !this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n this.update();\n }\n}\n","import { Tools } from \"../utils/Tools\";\nimport { Graph } from \"../objects/Graph\";\nimport { Layer, LayerLike } from \"../objects/Layers\";\nimport { PlottedObject, Point } from \"../objects/PlottedObject\";\nimport { Trajectory } from \"../objects/Trajectory\";\nimport { QELine } from \"./QELine\";\nimport { QEPoint } from \"./QEPoint\";\nimport { QETrajectory } from \"./QETrajectory\";\nimport { QEGraphElement } from \"./QEGraph\";\n\n\nconst { ArrayTools } = Tools;\nexport class QEArray extends Array<any> {\n constructor(...args: any[]) {\n super(...args);\n }\n\n search(key: string, name: string): LayerLike \| undefined {\n let found: LayerLike \| undefined;\n\n function fn(a: LayerLike): LayerLike \| undefined {\n return a.name === name ? a : undefined;\n }\n\n function recurse(obj: any, i?: number, parent: any = null): LayerLike \| undefined {\n if (ArrayTools.isArray(obj)) {\n for (const [i, o] of obj.entries()) {\n found = recurse(o, i, parent);\n if (found) {\n return found;\n }\n }\n } else {\n found = fn(obj);\n if (!found) {\n if (obj && ArrayTools.isArray(obj[key])) {\n for (const [i, o] of obj[key].entries()) {\n found = recurse(o, i, obj);\n if (found) {\n return found;\n }\n }\n }\n } else {\n return found;\n }\n }\n return found;\n }\n\n return recurse(this);\n }\n\n flatten(): LayerLike[] {\n return this.reduce<LayerLike[]>((a, l: LayerLike) => {\n a.push(l);\n if (l.layers && Array.isArray(l.layers)) {\n a.push(...l.layers);\n }\n return a;\n }, []);\n }\n}\n\nexport interface QEElement {\n svg_element: SVGElement;\n graph: QEGraphElement;\n parent: SVGElement \| null;\n __name__: string;\n __data__: Graph \| PlottedObject \| LayerLike;\n __children__: QEArray;\n draw(): void;\n update(): void;\n}\n\nconst\n QEElementConstructors: Record<string, new (d: any, p: SVGElement, g: QEGraphElement) => QEElement> =\n {\n \"AxisPoint\": QEPoint,\n \"AxisLine\": QELine,\n \"Point\": QEPoint,\n \"Line\": QELine,\n \"Edge\": QELine,\n \"TaperedEdge\": QELine,\n \"TaperedWeightedMidpointEdge\": QELine,\n \"NodeEdge\": QELine,\n \"Trajectory\": QETrajectory,\n }\n;\n\nexport class QELayer implements QEElement {\n static tagName = 'g';\n\n svg_element: SVGElement; \n __name__: string;\n\n constructor(\n public __data__: Layer, \n public parent: SVGElement, \n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray(),\n ) {\n this.__name__ = __data__.name \|\| \"unnamed-layer\";\n\n __data__.__state__.addListener(`layer_updated`, \"live\", ({ key, newValue, oldValue } : any) => {\n const childId = (child: QEElement) => (child.__data__ as PlottedObject)?.ID;\n\n const removing = this.__children__.filter((child: QEElement) =>\n !newValue.objects.has(childId(child))\n );\n const updating = this.__children__.filter((child: QEElement) =>\n newValue.objects.has(childId(child))\n );\n const adding = [...newValue.objects.values()].filter((obj: PlottedObject) =>\n !this.__children__.some((child: QEElement) => childId(child) === obj.ID)\n );\n\n adding.forEach((obj: PlottedObject) => {\n const obj_name = (obj as any)._typeName \|\| obj.constructor.name;\n let constructor = QEElementConstructors[obj_name];\n if (!constructor) {\n if (obj instanceof Trajectory) constructor = QETrajectory;\n else if (obj instanceof Point) constructor = QEPoint;\n else constructor = QELine;\n }\n const ena_element: QEElement = new constructor(obj, this.svg_element, this.graph);\n this.__children__.push(ena_element);\n });\n\n updating.forEach((child: QEElement) => {\n // Pull the new PlottedObject from the updated layer data so that any\n // changed properties (e.g. weight, color, meta flags) are picked up by\n // the child's update() call.\n const newData = newValue.objects.get(childId(child)) as PlottedObject;\n if (newData) (child as any).__data__ = newData;\n child.update();\n });\n\n removing.forEach((child: QEElement) => {\n if (child.svg_element.parentElement) {\n child.svg_element.parentElement.removeChild(child.svg_element);\n }\n const idx = this.__children__.indexOf(child);\n if (idx >= 0) this.__children__.splice(idx, 1);\n });\n\n this.update();\n });\n\n this.svg_element = this.create();\n }\n\n get name() {\n return this.__name__;\n }\n\n create(): SVGElement {\n if(!this.__data__) {\n throw new Error(\"Layer is null\");\n }\n let layer: Layer = this.__data__ as Layer;\n this.svg_element = document.createElementNS(\"http://www.w3.org/2000/svg\", QELayer.tagName);\n this.svg_element.setAttribute('data-layer-name', layer.name);\n this.svg_element.setAttribute('data-layer-id', layer.ID);\n\n (this.svg_element as any).__data__ = layer;\n\n this.svg_element.classList.add('ena-layer');\n\n if(this.__data__.layers && this.__data__.layers.length > 0) {\n this.__data__.layers.forEach((sublayer: LayerLike) => {\n const layer_g: QELayer = new QELayer(sublayer as any, this.svg_element, this.graph);\n this.__children__.push(layer_g);\n });\n }\n\n return this.svg_element;\n }\n\n update() {\n if(!this.__data__) {\n throw new Error(\"Layer is null\");\n }\n\n if(this.__data__.visible) {\n // Update layer properties here\n if(this.parent.nodeName.toLowerCase() === \"svg\") {\n // Compute the transform string based on the size of the parent SVG elemet. \n // -- a circle with radius 1 should be scaled to the size of the parent SVG element, \n // so that as the graph is zoomed in and out, the circle scales with it.\n // this.svg_element.style.transform = `scale(${this.parent.clientWidth / 100}, ${this.parent.clientHeight / 100})`;\n }\n\n // Update sublayers\n this.__children__.forEach((child: QEElement) => {\n child.update();\n });\n\n if(this.__data__.scale_objects === true) {\n if(this.__name__ === \"points\") {\n // this.svg_element.setAttribute('transform', `\n // scale(${this.graph.__data__.scale_x}, ${this.graph.__data__.scale_y})\n // `);\n }\n }\n else {\n // this.svg_element.setAttribute('transform', `scale(${this.graph.x_mirror()}, ${this.graph.y_mirror()})`); \n }\n }\n }\n\n draw(): void {\n this.parent?.appendChild(this.svg_element);\n\n this.__children__.forEach((child: QEElement) => {\n child.draw();\n });\n }\n\n add(child: QEElement) {\n this.__children__.push(child);\n }\n}","import { Label, Point } from \"../objects/PlottedObject\";\nimport { QEGraphElement } from \"./QEGraph\";\n\n/*\n SVG <text> drawable for a single ENA label.\n \n ── Display modes (Label.DISPLAY_TYPES) ──────────────────────────────────────\n * OFF (0) — never shown\n * AUTO (1) — shown on mouseover of the associated point, hidden on mouseout\n * CLICK (2) — toggled by clicking the associated point\n * ON (3) — always shown\n \n ── Position modes (Label.POSITION) ─────────────────────────────────────────\n * OBJECT (1) — offset near the point (quadrant-aware, default)\n * STATIC (2) — centered directly on the point (no offset; label overlaps point)\n * CONTAINER (3) — projected to the viewBox boundary in the point's direction;\n * useful for code-node labels that appear at the outer ring\n * CUSTOM (4) — caller provides explicit (customX, customY) coordinates\n /\nexport class QELabel {\n svg_element: SVGTextElement;\n private _visible: boolean = false;\n // Drag offset (graph-space units) and pin state for host-repositionable labels.\n private _offsetX = 0;\n private _offsetY = 0;\n pinned = false;\n\n constructor(\n public readonly text: string,\n public readonly point: Point,\n public readonly parent: SVGElement,\n public readonly graph: QEGraphElement,\n public readonly displayMode: number = Label.DISPLAY_TYPES.ON,\n public readonly position: number = Label.POSITION.OBJECT,\n public customX?: number,\n public customY?: number,\n ) {\n this.svg_element = this._create();\n\n // Set initial visibility without calling update() yet.\n // The QEGraphElement calls update_labels() after update_extremes() so that\n // the first real positioning uses the correct graph extent, not the default 1.\n if (displayMode === Label.DISPLAY_TYPES.ON) {\n this._visible = true;\n this.svg_element.setAttribute('display', 'block');\n } else {\n this._visible = false;\n this.svg_element.setAttribute('display', 'none');\n }\n }\n\n private _create(): SVGTextElement {\n const el = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n el.textContent = this.text;\n el.setAttribute('data-label-for', this.point.ID);\n el.setAttribute('pointer-events', 'auto'); // draggable\n el.style.cursor = 'grab';\n this._attachDrag(el);\n this.parent.appendChild(el);\n return el;\n }\n\n /* Drag to reposition; pins the label open and emits qe-label-move on drop. /\n private _attachDrag(el: SVGTextElement): void {\n el.addEventListener('mousedown', (ev: MouseEvent) => {\n ev.preventDefault();\n ev.stopPropagation(); // don't start a graph pan\n const svg = el.ownerSVGElement;\n if (!svg) return;\n const toUser = (cx: number, cy: number) => {\n const p = svg.createSVGPoint(); p.x = cx; p.y = cy;\n const m = svg.getScreenCTM();\n return m ? p.matrixTransform(m.inverse()) : ({ x: 0, y: 0 } as DOMPoint);\n };\n const start = toUser(ev.clientX, ev.clientY);\n const baseX = this._offsetX, baseY = this._offsetY;\n el.style.cursor = 'grabbing';\n\n const onMove = (e: MouseEvent) => {\n const p = toUser(e.clientX, e.clientY);\n this._offsetX = baseX + (p.x - start.x);\n this._offsetY = baseY + (p.y - start.y);\n this.pinned = true; // keep it shown once moved\n this._visible = true;\n this.svg_element.setAttribute('display', 'block');\n this.update();\n };\n const onUp = () => {\n document.removeEventListener('mousemove', onMove);\n document.removeEventListener('mouseup', onUp);\n el.style.cursor = 'grab';\n // Public event so the host can persist / mirror across coordinated plots.\n this.graph.dispatchEvent(new CustomEvent('qe-label-move', {\n detail: { id: this.point.ID, transform: { x: this._offsetX, y: this._offsetY } },\n bubbles: true, composed: true,\n }));\n };\n document.addEventListener('mousemove', onMove);\n document.addEventListener('mouseup', onUp);\n });\n }\n\n /\n Recompute position and font-size from current graph extents.\n * No-ops when the label is hidden (AUTO/CLICK modes while not hovered/clicked).\n /\n update(): void {\n if (!this._visible) return;\n\n const extent = this.graph.__data__.extremes.x_max;\n if (extent <= 0) return; // graph not initialised yet\n\n // qe_labels(font_size =) is in CSS pixels (constant on screen); default\n // scales with the plot extent.\n const font = (this.graph as any)._labelFont ?? {};\n const fontSize = font.size ? font.size (this.graph as any).unitsPerPixel() : extent * 0.06;\n const offset = fontSize * 1.2;\n\n let x: number, y: number, anchor: string;\n\n switch (this.position) {\n\n case Label.POSITION.STATIC: {\n // Centered on the point — label sits at exactly the point's coordinates.\n // Useful when the caller wants to control offset manually via customX/Y.\n x = this.point.x;\n y = this.point.y - offset * 0.3;\n anchor = 'middle';\n break;\n }\n\n case Label.POSITION.CONTAINER: {\n // Project from the view's centre (the origin, unless center=\"content\")\n // through the point onto the viewBox boundary. Labels ring the outer\n // edge of the plot, one per code/group direction.\n const { cx, cy } = this.graph.__data__.extremes;\n const px = this.point.x - cx;\n const py = this.point.y - cy;\n const dist = Math.sqrt(px * px + py * py) \|\| 1;\n const scale = (extent * 0.93) / dist;\n x = cx + px * scale;\n y = cy + py * scale - offset * 0.3;\n anchor = px >= 0 ? 'start' : 'end';\n break;\n }\n\n case Label.POSITION.CUSTOM: {\n // Caller-provided coordinates; fall back to OBJECT behaviour if unset.\n if (this.customX != null && this.customY != null) {\n x = this.customX;\n y = this.customY;\n anchor = 'start';\n break;\n }\n // fall through to OBJECT\n }\n\n default:\n case Label.POSITION.OBJECT: {\n // Quadrant-aware offset: push label away from origin.\n const dx = this.point.x >= 0 ? offset : -offset;\n anchor = this.point.x >= 0 ? 'start' : 'end';\n x = this.point.x + dx;\n y = this.point.y - offset * 0.4;\n break;\n }\n }\n\n this.svg_element.setAttribute('x', x.toString());\n this.svg_element.setAttribute('y', y.toString());\n // Host drag offset (graph-space units) composes on top of the computed spot.\n if (this._offsetX \|\| this._offsetY) {\n this.svg_element.setAttribute('transform', `translate(${this._offsetX}, ${this._offsetY})`);\n }\n this.svg_element.setAttribute('font-size', fontSize.toString());\n this.svg_element.setAttribute('font-family', font.family ?? 'system-ui, sans-serif');\n this.svg_element.setAttribute('font-weight', '500');\n this.svg_element.setAttribute('text-anchor', anchor);\n this.svg_element.setAttribute('fill', font.color ?? this.point.color?.toString() ?? '#333333');\n }\n\n /** Make the label visible and position it immediately. /\n show(): void {\n this._visible = true;\n this.svg_element.setAttribute('display', 'block');\n this.update();\n }\n\n hide(): void {\n if (this.pinned) return; // a dragged/pinned label stays visible\n this._visible = false;\n this.svg_element.setAttribute('display', 'none');\n }\n\n toggle(): void {\n this._visible ? this.hide() : this.show();\n }\n\n get visible(): boolean { return this._visible; }\n\n remove(): void {\n this.svg_element.remove();\n }\n}\n","/\n Declarative child layer elements for <qe-graph>.\n \n Each element is an inert configuration holder — no shadow DOM, no rendering\n * logic. <qe-graph> reads their presence and attributes via querySelector() to\n * configure each rendering layer.\n \n Presence = the layer is rendered.\n * Absence = the layer is hidden. (Code-node positions come from the\n * model and anchor the coordinate space whether or not\n * <qe-nodes> is present; the element only controls drawing.)\n \n HTML authoring example:\n \n <qe-graph width=\"100%\" height=\"440\">\n * <qe-nodes label=\"on\"></qe-nodes>\n * <qe-means groups=\"FirstGame,SecondGame\" confidence></qe-means>\n * <qe-points label=\"auto\"></qe-points>\n * <qe-edges group=\"FirstGame\" compare=\"SecondGame\"></qe-edges>\n * </qe-graph>\n /\n\n/\n <qe-nodes> — renders the code nodes.\n * Presence = draw nodes; absence = hide them (positions still set the extent).\n * A node's diameter equals the summed widths of its drawn edges: every edge\n * touching it (undirected), or the wide ends of the edges directed at it,\n * including its self-connection (directed / ONA).\n \n Attributes:\n * label \"on\" \| \"off\" \| \"click\" \| \"auto\" (default \"on\")\n * unconnected \"dot\" (default) — nodes with no drawn edges show as a tiny\n * dot; \"hide\" — hide them (and their labels).\n /\nexport class QENodesElement extends HTMLElement {\n static tagName = 'qe-nodes' as const;\n}\n\n/\n <qe-means> — renders group mean markers and optional CI boxes.\n * Presence = show means; absence = hide means.\n \n Attributes:\n * groups Comma-separated group names to show. Omit for all groups.\n * confidence Boolean — show 95% CI rectangles.\n * label \"on\" \| \"off\" \| \"click\" \| \"auto\" (default \"on\")\n * fixed-size Boolean — keep mean markers a constant on-screen pixel size\n * regardless of data extent, container size, or zoom (default:\n * markers scale with the coordinate space, like nodes and edges).\n /\nexport class QEMeansElement extends HTMLElement {\n static tagName = 'qe-means' as const;\n}\n\n/\n <qe-points> — renders individual unit scatter dots.\n * Presence = show unit points; absence = hide unit points.\n \n Attributes:\n * label \"on\" \| \"off\" \| \"click\" \| \"auto\" (default \"auto\")\n * size Numeric dot size (default 2.5), relative to the code-node size.\n * fixed-size Boolean — keep unit dots a constant on-screen pixel size\n * regardless of data extent, container size, or zoom (default:\n * dots scale with the coordinate space, like nodes and edges).\n /\nexport class QEPointsElement extends HTMLElement {\n static tagName = 'qe-points' as const;\n}\n\n/\n <qe-edges> — renders an edge network.\n * Presence = draw edges; absence = no edge network.\n \n Attributes:\n * group Group name whose mean network to draw.\n * unit Individual unit ID whose personal network to draw\n * (e.g. \"FirstGame::steven z\"). Mutually exclusive with `group`.\n * compare Second group to subtract (group − compare).\n * also Second group to overlay alongside `group`.\n * scale Reference node weight for mark sizes — the node drawn at\n * <qe-graph mark-size> × the plot width (edge widths follow):\n * \"model\" (default) — the largest node among the model's\n * group-mean networks, so separate plots of\n * one model are comparable;\n * \"plot\" — this plot's own largest node;\n * <number> — a fixed node weight.\n * magnify Multiply this plot's edge widths and node sizes (not colour),\n * e.g. to read a faint subtraction. Whenever the attribute is\n * present — any value, including \"1\" — the plot is labelled\n * \"(scaled N.Nx)\", so exported plots state their scaling.\n * color-scale How \|weight\| maps onto webENA's colour ramps (saturation\n * 0.25–1, opacity 0.3–1):\n * \"model\" (default) — rescaled from the model's smallest to largest\n * non-zero weight (every unit), so plots of one\n * model share a colour scale;\n * \"plot\" — rescaled within this plot (webENA);\n * \"absolute\" — no ramps: saturation = opacity = \|weight\|.\n /\nexport class QEEdgesElement extends HTMLElement {\n static tagName = 'qe-edges' as const;\n}\n\n/\n <qe-trajectories> — renders epistemic cognitive trajectory curves and steps.\n * Presence = draw trajectories; absence = no trajectories.\n \n Attributes:\n * units Comma-separated unit IDs to show. Omit for all.\n * smooth \"none\" \| \"poly\" (default \"none\")\n * max-degree Upper bound on polynomial degree if smooth=\"poly\" (default 3)\n * degree-selection \"loocv_2d\" \| \"fixed\" (default \"loocv_2d\"). \"loocv_2d\"\n * picks the degree in 1..max-degree by joint 2D leave-one-out CV;\n * \"fixed\" always uses max-degree. Near-origin points are excluded\n * from the fit (still drawn).\n * points \"true\" \| \"false\" — show discrete point markers along trajectory\n * tips \"true\" \| \"false\" — show leading tip marker\n * playhead Number — current turn / time index for filtering/animation\n * line-style \"uniform\" \| \"tapered\" (default \"uniform\")\n * stroke-width Number (default 2)\n * stroke-width-range \"min,max\" for tapered lines (default \"1,6\")\n * opacity-range \"min,max\" for tapered lines (default \"0.3,1\")\n /\nexport class QETrajectoriesElement extends HTMLElement {\n static tagName = 'qe-trajectories' as const;\n}\n\n/\n <qe-axes> — renders the x/y axis lines and, per axis, an optional title.\n * Presence = draw axes; absence = no axes.\n \n Attributes:\n * x Show the x-axis label. A value sets custom text; an empty/boolean\n * attribute defaults to the x dimension name (e.g. \"SVD1\").\n * y Show the y-axis label. Same rule with the y dimension name.\n \n Examples:\n * <qe-axes></qe-axes> lines only, no labels\n * <qe-axes x y></qe-axes> \"SVD1\" / \"SVD2\"\n * <qe-axes x=\"Task focus\" y> \"Task focus\" / \"SVD2\"\n /\nexport class QEAxesElement extends HTMLElement {\n static tagName = 'qe-axes' as const;\n}\n\ncustomElements.define(QENodesElement.tagName, QENodesElement);\ncustomElements.define(QEMeansElement.tagName, QEMeansElement);\ncustomElements.define(QEPointsElement.tagName, QEPointsElement);\ncustomElements.define(QEEdgesElement.tagName, QEEdgesElement);\ncustomElements.define(QETrajectoriesElement.tagName, QETrajectoriesElement);\ncustomElements.define(QEAxesElement.tagName, QEAxesElement);\n","import { DefaultGraphOptions, Graph } from \"../objects/Graph\";\nimport { DrawableElement } from \"./DrawableElement\";\nimport { QEArray, QEElement, QELayer } from \"./QELayer\";\nimport QEVisualElement from \"./QEVisual\";\nimport { DataFrameRow } from \"../types/DataFrame\";\nimport { NodeEdge, TaperedWeightedMidpointEdge } from \"../objects/Edges\";\nimport { Label, Line, Point } from \"../objects/PlottedObject\";\nimport { Trajectory } from \"../objects/Trajectory\";\nimport { LayerLike } from \"../objects/Layers\";\nimport { Color } from \"../objects/Color\";\nimport { Extremes } from \"../objects/Extremes\";\nimport { QELabel } from \"./QELabel\";\nimport { DEFAULT_EDGE_WIDTH, OPACITY_RANGE, SATURATION_RANGE, UNCONNECTED_NODE_SIZE, nodeSizeForEdges, rampFor, widthPerWeight } from \"../objects/Sizing\";\nimport \"./QEChildElements.js\";\n\n// Accessible color palette for group assignment (Paul Tol's bright scheme)\nconst GROUP_PALETTE = [\n '#4477AA', '#EE6677', '#228833', '#CCBB44',\n '#66CCEE', '#AA3377', '#BBBBBB', '#000000',\n];\n\n/\n Parse an edge column name into the two code IDs it connects.\n * Edge columns use \".\" as separator between the two codes, but codes can\n * themselves contain \".\" (e.g. \"Technical.Constraints\"). We resolve the\n * ambiguity by trying every prefix that matches a known code.\n \n Self-connections (\"A.A\") are detected first — they return [A, A].\n * In directed (ONA) mode the full unfolded matrix is expected, so A→B and\n * B→A are distinct columns; both resolve correctly as ordered pairs.\n /\nfunction parseEdgePair(colName: string, codes: string[]): [string, string] \| null {\n // Self-connections first: exact match \"code.code\"\n for (const c of codes) {\n if (colName === `${c}.${c}`) return [c, c];\n }\n // Directed or undirected pairs: longest-prefix wins to handle dotted code names\n for (const c1 of codes) {\n if (colName.startsWith(c1 + '.')) {\n const c2 = colName.slice(c1.length + 1);\n if (codes.includes(c2)) return [c1, c2];\n }\n }\n return null;\n}\n\n/\n Compute half-width and half-height for a 95% CI rectangle on the group mean.\n \n Each axis is treated independently: half-extent = t(df,0.975) × SE,\n * where SE = sqrt(variance / n) and df = n − 1. This matches the standard\n * ENA rectangular CI displayed in the rENA / Web ENA tools.\n \n Inputs are the raw (un-scaled) variances; pointScale is applied here so\n * the returned values are in SVG coordinate space.\n /\nfunction computeCIRect(\n varX: number, varY: number, n: number, pointScale: number\n): { halfW: number; halfH: number } {\n // t(df, 0.975) — rough approximation good to ±0.02 for df ≥ 3\n const df = Math.max(1, n - 1);\n const t95 = df >= 120 ? 1.960\n : df >= 60 ? 2.000\n : df >= 30 ? 2.042\n : df >= 20 ? 2.086\n : df >= 10 ? 2.228\n : df >= 5 ? 2.571\n : 4.303; // df = 1\n const seX = Math.sqrt(Math.max(0, varX) / n) pointScale;\n const seY = Math.sqrt(Math.max(0, varY) / n) * pointScale;\n return { halfW: t95 * seX, halfH: t95 * seY };\n}\n\n/** Mean markers never exceed this fraction of their interval box's shorter\n * half-side. Marker size is otherwise arbitrary (extent- or pixel-based), so\n * without a cap a tight CI disappears underneath the mean square. /\nconst MEAN_MAX_FRACTION_OF_INTERVAL = 0.5;\n\nfunction capMeanToInterval(meanPt: Point \| undefined, halfW: number, halfH: number): void {\n if (!meanPt) return;\n const half = Math.min(Math.abs(halfW), Math.abs(halfH));\n if (!(half > 0)) return; // degenerate interval (n = 1, zero variance): keep default size\n (meanPt as any).meta = { ...((meanPt as any).meta ?? {}), maxRadius: half MEAN_MAX_FRACTION_OF_INTERVAL };\n}\n\nfunction readIntervalBounds(\n row: DataFrameRow, dim0: string, dim1: string, prefix = ''\n): { x_low: number; x_high: number; y_low: number; y_high: number } \| null {\n // prefix '' → CI ({dim}.low / .high); 'o' → outlier ({dim}.olow / .ohigh).\n const get = (col: string) => {\n const i = row.names.indexOf(col);\n const raw = i >= 0 ? row[i] : null;\n if (raw == null \|\| raw === '') return undefined; // Number(null) would be 0\n const v = Number(raw);\n return Number.isFinite(v) ? v : undefined;\n };\n const xLow = get(`${dim0}.${prefix}low`) ?? get(`${dim0}_${prefix}low`);\n const xHigh = get(`${dim0}.${prefix}high`) ?? get(`${dim0}_${prefix}high`);\n const yLow = get(`${dim1}.${prefix}low`) ?? get(`${dim1}_${prefix}low`);\n const yHigh = get(`${dim1}.${prefix}high`) ?? get(`${dim1}_${prefix}high`);\n if (xLow == null \|\| xHigh == null \|\| yLow == null \|\| yHigh == null) return null;\n return { x_low: xLow, x_high: xHigh, y_low: yLow, y_high: yHigh };\n}\n\n/*\n <qe-edges color-scale>: the range that edge weights are rescaled from onto\n * webENA's saturation (0.25–1) and opacity (0.3–1) ramps.\n * \"model\" (default) — min / max non-zero \|weight\| across the whole model\n * (every unit), so separate plots of one model share\n * one colour scale.\n * \"plot\" — this plot's own min / max (webENA's per-network\n * behaviour).\n * \"absolute\" — no rescaling: saturation = opacity = \|weight\|.\n /\ntype ColorScale = 'model' \| 'plot' \| 'absolute';\n\n/* One <qe-edges> element: a named network or an explicit `network` row. /\ntype EdgeLayerSpec = {\n group: string \| null; unit: string \| null;\n compare: string \| null; also: string \| null;\n network: string \| null;\n colors: [string, string \| null] \| null; // positive, negative (null → complement)\n threshold: [number, number] \| null; // min, max (max = Infinity when omitted)\n name: string \| null;\n};\n\nfunction parseEdgeLayer(el: Element): EdgeLayerSpec {\n const a = (k: string) => el.getAttribute(k);\n const cols = a('colors')?.split(',').map(c => c.trim()).filter(Boolean) ?? [];\n const thr = a('threshold')?.split(',').map(Number).filter(Number.isFinite) ?? [];\n return {\n group: a('group'), unit: a('unit'), compare: a('compare'), also: a('also'),\n network: a('network'),\n colors: cols.length ? [cols[0], cols[1] ?? null] : null,\n threshold: thr.length ? [thr[0], thr.length > 1 ? thr[1] : Infinity] : null,\n name: a('name'),\n };\n}\n\n/* Complementary hue (rENA: one colour → negatives use hue + 180°). /\nfunction complementColor(hex: string): string {\n const { r, g, b } = Color.parseColor(hex);\n const mx = Math.max(r, g, b), mn = Math.min(r, g, b);\n const f = (c: number) => (mx + mn - c).toString(16).padStart(2, '0');\n return `#${f(r)}${f(g)}${f(b)}`;\n}\n\nfunction parseColorScale(attr: string \| null): ColorScale {\n const a = attr?.trim().toLowerCase();\n return a === 'plot' \|\| a === 'absolute' ? a : 'model';\n}\n\n/\n Parse a label-mode attribute string into a Label.DISPLAY_TYPES integer.\n * \"on\" → 3 (ON)\n * \"off\" → 0 (OFF)\n * \"click\" → 2 (CLICK)\n * \"auto\" → 1 (AUTO)\n * Returns `defaultMode` for any unrecognized value or null.\n /\nfunction parseLabelMode(attr: string \| null, defaultMode: number): number {\n switch (attr?.toLowerCase()) {\n case 'on': return 3;\n case 'off': return 0;\n case 'click': return 2;\n case 'auto': return 1;\n default: return defaultMode;\n }\n}\n\nexport class QEGraphElement extends DrawableElement implements QEElement {\n static tagName: string = \"qe-graph\";\n\n static get observedAttributes(): string[] {\n // Only layout / shorthand attributes live on <qe-graph> itself.\n // Layer-specific config (group, unit, compare, also, points, edges,\n // confidence, groups) lives on child elements and is observed via\n // MutationObserver in connectedCallback().\n return [\n 'width', 'height', 'for',\n 'scale-points', 'point-scale', 'center',\n 'labels', 'label-nodes', 'label-means', 'label-points',\n ];\n }\n\n static style: string = `\n ${DrawableElement.style}\n\n :host {\n display: block;\n }\n\n .wrapper {\n width: 100%;\n height: 100%;\n }\n\n svg {\n width: 100%;\n height: 100%;\n aspect-ratio: 1 / 1;\n background-color: #FFF;\n }\n `;\n\n svg_element: SVGElement;\n graph: QEGraphElement;\n parent: SVGElement \| null;\n zoom_level: number = 1;\n\n __data__: Graph;\n __children__: QEArray = new QEArray();\n __name__: string;\n \n\n private _vizena!: QEVisualElement;\n get vizena() {\n return this._vizena;\n }\n\n private _hasModel = false;\n private _renderPending = false;\n private _childObserver: MutationObserver \| null = null;\n\n // SVG <rect> elements for per-group CI boxes, keyed by group name.\n // Managed directly (not via QELayer) so they render behind unit points.\n private _ciRects: Map<string, SVGRectElement> = new Map();\n private _outlierRects: Map<string, SVGRectElement> = new Map();\n private _ciCross: Map<string, SVGPathElement> = new Map();\n\n // Cached reference to the labels <g> layer — set once in connectedCallback()\n // after draw() so it is guaranteed to be in the SVG DOM.\n private _labelsGroup: SVGGElement \| null = null;\n\n // SVG <text> label elements for nodes, mean points, and unit points.\n private _nodeLabels: Map<string, QELabel> = new Map();\n private _meanLabels: Map<string, QELabel> = new Map();\n private _pointLabels: Map<string, QELabel> = new Map();\n\n // Axes (<qe-axes>): whether to show axis lines, and resolved label text\n // (null = no label for that axis). SVG <text> nodes are cached and positioned\n // in update_axis_labels() using the freshly-computed extremes.\n private _showAxes = false;\n private _axisXText: string \| null = null;\n private _axisYText: string \| null = null;\n private _axisLabelEls: Map<'x' \| 'y', SVGTextElement> = new Map();\n // \"(scaled 1.5x)\" label, drawn whenever <qe-edges magnify> is present.\n private _magnifyText: string \| null = null;\n private _magnifyEl: SVGTextElement \| null = null;\n // <qe-graph range> / plot-title / label-font- (qe_plot(range =, title =),\n // qe_labels(font_)); resolved each render.\n private _rangeExtent: number \| null = null;\n private _rangeMode: 'network' \| 'points' \| 'number' \| null = null;\n /* center=\"content\": centre the view on the drawn content, not the origin /\n private _centerContent = false;\n private _plotTitle: string \| null = null;\n private _titleEl: SVGTextElement \| null = null;\n private _resizeObs: ResizeObserver \| null = null;\n _labelFont: { size: number \| null; family: string \| null; color: string \| null } =\n { size: null, family: null, color: null };\n\n /* SVG user units per CSS pixel at the current size / zoom. /\n unitsPerPixel(): number {\n const extent = this.__data__.extremes.x_max \|\| 1;\n const rect = this.svg_element?.getBoundingClientRect?.();\n const zoom = (this as any).zoom_level \|\| 1;\n return rect && rect.width > 0 ? (2 extent / rect.width) / zoom : extent * 0.004;\n }\n\n constructor() {\n super();\n\n this.graph = this;\n this.parent = null;\n\n this.__data__ = new Graph(DefaultGraphOptions);\n this.__name__ = this.__data__.name \|\| \"unnamed-graph\";\n this.svg_element = this.create();\n\n console.log(\"Created ena-graph svg element: \", this.svg_element);\n\n // Listen for the model-updated CustomEvent dispatched by VisualQEElement.\n // The Model object is carried in event.detail, so ena-graph works whether it\n // is a child, sibling, or anywhere else relative to ena-visual.\n document.addEventListener('model-updated', (e: Event) => {\n // When multiple qe-visual elements exist on the page, each qe-graph must\n // only react to events from its own associated visual. _vizena is resolved\n // in connectedCallback(); before that point we accept all events (initial\n // load), but once the association is known we filter strictly.\n // composedPath()[0]: inside a shadow root (e.g. a qe-visual in another\n // component), e.target is retargeted to the shadow host\n const origin = e.composedPath?.()[0] ?? e.target;\n if (this._vizena && origin !== this._vizena) return;\n\n const model = (e as CustomEvent).detail;\n if (!model) return;\n\n // Tweening (opt-in via `animate`): snapshot current mark/edge positions\n // BEFORE the rebuild so we can animate old→new after this.update().\n this._animateMs = this.hasAttribute('animate')\n ? (parseInt(this.getAttribute('animate') \|\| '', 10) \|\| 300)\n : 0;\n const tweenFrom = (this._animateMs > 0 && this._hasModel) ? this._captureTween() : null;\n\n this._hasModel = true;\n\n const dims = model.dimensions as string[];\n\n // Resolved column names from setModelData (auto-detected or caller-supplied)\n const unitIdCol = model.unit_id_col;\n const nodeIdCol = model.node_id_col;\n const groupColName = model.group_col;\n\n // ── Layer config (read once from child elements) ─────────────────────────\n const config = this._readLayerConfig();\n\n // ── Axes (<qe-axes>) ─────────────────────────────────────────────────────\n // Resolve label text now that dims are known: empty x/y attribute falls\n // back to the dimension name; a value is used verbatim; null = no label.\n this._showAxes = config.showAxes;\n this._axisXText = config.axisXLabel === null ? null : (config.axisXLabel \|\| String(dims?.[0] ?? 'x'));\n // Present on any <qe-edges magnify>, including \"1\" — as webENA labels\n // its side plots \"(scaled 1.0x)\" so an exported set says which plot was\n // magnified.\n this._magnifyText = config.edgeMagnify == null ? null\n : `(scaled ${config.edgeMagnify.toFixed(1)}x)`;\n this._axisYText = config.axisYLabel === null ? null : (config.axisYLabel \|\| String(dims?.[1] ?? 'y'));\n\n // ── Group color map ──────────────────────────────────────────────────────\n // Priority: (1) points groupCol, (2) groups frame row names, (3) empty.\n const groupColorMap: Record<string, string> = {};\n // Model palette (qe_plot(palette =)) or the default Tol \"bright\" scheme.\n const PALETTE: string[] = (model as any).palette?.length ? (model as any).palette : GROUP_PALETTE;\n if (groupColName && model.points?.names) {\n const groupCol = model.points.col(groupColName);\n if (groupCol) {\n const uniqueGroups: string[] = [...new Set([...groupCol].map(String))];\n uniqueGroups.forEach((g, i) => {\n groupColorMap[g] = PALETTE[i % PALETTE.length];\n });\n }\n }\n // Groups-frame rows: a `color` column overrides the palette, and rows that\n // are not groups of the points (e.g. the mean of an arbitrary subset,\n // qe_group(points =)) still get a colour so they count as known groups.\n if (model.groups?.rows && model.groups.rows().length > 0) {\n model.groups.rows().forEach((row: DataFrameRow) => {\n const g = row.rowName ?? String(row[0]);\n const ci = row.names.indexOf('color');\n const c = ci >= 0 ? row[ci] : null;\n if (c && String(c) !== 'NA') groupColorMap[g] = String(c);\n else if (!groupColorMap[g]) {\n groupColorMap[g] = PALETTE[Object.keys(groupColorMap).length % PALETTE.length];\n }\n });\n }\n\n // ── Active groups for MEANS display ─────────────────────────────────────\n // `groups` attribute: comma-separated list of group names whose means and\n // CI boxes should be rendered. Default (attribute absent or empty): show\n // means for ALL groups present in the model.\n //\n // Means display is intentionally independent of edge selection. The edge\n // section below reads `group` / `compare` / `also` to determine which\n // network(s) to draw; those attributes have no effect here.\n const _allGroupNames_ = Object.keys(groupColorMap);\n const activeMeanGroups: Set<string> = (config.activeMeanGroups && config.activeMeanGroups.trim())\n ? new Set(\n config.activeMeanGroups.split(',')\n .map(s => s.trim())\n .filter(g => groupColorMap[g]) // silently drop names not in model\n )\n : new Set(_allGroupNames_); // default: every group\n\n // ── Point-to-node coordinate scaling ────────────────────────────────────\n // Unit point coordinates are in a different (typically much smaller) range\n // Unit/mean point coordinates are rescaled by default so the outermost point\n // aligns with the outermost code node — matching the ENA Web Tool default.\n // Set scale-points=\"false\" on <qe-graph> to show raw SVD coordinates\n // (points cluster near origin relative to code nodes).\n const scalePointsEnabled = config.scalePoints;\n\n const getExtent = (rows: DataFrameRow[]): number => {\n let max = 0;\n rows.forEach(row => {\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n if (xIdx >= 0) max = Math.max(max, Math.abs(Number(row[xIdx])));\n if (yIdx >= 0) max = Math.max(max, Math.abs(Number(row[yIdx])));\n });\n return max;\n };\n\n const maxNodeExtent = model.nodes?.rows ? getExtent(model.nodes.rows()) : 0;\n const maxPointExtent = model.points?.rows ? getExtent(model.points.rows()) : 0;\n const maxTrajExtent = model.trajectories?.rows ? getExtent(model.trajectories.rows()) : 0;\n const effectivePointExtent = maxPointExtent > 0 ? maxPointExtent : maxTrajExtent;\n // point-scale=\"N\" (optional, unset by default): an explicit factor, e.g.\n // 1 for raw coordinates or another tool's rescaling, instead of fitting\n // the outermost point to the outermost node\n const pointScale = config.pointScale !== null ? config.pointScale\n : (scalePointsEnabled && effectivePointExtent > 0 && maxNodeExtent > 0)\n ? maxNodeExtent / effectivePointExtent\n : 1;\n\n // <qe-graph range>: a symmetric axis range, as rENA's scale.to —\n // \"network\" = ±max \|node\| × 1.2, \"points\" = ±max \|drawn point\| × 1.2, or\n // a number. Absent → qeviz's default (1.3 × the largest drawn mark).\n this._rangeExtent =\n config.range === 'network' ? maxNodeExtent * 1.2\n : config.range === 'points' ? effectivePointExtent * pointScale * 1.2\n : typeof config.range === 'number' ? config.range\n : null;\n this._rangeMode = config.range === 'network' \|\| config.range === 'points' ? config.range\n : typeof config.range === 'number' ? 'number' : null;\n this._centerContent = config.centerContent;\n this._plotTitle = config.plotTitle;\n this._labelFont = config.labelFont;\n\n // ── Label display modes — sourced from config (child elements or shorthand) ──\n const labelNodes = config.labelNodes;\n const labelMeans = config.labelMeans;\n const labelPoints = config.labelPoints;\n\n // Use the cached labels <g> reference (set once in connectedCallback).\n const labelSvg = this._labelsGroup;\n\n // ── Helper: build a Point from a DataFrame row ───────────────────────────\n // Looks up dimension values by column name so it works with any data format.\n // Y is negated because SVG y-axis points down while ENA convention is y-up.\n // `scale` multiplies x/y — use pointScale for unit/mean points, 1 for nodes.\n const rowToPoint = (row: DataFrameRow, idCol: string, colorStr?: string, scale = 1): Point => {\n const idIdx = row.names.indexOf(idCol);\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n const pt = new Point({\n ID: idIdx >= 0 ? String(row[idIdx]) : (row.rowName \|\| `pt-${Math.random().toString(36).slice(2)}`),\n dimensions: [\n xIdx >= 0 ? Number(row[xIdx]) * scale : 0,\n yIdx >= 0 ? -Number(row[yIdx]) * scale : 0, // negate Y: SVG y-down vs ENA y-up\n ],\n meta: {},\n });\n if (colorStr) pt.color = new Color(colorStr);\n return pt;\n };\n\n // ── Unit points + group means ────────────────────────────────────────────\n // groupSums is used later for mean edges and CI ellipses.\n // x2/y2/xy accumulate Σ(raw²) for variance computation.\n const groupSums: Record<string, {\n x: number; y: number; x2: number; y2: number; xy: number;\n n: number; color: string;\n }> = {};\n\n // <qe-points> presence controls unit-dot visibility.\n // <qe-means> presence controls mean markers and CI boxes.\n const showUnitPoints = config.showPoints;\n\n // ── Explicit point sets (qe_points(units =, points =)) ─────────────────\n // Each <qe-points set=\"…\"> draws that set's rows of model.pointsets, on\n // the same point scale as the unit points.\n const pointSetFrame = (model as any).pointsets;\n if (config.pointSets.length && pointSetFrame?.rows) {\n const psLayer = this.__children__.search('__children__', 'points') as QELayer;\n const col = (r: DataFrameRow, k: string) => { const i = r.names.indexOf(k); return i >= 0 ? r[i] : null; };\n config.pointSets.forEach((ps, si) => {\n pointSetFrame.rows().forEach((row: DataFrameRow) => {\n if (String(col(row, 'set')) !== ps.set) return;\n const id = String(col(row, 'id'));\n const group = col(row, 'group') != null && String(col(row, 'group')) !== 'NA' ? String(col(row, 'group')) : null;\n const color = col(row, 'color') && String(col(row, 'color')) !== 'NA' ? String(col(row, 'color'))\n : group && groupColorMap[group] ? groupColorMap[group]\n : PALETTE[si % PALETTE.length];\n const pt = rowToPoint(row, 'id', color, pointScale);\n pt.ID = `${ps.set}::${id}`;\n pt.size = ps.size ?? config.pointSize ?? 2.5;\n const shape = col(row, 'shape');\n if (shape && String(shape) !== 'NA') pt.shape = String(shape);\n const label = col(row, 'label');\n (pt as any).meta = {\n stroke: '#ffffff', kind: 'point',\n name: label != null && String(label) !== 'NA' ? String(label) : id,\n group: group ?? undefined, unit: id, set: ps.set,\n fixedSize: ps.fixedSize,\n };\n this.__data__.points.set(pt.ID, pt);\n psLayer?.__data__.objects.set(pt.ID, pt);\n });\n });\n }\n\n if (model.points?.rows) {\n const pointsLayer = this.__children__.search('__children__', 'points') as QELayer;\n if (pointsLayer) {\n model.points.rows().forEach((row: DataFrameRow) => {\n // Determine this point's group color\n const groupColIdx = groupColName ? row.names.indexOf(groupColName) : -1;\n const group = groupColIdx >= 0 ? String(row[groupColIdx]) : null;\n const colorStr = group ? (groupColorMap[group] ?? '#888888') : '#888888';\n\n // Only add unit dots to the layer when 'points' attribute is present.\n if (showUnitPoints) {\n const pt = rowToPoint(row, unitIdCol, colorStr, pointScale);\n // Unit-point size: <qe-points size=…> overrides the default 2.5.\n // (Point() defaults to 1, which renders smaller than code nodes.)\n pt.size = config.pointSize ?? 2.5;\n // White halo separates overlapping dots in dense clusters.\n // meta.kind/name/group feed the qe-node-* interaction events.\n (pt as any).meta = {\n ...((pt as any).meta ?? {}),\n stroke: '#ffffff', kind: 'point', name: pt.ID,\n group: group ?? undefined, unit: pt.ID,\n fixedSize: config.pointFixedSize,\n };\n this.__data__.points.set(pt.ID, pt);\n pointsLayer.__data__.objects.set(pt.ID, pt);\n }\n\n // Always accumulate for mean + variance (needed for Path B even without dots)\n if (group) {\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n if (!groupSums[group]) groupSums[group] = { x: 0, y: 0, x2: 0, y2: 0, xy: 0, n: 0, color: colorStr };\n const rx = xIdx >= 0 ? Number(row[xIdx]) : 0;\n const ry = yIdx >= 0 ? Number(row[yIdx]) : 0;\n groupSums[group].x += rx;\n groupSums[group].y += ry;\n groupSums[group].x2 += rx * rx;\n groupSums[group].y2 += ry * ry;\n groupSums[group].xy += rx * ry;\n groupSums[group].n += 1;\n }\n });\n\n // ── Group means + bounds ──────────────────────────────────────────────\n // Two paths:\n // A) model.groups frame present → use pre-computed means + bounds.\n // This is the Phase 3+ preferred path. qeviz renders; adapters compute.\n // B) No groups frame → compute means from unit-point accumulations\n // (legacy fallback; also used when only points are provided).\n //\n // Deprecated frames (model.confidence, model.outlier) are still respected\n // in path B for backward compatibility with rENA adapters not yet updated.\n //\n // Means rendering is guarded by config.showMeans (<qe-means> presence).\n // When absent, activeGroupRows is kept empty so the labels section below\n // also skips mean labels cleanly.\n\n const hasGroupsFrame = !!(model.groups?.rows && model.groups.rows().length > 0);\n\n // Rows from the groups frame that are active in the current view.\n // Empty when <qe-means> is absent so downstream label logic is consistent.\n const activeGroupRows: DataFrameRow[] = (config.showMeans && hasGroupsFrame)\n ? model.groups.rows().filter((r: DataFrameRow) => {\n const g = r.rowName ?? String(r[0]);\n return activeMeanGroups.size === 0 \|\| activeMeanGroups.has(g);\n })\n : [];\n\n if (config.showMeans) {\n const pointsLayerSvg = pointsLayer.svg_element as SVGGElement \| null;\n const sw = (maxNodeExtent > 0 ? maxNodeExtent : 1) * 0.008;\n\n if (hasGroupsFrame) {\n // ── Path A: groups frame ─────────────────────────────────────────\n // Remove CI/outlier rects for groups no longer active.\n const activeNames = new Set(activeGroupRows.map((r: DataFrameRow) => r.rowName ?? String(r[0])));\n this._ciRects.forEach((el, g) => { if (!activeNames.has(g)) { el.remove(); this._ciRects.delete(g); } });\n this._outlierRects.forEach((el, g) => { if (!activeNames.has(g)) { el.remove(); this._outlierRects.delete(g); } });\n this._ciCross.forEach((el, k) => { if (!activeNames.has(k.slice(2))) { el.remove(); this._ciCross.delete(k); } });\n\n activeGroupRows.forEach((row: DataFrameRow) => {\n const group = row.rowName ?? String(row[0]);\n const color = groupColorMap[group] ?? '#888888';\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n const mx = xIdx >= 0 ? Number(row[xIdx]) * pointScale : 0;\n const my = yIdx >= 0 ? -Number(row[yIdx]) * pointScale : 0;\n\n // Mean marker — square, larger than unit points\n const meanPt = new Point({\n ID: `mean-${group}`,\n dimensions: [mx, my],\n meta: { kind: 'mean', name: group, group, fixedSize: config.meanFixedSize },\n });\n meanPt.color = new Color(color);\n meanPt.size = 4; // radius = extent × 0.006 × 4 ≈ 0.024 for a unit extent\n const shapeIdx = row.names.indexOf('shape');\n const rowShape = shapeIdx >= 0 ? row[shapeIdx] : null;\n meanPt.shape = rowShape && String(rowShape) !== 'NA' ? String(rowShape) : 'rect';\n this.__data__.points.set(meanPt.ID, meanPt);\n pointsLayer.__data__.objects.set(meanPt.ID, meanPt);\n\n // Per-mean overrides (explicit means, as rENA's ena.plot.group\n // sets them per call): groups-frame `intervals` / `outlier`\n // columns win over the <qe-means> attributes when present.\n const cell = (name: string): any => {\n const i = row.names.indexOf(name);\n const v = i >= 0 ? row[i] : null;\n return v == null \|\| String(v) === 'NA' \|\| String(v) === '' ? null : v;\n };\n const rowIv = cell('intervals');\n const iv: 'box' \| 'crosshairs' \| 'none' =\n rowIv === 'box' \|\| rowIv === 'crosshairs' \|\| rowIv === 'none' ? rowIv : config.intervals;\n const rowOut = cell('outlier');\n const showOut = rowOut == null ? config.showOutlier : (rowOut === true \|\| String(rowOut) === 'true');\n\n // Outlier interval (qe_group(outlier = TRUE)): {dim}.olow / .ohigh.\n const ob = showOut\n ? readIntervalBounds(row, dims[0] as string, dims[1] as string, 'o')\n : null;\n if (!ob) {\n this._outlierRects.get(group)?.remove(); this._outlierRects.delete(group);\n } else {\n let oel = this._outlierRects.get(group);\n if (!oel) {\n oel = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n oel.setAttribute('data-outlier-group', group);\n this._outlierRects.set(group, oel);\n }\n oel.setAttribute('x', (ob.x_low * pointScale).toString());\n oel.setAttribute('y', (-ob.y_high * pointScale).toString());\n oel.setAttribute('width', ((ob.x_high - ob.x_low) * pointScale).toString());\n oel.setAttribute('height', ((ob.y_high - ob.y_low) * pointScale).toString());\n oel.setAttribute('fill', 'none');\n oel.setAttribute('stroke', color);\n oel.setAttribute('stroke-width', sw.toString());\n oel.setAttribute('stroke-opacity', '0.5');\n oel.setAttribute('stroke-dasharray', `${sw * 2} ${sw * 2}`);\n if (pointsLayerSvg && !oel.parentElement) pointsLayerSvg.insertBefore(oel, pointsLayerSvg.firstChild);\n }\n\n // CI (<qe-means intervals=\"box\|crosshairs\|none\">, or the legacy\n // `confidence` flag = box). Gated so qe_group(intervals = \"none\")\n // draws nothing.\n const bounds = iv !== 'none'\n ? readIntervalBounds(row, dims[0] as string, dims[1] as string)\n : null;\n const crossKey = `x:${group}`;\n if (!bounds \|\| iv !== 'crosshairs') {\n this._ciCross.get(crossKey)?.remove(); this._ciCross.delete(crossKey);\n }\n if (bounds && iv === 'crosshairs') {\n this._ciRects.get(group)?.remove(); this._ciRects.delete(group);\n // Two arms through the mean: x_lo..x_hi at the mean's y, and\n // y_lo..y_hi at the mean's x.\n const x0 = bounds.x_low * pointScale, x1 = bounds.x_high * pointScale;\n const y0 = -bounds.y_high * pointScale, y1 = -bounds.y_low * pointScale;\n capMeanToInterval(meanPt, (x1 - x0) / 2, (y1 - y0) / 2);\n let cel = this._ciCross.get(crossKey);\n if (!cel) {\n cel = document.createElementNS('http://www.w3.org/2000/svg', 'path') as SVGPathElement;\n cel.setAttribute('data-ci-group', group);\n cel.setAttribute('data-ci-kind', 'crosshairs');\n this._ciCross.set(crossKey, cel);\n }\n cel.setAttribute('d', `M${x0} ${my} L${x1} ${my} M${mx} ${y0} L${mx} ${y1}`);\n cel.setAttribute('fill', 'none');\n cel.setAttribute('stroke', color);\n cel.setAttribute('stroke-width', (sw * 1.25).toString());\n cel.setAttribute('stroke-opacity', '0.8');\n if (pointsLayerSvg && !cel.parentElement) pointsLayerSvg.insertBefore(cel, pointsLayerSvg.firstChild);\n } else if (!bounds) {\n const stale = this._ciRects.get(group);\n if (stale) { stale.remove(); this._ciRects.delete(group); }\n } else {\n const rect_x = bounds.x_low * pointScale;\n const rect_y = -bounds.y_high * pointScale;\n const rect_width = (bounds.x_high - bounds.x_low) * pointScale;\n const rect_height = (bounds.y_high - bounds.y_low) * pointScale;\n capMeanToInterval(meanPt, rect_width / 2, rect_height / 2);\n\n let el = this._ciRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-ci-group', group);\n this._ciRects.set(group, el);\n }\n el.setAttribute('x', rect_x.toString());\n el.setAttribute('y', rect_y.toString());\n el.setAttribute('width', rect_width.toString());\n el.setAttribute('height', rect_height.toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.8');\n el.setAttribute('stroke-dasharray', `${sw * 4} ${sw * 3}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n }\n });\n\n } else {\n // ── Path B: legacy — compute means from groupSums ────────────────\n // Add one mean point per group — larger (size=1.5) and same group color\n Object.entries(groupSums).forEach(([group, { x, y, n, color }]) => {\n const meanPt = new Point({\n ID: `mean-${group}`,\n dimensions: [x / n * pointScale, -(y / n) * pointScale],\n meta: { kind: 'mean', name: group, group, fixedSize: config.meanFixedSize },\n });\n meanPt.color = new Color(color);\n meanPt.size = 4; // radius = extent × 0.006 × 4 ≈ 0.024 for a unit extent\n meanPt.shape = 'rect';\n this.__data__.points.set(meanPt.ID, meanPt);\n pointsLayer.__data__.objects.set(meanPt.ID, meanPt);\n });\n\n // ── CI boxes (deprecated confidence frame or JS fallback) ────────\n const showCI = config.showCI;\n if (showCI) {\n this._ciRects.forEach((el, g) => {\n if (!groupSums[g]) { el.remove(); this._ciRects.delete(g); }\n });\n\n if (model.confidence?.rows) {\n // Pre-computed path: deprecated model.confidence frame\n model.confidence.rows().forEach((row: DataFrameRow) => {\n const groupIdx = row.names.indexOf(groupColName ?? 'group');\n const group = groupIdx >= 0 ? String(row[groupIdx]) : (row.rowName ?? null);\n if (!group) return;\n const color = groupColorMap[group] ?? '#888888';\n const bounds = readIntervalBounds(row, dims[0] as string, dims[1] as string);\n if (!bounds) return;\n const rect_x = bounds.x_low * pointScale;\n const rect_y = -bounds.y_high * pointScale;\n const rect_width = (bounds.x_high - bounds.x_low) * pointScale;\n const rect_height = (bounds.y_high - bounds.y_low) * pointScale;\n capMeanToInterval(this.__data__.points.get(`mean-${group}`) as Point \| undefined,\n rect_width / 2, rect_height / 2);\n let el = this._ciRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-ci-group', group);\n this._ciRects.set(group, el);\n }\n el.setAttribute('x', rect_x.toString());\n el.setAttribute('y', rect_y.toString());\n el.setAttribute('width', rect_width.toString());\n el.setAttribute('height', rect_height.toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.8');\n el.setAttribute('stroke-dasharray', `${sw * 4} ${sw * 3}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n });\n } else {\n // JS fallback: compute CI from accumulated variance\n Object.entries(groupSums).forEach(([group, { x, y, x2, y2, n, color }]) => {\n if (n < 2) return;\n const μx = x / n, μy = y / n;\n const rawVarX = x2 / n - μx * μx;\n const rawVarY = y2 / n - μy * μy;\n const { halfW, halfH } = computeCIRect(rawVarX, rawVarY, n, pointScale);\n const cx = μx * pointScale, cy = -(μy) * pointScale;\n capMeanToInterval(this.__data__.points.get(`mean-${group}`) as Point \| undefined,\n halfW, halfH);\n let el = this._ciRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-ci-group', group);\n this._ciRects.set(group, el);\n }\n el.setAttribute('x', (cx - halfW).toString());\n el.setAttribute('y', (cy - halfH).toString());\n el.setAttribute('width', (halfW * 2).toString());\n el.setAttribute('height', (halfH * 2).toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.8');\n el.setAttribute('stroke-dasharray', `${sw * 4} ${sw * 3}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n });\n }\n }\n\n // ── Outlier boxes (deprecated model.outlier frame) ───────────────\n const showOutlier = true; // legacy frame; presence of model.outlier guards rendering\n if (showOutlier && model.outlier?.rows) {\n this._outlierRects.forEach((el, g) => {\n if (!groupColorMap[g]) { el.remove(); this._outlierRects.delete(g); }\n });\n model.outlier.rows().forEach((row: DataFrameRow) => {\n const groupIdx = row.names.indexOf(groupColName ?? 'group');\n const group = groupIdx >= 0 ? String(row[groupIdx]) : (row.rowName ?? null);\n if (!group) return;\n const color = groupColorMap[group] ?? '#888888';\n const bounds = readIntervalBounds(row, dims[0] as string, dims[1] as string);\n if (!bounds) return;\n const rect_x = bounds.x_low * pointScale;\n const rect_y = -bounds.y_high * pointScale;\n const rect_width = (bounds.x_high - bounds.x_low) * pointScale;\n const rect_height = (bounds.y_high - bounds.y_low) * pointScale;\n let el = this._outlierRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-outlier-group', group);\n this._outlierRects.set(group, el);\n }\n el.setAttribute('x', rect_x.toString());\n el.setAttribute('y', rect_y.toString());\n el.setAttribute('width', rect_width.toString());\n el.setAttribute('height', rect_height.toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.5');\n el.setAttribute('stroke-dasharray', `${sw * 2} ${sw * 2}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n });\n }\n } // end Path B\n } // end config.showMeans\n\n // ── Labels ──────────────────────────────────────────────────────────\n if (labelSvg) {\n // Remove labels for objects that no longer exist\n this._pointLabels.forEach((lbl, id) => {\n if (!pointsLayer.__data__.objects.get(id)) { lbl.remove(); this._pointLabels.delete(id); }\n });\n this._meanLabels.forEach((lbl, id) => {\n if (!pointsLayer.__data__.objects.get(`mean-${id}`)) { lbl.remove(); this._meanLabels.delete(id); }\n });\n\n // Unit point labels\n if (labelPoints !== 0) {\n model.points.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n const unitId = qIdx >= 0 ? String(row[qIdx]) : null;\n if (!unitId) return;\n const pt = pointsLayer.__data__.objects.get(unitId) as Point \| undefined;\n if (!pt) return;\n // Use the raw unit ID as the label text.\n // TODO: support a label-format attribute or callback so callers\n // can supply a custom display string (e.g. strip a prefix,\n // extract a sub-field from a compound ID, etc.)\n const displayText = unitId;\n let lbl = this._pointLabels.get(unitId);\n if (!lbl) {\n lbl = new QELabel(displayText, pt, labelSvg, this, labelPoints);\n this._pointLabels.set(unitId, lbl);\n } else {\n labelPoints === Label.DISPLAY_TYPES.ON ? lbl.show() : lbl.hide();\n }\n });\n }\n\n // Mean labels — use active groups frame rows if available, else groupSums keys\n if (labelMeans !== 0) {\n const meanGroupNames: string[] = hasGroupsFrame\n ? activeGroupRows.map((r: DataFrameRow) => r.rowName ?? String(r[0]))\n : Object.keys(groupSums);\n\n meanGroupNames.forEach((group: string) => {\n const meanId = `mean-${group}`;\n const pt = pointsLayer.__data__.objects.get(meanId) as Point \| undefined;\n if (!pt) return;\n let lbl = this._meanLabels.get(group);\n if (!lbl) {\n lbl = new QELabel(group, pt, labelSvg, this, labelMeans);\n this._meanLabels.set(group, lbl);\n } else {\n labelMeans === Label.DISPLAY_TYPES.ON ? lbl.show() : lbl.hide();\n }\n });\n }\n }\n\n pointsLayer.__data__.__state__.setVariable('layer_updated', pointsLayer.__data__);\n }\n }\n\n // ── Cognitive Trajectories Layer ──────────────────────────────────────────\n const trajectoriesLayer = this.__children__.search('__children__', 'trajectories') as QELayer;\n const trajectoriesEnabled = config.showTrajectories;\n if (trajectoriesEnabled && trajectoriesLayer) {\n trajectoriesLayer.__data__.objects.clear();\n this.__data__.trajectories.clear();\n\n const trajSource = model.trajectories?.rows ? model.trajectories : model.points;\n if (trajSource?.rows) {\n const unitRows: Record<string, Array<{ x: number; y: number; time: number }>> = {};\n const selectedUnits = config.trajectoryUnits ? config.trajectoryUnits.split(',').map(s => s.trim()) : null;\n\n trajSource.rows().forEach((row: DataFrameRow) => {\n const uIdx = row.names.indexOf(unitIdCol) >= 0 ? row.names.indexOf(unitIdCol) : (row.names.indexOf('unit') >= 0 ? row.names.indexOf('unit') : (row.names.indexOf('ENA_UNIT') >= 0 ? row.names.indexOf('ENA_UNIT') : -1));\n const unit = uIdx >= 0 ? String(row[uIdx]) : (row.rowName \|\| 'unit-1');\n\n if (selectedUnits && !selectedUnits.includes(unit)) return;\n\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n const tIdx = row.names.indexOf('time') >= 0 ? row.names.indexOf('time') : (row.names.indexOf('ActivityNumber') >= 0 ? row.names.indexOf('ActivityNumber') : (row.names.indexOf('RowID') >= 0 ? row.names.indexOf('RowID') : -1));\n\n const time = tIdx >= 0 ? Number(row[tIdx]) : (unitRows[unit] ? unitRows[unit].length + 1 : 1);\n // Keep every row: the playhead is applied inside Trajectory via\n // currentTime so degree selection can run on the full trajectory\n // while only the visible prefix is fit and drawn.\n\n if (xIdx >= 0 && yIdx >= 0) {\n if (!unitRows[unit]) unitRows[unit] = [];\n unitRows[unit].push({\n x: Number(row[xIdx]) * pointScale,\n y: -Number(row[yIdx]) * pointScale,\n time\n });\n }\n });\n\n const unitKeys = Object.keys(unitRows);\n unitKeys.forEach((unitKey, uIdx) => {\n const rawPts = unitRows[unitKey];\n if (rawPts.length === 0) return;\n\n const colorStr = PALETTE[uIdx % PALETTE.length];\n\n const trajObj = new Trajectory({\n ID: `traj-${unitKey}`,\n unitId: unitKey,\n color: new Color(colorStr),\n lineStyle: config.trajectoryLineStyle,\n strokeWidth: config.trajectoryStrokeWidth,\n strokeWidthRange: config.trajectoryStrokeWidthRange,\n opacityRange: config.trajectoryOpacityRange,\n smooth: config.trajectorySmooth,\n maxDegree: config.trajectoryMaxDegree,\n degreeSelection: config.trajectoryDegreeSelection,\n currentTime: config.trajectoryPlayhead ?? Infinity,\n showPoints: config.trajectoryShowPoints,\n showTips: config.trajectoryShowTips,\n points: rawPts.map(p => ({ x: p.x, y: p.y, time: p.time }))\n });\n\n this.__data__.trajectories.set(unitKey, trajObj);\n trajectoriesLayer.__data__.objects.set(trajObj.ID, trajObj);\n });\n }\n trajectoriesLayer.__data__.__state__.setVariable('layer_updated', trajectoriesLayer.__data__);\n }\n\n // ── Mean network edges ───────────────────────────────────────────────────\n // For each group, compute the mean weight of every edge column across its\n // unit rows, then draw a Line for pairs whose mean weight is non-zero.\n const networkLayer = this.__children__.search('__children__', 'network') as QELayer;\n const edgeLayer = networkLayer?.__children__.search('__children__', 'edges') as QELayer;\n const nodeLayer = networkLayer?.__children__.search('__children__', 'nodes') as QELayer;\n // edgenodes sits above `nodes` in the layer tree — self-connections (NodeEdge)\n // must be drawn here so the dot is visible on top of the code node.\n const edgenodeLayer = networkLayer?.__children__.search('__children__', 'edgenodes') as QELayer;\n\n const edgesEnabled = config.showEdges;\n if (model.nodes?.rows && nodeLayer) {\n // ── Step 1: Populate node positions first ─────────────────────────────\n // Nodes are always placed so they anchor the coordinate space (extremes).\n // Sizes will be overwritten after edge weights are computed; when edges\n // are hidden the default size is used instead.\n model.nodes.rows().forEach((row: DataFrameRow) => {\n const pt = rowToPoint(row, nodeIdCol, '#444444');\n pt.size = 2; // default when no edge weights available\n // Display text: the nodes frame's optional `label` column\n // (qe_nodes(labels =)); the code id stays the node's identity.\n const li = row.names.indexOf('label');\n const lv = li >= 0 ? row[li] : null;\n (pt as any).meta = { ...((pt as any).meta ?? {}), kind: 'node',\n name: lv != null && String(lv) !== 'NA' && String(lv) !== '' ? String(lv) : pt.ID };\n nodeLayer.__data__.objects.set(pt.ID, pt);\n });\n\n if (edgesEnabled && edgeLayer && model.edges?.rows) {\n // ── Step 2: Build unit→group lookup from points data ─────────────────\n const unitGroupMap: Record<string, string> = {};\n if (groupColName && model.points?.rows) {\n model.points.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n const gIdx = row.names.indexOf(groupColName!);\n if (qIdx >= 0 && gIdx >= 0) unitGroupMap[String(row[qIdx])] = String(row[gIdx]);\n });\n }\n\n // ── Step 3: Collect valid edge-column → code-pair mappings ───────────\n const codeNames: string[] = model.nodes.rows().map((r: DataFrameRow) => {\n const idx = r.names.indexOf(nodeIdCol);\n return idx >= 0 ? String(r[idx]) : '';\n }).filter(Boolean);\n\n const edgePairs: Array<{ col: string; pair: [string, string] }> = [];\n (model.edges.names ?? []).forEach((col: string) => {\n const pair = parseEdgePair(col, codeNames);\n if (pair) edgePairs.push({ col, pair });\n });\n\n // ── Step 4: Edge-weight helpers ───────────────────────────────────────\n type EdgeWeights = Record<string, number>;\n\n /** Raw weights for a single unit row. /\n const getUnitEdges = (unitId: string): EdgeWeights => {\n const result: EdgeWeights = {};\n model.edges.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n if (qIdx < 0 \|\| String(row[qIdx]) !== unitId) return;\n edgePairs.forEach(({ col }) => {\n const colIdx = row.names.indexOf(col);\n if (colIdx >= 0) result[col] = Number(row[colIdx]) \|\| 0;\n });\n });\n return result;\n };\n\n /* Mean weights across all units in a group. /\n const getGroupEdges = (groupName: string): EdgeWeights => {\n const sums: EdgeWeights = {};\n let count = 0;\n model.edges.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n const unitId = qIdx >= 0 ? String(row[qIdx]) : null;\n const gColIdx = groupColName ? row.names.indexOf(groupColName) : -1;\n const group = gColIdx >= 0 ? String(row[gColIdx]) : (unitId ? unitGroupMap[unitId] : null);\n if (group !== groupName) return;\n count++;\n edgePairs.forEach(({ col }) => {\n const colIdx = row.names.indexOf(col);\n if (colIdx >= 0) { const v = Number(row[colIdx]); if (!isNaN(v)) sums[col] = (sums[col] ?? 0) + v; }\n });\n });\n if (count === 0) return {};\n const result: EdgeWeights = {};\n edgePairs.forEach(({ col }) => { result[col] = (sums[col] ?? 0) / count; });\n return result;\n };\n\n /* Resolve an identifier to edge weights + color.\n * Checks group names first, then treats the value as a unit ID. /\n const resolve = (id: string): { weights: EdgeWeights; color: string; label: string } => {\n if (groupColorMap[id]) {\n return { weights: getGroupEdges(id), color: groupColorMap[id], label: id };\n }\n // Unit: color from its group, or neutral grey\n const groupOfUnit = unitGroupMap[id] ?? null;\n const color = groupOfUnit ? (groupColorMap[groupOfUnit] ?? '#888888') : '#888888';\n return { weights: getUnitEdges(id), color, label: id };\n };\n\n // ── Steps 5–6: Build the edges to draw, one <qe-edges> layer at a time ─\n //\n // Named layers (as before):\n // group=\"A\" — group mean\n // unit=\"u\" — one unit's network\n // group=\"A\" compare=\"B\" — subtraction A − B (sign → colour)\n // group=\"A\" also=\"B\" — two groups overlaid\n // Explicit layers (0.5):\n // network=\"n1\" — a row of model.networks (signed)\n // Per layer: colors=\"pos,neg\" overrides the palette; threshold=\"min,max\"\n // drops \|w\| < min and caps \|w\| > max (rENA semantics).\n // Each entry's weight is ≥ 0; the sign is carried by its colour.\n type DrawEdge = { col: string; pair: [string, string]; weight: number; color: string;\n layer: number; name?: string; group?: string; unit?: string };\n const drawEdges: DrawEdge[] = [];\n\n const networkRow = (name: string): EdgeWeights \| null => {\n const frame = (model as any).networks;\n const row = frame?.rows?.().find((r: DataFrameRow) => r.rowName === name);\n if (!row) return null;\n const w: EdgeWeights = {};\n edgePairs.forEach(({ col }) => {\n const i = row.names.indexOf(col);\n if (i >= 0) { const v = Number(row[i]); if (Number.isFinite(v)) w[col] = v; }\n });\n return w;\n };\n const thresholded = (w: number, thr: [number, number] \| null): number => {\n if (!thr) return w;\n const a = Math.abs(w);\n if (a < thr[0]) return 0;\n return a > thr[1] ? Math.sign(w) thr[1] : w;\n };\n\n config.edgeLayers.forEach((L, li) => {\n const push = (col: string, pair: [string, string], w: number, color: string,\n meta: { name?: string; group?: string; unit?: string }) => {\n w = thresholded(w, L.threshold);\n if (Math.abs(w) < 1e-6) return;\n drawEdges.push({ col: `${li}:${col}`, pair, weight: Math.abs(w), color, layer: li, ...meta });\n };\n const signColors = (pos: string, neg: string): [string, string] => {\n if (!L.colors) return [pos, neg];\n return [L.colors[0], L.colors[1] ?? complementColor(L.colors[0])];\n };\n\n if (L.network) {\n // Explicit network: signed weights from model.networks.\n const w = networkRow(L.network);\n if (!w) return;\n const [pos, neg] = signColors(PALETTE[0], PALETTE[1]);\n const meta = { name: L.name ?? L.network };\n edgePairs.forEach(({ col, pair }) => {\n const v = w[col] ?? 0;\n push(col, pair, v, v >= 0 ? pos : neg, meta);\n });\n return;\n }\n\n // Named layer — unit overrides group; no default to the first group.\n const primaryId = L.unit ?? L.group ?? null;\n if (!primaryId) return;\n const primary = resolve(primaryId);\n const secondaryId = L.compare ?? L.also ?? null;\n const secondary = secondaryId ? resolve(secondaryId) : null;\n const meta = { name: L.name ?? primaryId, group: L.group ?? undefined, unit: L.unit ?? undefined };\n const [pos, neg] = signColors(primary.color, secondary?.color ?? primary.color);\n\n if (secondary && L.compare) {\n // A − B: positive → primary colour, negative → secondary colour\n edgePairs.forEach(({ col, pair }) => {\n const d = (primary.weights[col] ?? 0) - (secondary.weights[col] ?? 0);\n push(col, pair, d, d > 0 ? pos : neg, meta);\n });\n } else if (secondary && L.also) {\n // Overlay: both networks, each in its own colour\n edgePairs.forEach(({ col, pair }) => {\n const wA = primary.weights[col] ?? 0, wB = secondary.weights[col] ?? 0;\n if (wA > 0) push(col + '-a', pair, wA, pos, meta);\n if (wB > 0) push(col + '-b', pair, wB, neg, { ...meta, name: L.also ?? undefined, group: L.also ?? undefined });\n });\n } else {\n edgePairs.forEach(({ col, pair }) => {\n const w = primary.weights[col] ?? 0;\n if (w > 0) push(col, pair, w, pos, meta);\n });\n }\n });\n\n // Thin edges on top (rENA's thin.lines.in.front): later objects draw\n // over earlier ones, so add the heaviest first.\n drawEdges.sort((a, b) => b.weight - a.weight);\n\n // ── Step 7: Mark sizes and colour ────────────────────────────────────\n // Width is absolute (webENA): raw weight × one width-per-weight set by\n // <qe-graph edge-width>, shared by edges, directed wide ends,\n // self-connection dots and nodes (diameter = Σ edge widths).\n const isDirected = !!(model as any).directed;\n // <qe-edges magnify> scales this plot's widths and node sizes (not\n // colour) — e.g. to read a faint subtraction — and is always\n // labelled \"(scaled Nx)\" so it is never mistaken for the shared scale.\n const widthFrac = widthPerWeight(config.edgeWidth) * (config.edgeMagnify ?? 1);\n\n // Colour (webENA ramps): each class (lines vs self-loops) rescales\n // \|weight\| from [min, max] onto saturation 0.25–1 / opacity 0.3–1.\n // The range comes from the whole model — every non-zero weight in\n // the edges frame — so plots of one model share a colour scale;\n // webENA takes it from each plotted network (\"plot\").\n const rangeOf = (ws: number[]): [number, number] => {\n const nz = ws.map(Math.abs).filter(v => v > 0);\n return nz.length ? [Math.min(...nz), Math.max(...nz)] : [0, 0];\n };\n const modelRange = (self: boolean): [number, number] => {\n const vals: number[] = [];\n edgePairs.forEach(({ col, pair }) => {\n if ((pair[0] === pair[1]) !== self) return;\n const column = model.edges.col(col);\n if (column) for (const v of column) vals.push(Number(v));\n });\n return rangeOf(vals);\n };\n const plotRange = (self: boolean): [number, number] =>\n rangeOf(drawEdges.filter(e => (e.pair[0] === e.pair[1]) === self).map(e => e.weight));\n const cscale = config.edgeColorScale;\n const colourRange = (self: boolean): [number, number] =>\n cscale === 'plot' ? plotRange(self) : modelRange(self);\n const lineRange = colourRange(false), selfRange = colourRange(true);\n const colourOf = (w: number, self: boolean) => {\n if (cscale === 'absolute') { const a = Math.min(1, Math.abs(w)); return { saturation: a, opacity: a }; }\n const [lo, hi] = self ? selfRange : lineRange;\n return { saturation: rampFor(w, lo, hi, SATURATION_RANGE), opacity: rampFor(w, lo, hi, OPACITY_RANGE) };\n };\n\n // Weight accumulated at each node:\n // Undirected: every edge touching the node (both endpoints).\n // Directed: only edges directed at the node (pair[1] is the\n // target; its wide end is drawn there), including the\n // node's self-connection.\n const nodeWeightSum: Record<string, number> = {};\n drawEdges.forEach(({ pair, weight }) => {\n const isSelf = pair[0] === pair[1];\n if (isSelf && !isDirected) return; // skip illegal undirected diagonals\n const add = (id: string) => { nodeWeightSum[id] = (nodeWeightSum[id] ?? 0) + Math.abs(weight); };\n if (isDirected) { add(pair[1]); return; }\n add(pair[0]); add(pair[1]);\n });\n\n // Node sizes: diameter = Σ widths of the edges counted above. Nodes\n // with nothing counted get a tiny dot, or are hidden with\n // <qe-nodes unconnected=\"hide\">.\n model.nodes.rows().forEach((row: DataFrameRow) => {\n const codeIdx = row.names.indexOf(nodeIdCol);\n const id = codeIdx >= 0 ? String(row[codeIdx]) : '';\n if (!id) return;\n const pt = nodeLayer.__data__.objects.get(id) as Point \| undefined;\n if (!pt) return;\n const w = nodeWeightSum[id] ?? 0;\n const unconnected = !(w > 0);\n pt.size = unconnected ? (config.hideUnconnectedNodes ? 0 : UNCONNECTED_NODE_SIZE)\n : nodeSizeForEdges(w, widthFrac);\n (pt as any).meta = { ...((pt as any).meta ?? {}),\n hidden: unconnected && config.hideUnconnectedNodes };\n });\n\n // ── Step 8: Create edge objects ───────────────────────────────────────\n // For directed models, TaperedWeightedMidpointEdge needs the combined\n // weight of both directions (A→B + B→A) so the apex can be positioned\n // proportionally along the edge. Build a lookup keyed by \"A.B\" per\n // drawn network: an `also` overlay draws two networks in one layer,\n // and pooling them left every triangle short of its counterpart.\n const totalWeightByPair: Record<string, number> = {};\n const pairKey = (layer: number, net: string \| undefined, a: string, b: string) =>\n `${layer}:${net ?? ''}:${a}.${b}`;\n if (isDirected) {\n drawEdges.forEach(({ pair, weight, layer, name }) => {\n const key = pairKey(layer, name, pair[0], pair[1]);\n totalWeightByPair[key] = (totalWeightByPair[key] ?? 0) + weight;\n });\n }\n\n drawEdges.forEach(({ col, pair, weight, color, layer, name, group, unit }) => {\n const fromNode = nodeLayer.__data__.objects.get(pair[0]);\n const toNode = nodeLayer.__data__.objects.get(pair[1]);\n if (!fromNode \|\| !toNode) return;\n\n const isSelf = pair[0] === pair[1];\n if (isSelf && !isDirected) return; // undirected ENA has zero diagonal\n\n // Colour ramps rescale within each visual class (lines vs\n // self-loops), since self-weights are typically smaller.\n const { saturation, opacity } = colourOf(weight, isSelf);\n const fromPt = new Point({ ID: `${pair[0]}-src`, dimensions: [fromNode.x, fromNode.y], meta: {} });\n const toPt = new Point({ ID: `${pair[1]}-dst`, dimensions: [toNode.x, toNode.y], meta: {} });\n // Pick the edge class by topology:\n // • self-connection (A→A) → NodeEdge (filled circle at the node)\n // • directed (A→B) → TaperedWeightedMidpointEdge (triangle\n // whose apex is placed proportionally\n // to weight(A→B) / (weight(A→B) + weight(B→A)))\n // • undirected → Line (straight stroke)\n let edgeLine: Line;\n if (isSelf) {\n edgeLine = new NodeEdge({}, fromPt as any, toPt as any);\n // Actual display size is deferred to QELine.update() so it uses\n // the live extremes.x_max (which is not yet computed here).\n // Set a placeholder weight; update() will overwrite it.\n (edgeLine as any).weight = 0;\n } else if (isDirected) {\n const fwd = totalWeightByPair[pairKey(layer, name, pair[0], pair[1])] ?? weight;\n const bwd = totalWeightByPair[pairKey(layer, name, pair[1], pair[0])] ?? 0;\n const totalweight = fwd + bwd;\n edgeLine = new TaperedWeightedMidpointEdge(\n { weight, totalweight },\n fromPt as any,\n toPt as any\n );\n } else {\n edgeLine = new Line({}, fromPt, toPt);\n }\n edgeLine.ID = `edge-${col}`;\n edgeLine.color = new Color(color);\n (edgeLine as any).meta = {\n isMeanEdge: true,\n weight,\n // Width per unit weight (extent units), shared by all marks.\n widthFrac,\n saturation,\n opacity,\n isDirected,\n isSelf,\n // Identity for the qe-edge-* interaction events.\n source: pair[0],\n target: pair[1],\n group,\n unit,\n layer: name,\n };\n // Self-connections go in the `edgenodes` layer (above `nodes` in\n // draw order) so the dot is visible on top of the code node.\n const targetLayer = isSelf ? (edgenodeLayer ?? edgeLayer) : edgeLayer;\n targetLayer.__data__.objects.set(edgeLine.ID, edgeLine);\n });\n\n edgeLayer.__data__.__state__.setVariable('layer_updated', edgeLayer.__data__);\n if (edgenodeLayer) edgenodeLayer.__data__.__state__.setVariable('layer_updated', edgenodeLayer.__data__);\n }\n\n // ── Node visibility ──────────────────────────────────────────────────\n // Node positions come from the model and stay in the layer either way,\n // so they keep anchoring the extent (the plot does not rescale when\n // nodes are toggled); <qe-nodes> presence only controls the drawing,\n // as <qe-axes> does for the axis sub-tree.\n const nodesVisible = config.showNodes;\n if (nodeLayer.svg_element) {\n (nodeLayer.svg_element as SVGElement).style.display = nodesVisible ? '' : 'none';\n }\n if (!nodesVisible) {\n this._nodeLabels.forEach(lbl => lbl.remove());\n this._nodeLabels.clear();\n }\n\n // ── Node labels ──────────────────────────────────────────────────────\n if (labelSvg && labelNodes !== 0 && nodesVisible) {\n // Clean up stale node labels\n this._nodeLabels.forEach((lbl, id) => {\n if (!nodeLayer.__data__.objects.get(id)) { lbl.remove(); this._nodeLabels.delete(id); }\n });\n model.nodes.rows().forEach((row: DataFrameRow) => {\n const codeIdx = row.names.indexOf(nodeIdCol);\n const id = codeIdx >= 0 ? String(row[codeIdx]) : '';\n if (!id) return;\n const pt = nodeLayer.__data__.objects.get(id) as Point \| undefined;\n if (!pt) return;\n if ((pt as any).meta?.hidden) {\n this._nodeLabels.get(id)?.remove();\n this._nodeLabels.delete(id);\n return;\n }\n const text = String((pt as any).meta?.name ?? id);\n let lbl = this._nodeLabels.get(id);\n if (lbl && lbl.text !== text) { lbl.remove(); this._nodeLabels.delete(id); lbl = undefined; }\n if (!lbl) {\n lbl = new QELabel(text, pt, labelSvg, this, labelNodes);\n this._nodeLabels.set(id, lbl);\n } else {\n labelNodes === Label.DISPLAY_TYPES.ON ? lbl.show() : lbl.hide();\n }\n });\n }\n\n // Fire after both positions and sizes are set\n nodeLayer.__data__.__state__.setVariable('layer_updated', nodeLayer.__data__);\n }\n\n // ── Axis lines / points ──────────────────────────────────────────────────\n const axisPointsLayer = this.__children__.search('__children__', 'axis_points');\n const axisLinesLayer = this.__children__.search('__children__', 'axis_lines');\n if (axisPointsLayer) this.__data__.__state__.setVariable('graph_updated_axis_points', axisPointsLayer.__data__.objects);\n if (axisLinesLayer) this.__data__.__state__.setVariable('graph_updated_axis_lines', axisLinesLayer.__data__.objects);\n\n this.update();\n\n // Animate marks/edges from their pre-rebuild positions to the new ones.\n if (tweenFrom) this._runTween(tweenFrom);\n });\n }\n\n // ── Shared re-render scheduler ───────────────────────────────────────────────\n // Batches synchronous attribute / child-list changes into a single microtask\n // so that e.g. adding <qe-edges> and setting its attributes in the same tick\n // only triggers one render cycle.\n private _scheduleRerender(): void {\n if (!this._vizena \|\| !this._hasModel) return;\n if (this._renderPending) return;\n this._renderPending = true;\n queueMicrotask(() => {\n this._renderPending = false;\n this._vizena?.dispatchEvent(new CustomEvent('model-updated', {\n detail: this._vizena.model,\n bubbles: true,\n composed: true,\n }));\n });\n }\n\n // ── Layer configuration reader ────────────────────────────────────────────────\n // Reads child element presence / attributes to determine what each layer\n // should render. Called once at the top of every model-updated handler so\n // all rendering decisions are derived from a single snapshot.\n private _readLayerConfig(): {\n // Nodes\n labelNodes: number;\n showNodes: boolean;\n edgeWidth: number;\n range: 'network' \| 'points' \| number \| null;\n centerContent: boolean;\n plotTitle: string \| null;\n labelFont: { size: number \| null; family: string \| null; color: string \| null };\n hideUnconnectedNodes: boolean;\n scalePoints: boolean;\n pointScale: number \| null;\n // Means\n showMeans: boolean;\n activeMeanGroups: string \| null;\n showCI: boolean;\n intervals: 'box' \| 'crosshairs' \| 'none';\n showOutlier: boolean;\n labelMeans: number;\n meanFixedSize: boolean;\n // Points\n showPoints: boolean;\n pointSets: Array<{ set: string; size: number \| null; fixedSize: boolean }>;\n labelPoints: number;\n pointSize: number \| null;\n pointFixedSize: boolean;\n // Edges\n showEdges: boolean;\n edgeLayers: EdgeLayerSpec[];\n edgeColorScale: ColorScale;\n edgeMagnify: number \| null;\n\n showTrajectories: boolean;\n trajectoryUnits: string \| null;\n trajectorySmooth: 'none' \| 'poly';\n trajectoryMaxDegree: number;\n trajectoryDegreeSelection: 'loocv_2d' \| 'fixed';\n trajectoryShowPoints: boolean;\n trajectoryShowTips: boolean;\n trajectoryPlayhead: number \| null;\n trajectoryLineStyle: 'uniform' \| 'tapered';\n trajectoryStrokeWidth: number;\n trajectoryStrokeWidthRange: [number, number];\n trajectoryOpacityRange: [number, number];\n // Axes\n showAxes: boolean;\n axisXLabel: string \| null;\n axisYLabel: string \| null;\n } {\n const nodesEl = this.querySelector('qe-nodes');\n const meansEl = this.querySelector('qe-means');\n // <qe-points> without `set` = all unit points; with `set` = an explicit set.\n const allPointsEls = [...this.querySelectorAll('qe-points')];\n const pointsEl = allPointsEls.find(e => !e.hasAttribute('set')) ?? null;\n const setEls = allPointsEls.filter(e => e.hasAttribute('set'));\n // Every <qe-edges> child is one layer (0.5): a named network (group / unit\n // / compare / also) or an explicit one (network=\"name\" → model.networks).\n const edgeEls = [...this.querySelectorAll('qe-edges')];\n const firstAttr = (a: string) => edgeEls.find(e => e.hasAttribute(a))?.getAttribute(a) ?? null;\n const magnifyEl = edgeEls.find(e => e.hasAttribute('magnify'));\n const trajectoriesEl = this.querySelector('qe-trajectories');\n const axesEl = this.querySelector('qe-axes');\n const labelsShorthand = this.getAttribute('labels');\n\n return {\n // Nodes — always placed from the model (they anchor the coordinate\n // space); <qe-nodes> presence draws them, like every other layer.\n labelNodes: parseLabelMode(\n nodesEl?.getAttribute('label') ?? this.getAttribute('label-nodes') ?? labelsShorthand,\n Label.DISPLAY_TYPES.ON\n ),\n showNodes: !!nodesEl,\n range: (() => {\n const v = this.getAttribute('range');\n if (v === 'network' \|\| v === 'points') return v;\n const n = Number(v);\n return v != null && Number.isFinite(n) && n > 0 ? n : null;\n })(),\n plotTitle: this.getAttribute('plot-title') \|\| null,\n labelFont: {\n size: (() => { const n = Number(this.getAttribute('label-font-size'));\n return Number.isFinite(n) && n > 0 ? n : null; })(),\n family: this.getAttribute('label-font-family') \|\| null,\n color: this.getAttribute('label-font-color') \|\| null,\n },\n edgeWidth: (() => {\n const v = Number(this.getAttribute('edge-width'));\n return Number.isFinite(v) && v > 0 && v <= 1 ? v : DEFAULT_EDGE_WIDTH;\n })(),\n hideUnconnectedNodes: nodesEl?.getAttribute('unconnected')?.toLowerCase() === 'hide',\n scalePoints: this.getAttribute('scale-points') !== 'false',\n pointScale: (() => {\n const v = Number(this.getAttribute('point-scale'));\n return this.hasAttribute('point-scale') && Number.isFinite(v) && v > 0 ? v : null;\n })(),\n centerContent: this.getAttribute('center') === 'content',\n\n // Means — presence of <qe-means> = show; absence = hide.\n showMeans: !!meansEl,\n activeMeanGroups: meansEl?.getAttribute('groups') ?? null,\n showCI: !!meansEl && meansEl.hasAttribute('confidence'),\n // intervals=\"box\|crosshairs\|none\"; absent → the legacy `confidence` flag.\n intervals: (() => {\n const v = meansEl?.getAttribute('intervals');\n if (v === 'box' \|\| v === 'crosshairs' \|\| v === 'none') return v;\n return meansEl?.hasAttribute('confidence') ? 'box' : 'none';\n })() as 'box' \| 'crosshairs' \| 'none',\n showOutlier: !!meansEl && meansEl.hasAttribute('outlier'),\n labelMeans: parseLabelMode(\n meansEl?.getAttribute('label') ?? this.getAttribute('label-means') ?? labelsShorthand,\n Label.DISPLAY_TYPES.ON\n ),\n // fixed-size keeps mean markers a constant on-screen px size (webENA parity).\n meanFixedSize: !!meansEl && meansEl.hasAttribute('fixed-size'),\n\n // Points — presence of <qe-points> = show unit dots.\n showPoints: !!pointsEl,\n pointSets: setEls.map(e => ({\n set: e.getAttribute('set')!,\n size: e.getAttribute('size') ? parseFloat(e.getAttribute('size')!) : null,\n fixedSize: e.hasAttribute('fixed-size'),\n })),\n labelPoints: parseLabelMode(\n pointsEl?.getAttribute('label') ?? this.getAttribute('label-points') ?? labelsShorthand,\n Label.DISPLAY_TYPES.OFF\n ),\n pointSize: pointsEl?.getAttribute('size') ? parseFloat(pointsEl.getAttribute('size')!) : null,\n // fixed-size keeps unit dots a constant on-screen px size (webENA parity).\n pointFixedSize: !!pointsEl && pointsEl.hasAttribute('fixed-size'),\n\n // Edges — presence of <qe-edges> = draw a network.\n showEdges: edgeEls.length > 0,\n edgeLayers: edgeEls.map(parseEdgeLayer),\n // Plot-wide edge settings: the first <qe-edges> that sets them.\n edgeColorScale: parseColorScale(firstAttr('color-scale')),\n edgeMagnify: magnifyEl ? (() => {\n const v = Number(magnifyEl.getAttribute('magnify'));\n return Number.isFinite(v) && v > 0 ? v : 1;\n })() : null,\n\n // Trajectories — presence of <qe-trajectories> = draw cognitive trajectories\n showTrajectories: !!trajectoriesEl,\n trajectoryUnits: trajectoriesEl?.getAttribute('units') ?? null,\n trajectorySmooth: (trajectoriesEl?.getAttribute('smooth') as 'none' \| 'poly') ?? 'none',\n trajectoryMaxDegree: trajectoriesEl?.getAttribute('max-degree') ? parseInt(trajectoriesEl.getAttribute('max-degree')!, 10) : 3,\n trajectoryDegreeSelection: (trajectoriesEl?.getAttribute('degree-selection') as 'loocv_2d' \| 'fixed') ?? 'loocv_2d',\n trajectoryShowPoints: trajectoriesEl?.getAttribute('points') !== 'false',\n trajectoryShowTips: trajectoriesEl?.getAttribute('tips') !== 'false',\n trajectoryPlayhead: trajectoriesEl?.getAttribute('playhead') ? parseFloat(trajectoriesEl.getAttribute('playhead')!) : null,\n trajectoryLineStyle: (trajectoriesEl?.getAttribute('line-style') as 'uniform' \| 'tapered') ?? 'uniform',\n trajectoryStrokeWidth: trajectoriesEl?.getAttribute('stroke-width') ? parseFloat(trajectoriesEl.getAttribute('stroke-width')!) : 2,\n trajectoryStrokeWidthRange: this._parseNumberPair(trajectoriesEl?.getAttribute('stroke-width-range'), [1, 6]),\n trajectoryOpacityRange: this._parseNumberPair(trajectoriesEl?.getAttribute('opacity-range'), [0.3, 1]),\n\n // Axes — presence of <qe-axes> = draw axis lines. The x / y attributes add\n // a per-axis label: a value is used verbatim, an empty attribute falls back\n // to the dimension name (resolved later, where dims are known). null = no\n // label for that axis.\n showAxes: !!axesEl,\n axisXLabel: axesEl?.hasAttribute('x') ? (axesEl.getAttribute('x') ?? '') : null,\n axisYLabel: axesEl?.hasAttribute('y') ? (axesEl.getAttribute('y') ?? '') : null,\n };\n }\n\n private _parseNumberPair(value: string \| null \| undefined, fallback: [number, number]): [number, number] {\n if (!value) return fallback;\n const parts = value.split(',').map(part => Number(part.trim()));\n if (parts.length < 2 \|\| !parts.every(Number.isFinite)) return fallback;\n return [parts[0], parts[1]];\n }\n\n attributeChangedCallback(_name: string, oldValue: string \| null, newValue: string \| null): void {\n if (oldValue === newValue) return;\n this._scheduleRerender();\n }\n\n connectedCallback(): void {\n // Apply width/height HTML attributes as CSS dimensions on the host element\n // so the shadow-DOM wrapper's height:100% resolves to a real pixel value.\n const w = this.getAttribute('width');\n const h = this.getAttribute('height');\n this.style.display = 'block'; // custom elements are inline by default\n if (w) this.style.width = isNaN(Number(w)) ? w : `${w}px`;\n if (h) this.style.height = isNaN(Number(h)) ? h : `${h}px`;\n\n this.appendChild(this.svg_element);\n QEGraphElement._instances.add(this); // registry for getGraph()/instances()\n\n // Watch for child layer element additions/removals and attribute changes.\n // Any mutation schedules a re-render via the same microtask batch used by\n // attributeChangedCallback, so synchronous DOM mutations collapse to one pass.\n this._childObserver = new MutationObserver(() => this._scheduleRerender());\n this._childObserver.observe(this, {\n childList: true,\n attributes: true,\n subtree: true,\n attributeFilter: [\n 'group', 'unit', 'compare', 'also', 'color-scale', 'magnify',\n 'network', 'colors', 'threshold', 'name',\n 'groups', 'confidence', 'label', 'intervals', 'outlier', 'set', 'unconnected',\n 'scale-points', 'point-scale', 'edge-width', 'labels', 'range', 'center', 'plot-title',\n 'label-font-size', 'label-font-family', 'label-font-color', 'label-nodes', 'label-means', 'label-points',\n 'units', 'smooth', 'degree', 'points', 'tips', 'playhead',\n 'line-style', 'stroke-width', 'stroke-width-range', 'opacity-range',\n 'x', 'y', 'size', 'fixed-size',\n ],\n });\n // Find the associated ena-visual: check 'for' attribute first, then nearest\n // ancestor, then first one on the page. This lets ena-graph work as a child,\n // a sibling, or anywhere else in the document.\n const forId = this.getAttribute('for');\n this._vizena = (\n (forId ? document.getElementById(forId) : null) ??\n this.closest('qe-visual') ??\n this.parentElement?.closest('qe-visual') ??\n document.querySelector('qe-visual')\n ) as QEVisualElement;\n this.draw();\n\n // Cache the labels <g> after draw() has connected all layer elements to\n // the SVG DOM. We do this once here rather than searching on every\n // model-updated event to guarantee we always have a valid reference.\n const labelsLayer = this.__children__.search('__children__', 'labels') as QELayer;\n if (labelsLayer?.svg_element) {\n this._labelsGroup = labelsLayer.svg_element as SVGGElement;\n } else {\n // Fallback: create a new <g> directly inside the outermost graph layer.\n console.warn('[ena-graph] labels layer not found in layer tree; creating fallback <g>');\n const graphLayer = this.__children__[0] as QELayer;\n if (graphLayer?.svg_element) {\n this._labelsGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g') as SVGGElement;\n this._labelsGroup.setAttribute('data-layer-name', 'labels-fallback');\n graphLayer.svg_element.appendChild(this._labelsGroup);\n }\n }\n }\n\n disconnectedCallback(): void {\n this._childObserver?.disconnect();\n this._childObserver = null;\n this._resizeObs?.disconnect();\n this._resizeObs = null;\n QEGraphElement._instances.delete(this);\n // Remove the body-level tooltip node so it doesn't outlive the graph.\n this._tooltipEl?.remove();\n this._tooltipEl = null;\n }\n\n // ── Instance registry + read APIs (webENA integration) ──────────────────────\n private static _instances: Set<QEGraphElement> = new Set();\n\n /** All connected <qe-graph> instances (newest membership order). /\n static instances(): QEGraphElement[] { return [...QEGraphElement._instances]; }\n\n /* Look up a graph by its `id` or `plot-group` attribute. /\n static getGraph(key: string): QEGraphElement \| null {\n for (const g of QEGraphElement._instances) {\n if (g.id === key \|\| g.getAttribute('plot-group') === key) return g;\n }\n return null;\n }\n\n /* Resolved code nodes with their current graph-space coordinates. /\n getNodes(): Array<{ id: string; name: string; x: number; y: number }> {\n const layer = this.__children__.search('__children__', 'nodes') as QELayer \| undefined;\n if (!layer) return [];\n return [...layer.__data__.objects.values()].map((o: any) => ({\n id: o.ID, name: o.meta?.name ?? o.ID, x: o.x, y: o.y,\n }));\n }\n\n /* Resolved edges of the current network with weights and direction. /\n getEdges(): Array<{ source: string; target: string; weight: number; directed: boolean; self: boolean }> {\n const collect = (name: string) => {\n const l = this.__children__.search('__children__', name) as QELayer \| undefined;\n return l ? [...l.__data__.objects.values()] : [];\n };\n return [...collect('edges'), ...collect('edgenodes')]\n .map((o: any) => {\n const m = o.meta ?? {};\n return { source: m.source, target: m.target, weight: m.weight ?? 0,\n directed: !!m.isDirected, self: !!m.isSelf };\n })\n .filter(e => e.source != null && e.target != null);\n }\n\n // ── Transition tweening (opt-in via the `animate` attribute; webENA P2.1) ───\n private _animateMs = 0;\n private _tweenRaf: number \| null = null;\n\n /* Matches every numeric token in an SVG path `d` string (ints, decimals,\n * scientific notation, leading sign) while leaving command letters intact. /\n private static _PATH_NUM_RE = /-?\\d\\.?\\d+(?:e[-+]?\\d+)?/gi;\n\n /** Marks (circles/rects), undirected edge lines, and directed / self-edge\n * triangle paths all participate in tweening. /\n private _tweenTargets(): SVGElement[] {\n return [...this.svg_element.querySelectorAll(\n 'circle[data-point-id], rect[data-point-id], line[data-edge-source], path[data-edge-source]'\n )] as SVGElement[];\n }\n\n private _readCoords(el: SVGElement): any {\n const tag = el.tagName.toLowerCase();\n const n = (a: string) => parseFloat(el.getAttribute(a) \|\| '0');\n if (tag === 'circle') return { t: 'c', cx: n('cx'), cy: n('cy') };\n if (tag === 'rect') return { t: 'r', x: n('x'), y: n('y') };\n if (tag === 'line') return { t: 'l', x1: n('x1'), y1: n('y1'), x2: n('x2'), y2: n('y2') };\n if (tag === 'path') {\n const d = el.getAttribute('d') \|\| '';\n return { t: 'p', d, nums: (d.match(QEGraphElement._PATH_NUM_RE) \|\| []).map(Number) };\n }\n return null;\n }\n\n /* Snapshot current tween-target positions keyed by element. /\n private _captureTween(): Map<SVGElement, any> {\n const m = new Map<SVGElement, any>();\n this._tweenTargets().forEach(el => { const c = this._readCoords(el); if (c) m.set(el, c); });\n return m;\n }\n\n /* Animate each still-present element from its snapshot to its new position. /\n private _runTween(from: Map<SVGElement, any>): void {\n if (this._tweenRaf !== null) { cancelAnimationFrame(this._tweenRaf); this._tweenRaf = null; }\n const to = new Map<SVGElement, any>();\n this._tweenTargets().forEach(el => { if (from.has(el)) { const c = this._readCoords(el); if (c) to.set(el, c); } });\n if (!to.size) return;\n\n const dur = this._animateMs;\n const t0 = performance.now();\n const ease = (t: number) => (t < 0.5 ? 2 t * t : 1 - Math.pow(-2 * t + 2, 2) / 2);\n const lerp = (a: number, b: number, k: number) => a + (b - a) * k;\n\n const step = (now: number) => {\n const t = Math.min(1, (now - t0) / dur);\n const k = ease(t);\n to.forEach((nc, el) => {\n const oc = from.get(el);\n if (!oc \|\| oc.t !== nc.t) return;\n if (nc.t === 'c') {\n el.setAttribute('cx', String(lerp(oc.cx, nc.cx, k)));\n el.setAttribute('cy', String(lerp(oc.cy, nc.cy, k)));\n } else if (nc.t === 'r') {\n el.setAttribute('x', String(lerp(oc.x, nc.x, k)));\n el.setAttribute('y', String(lerp(oc.y, nc.y, k)));\n } else if (nc.t === 'l') {\n el.setAttribute('x1', String(lerp(oc.x1, nc.x1, k)));\n el.setAttribute('y1', String(lerp(oc.y1, nc.y1, k)));\n el.setAttribute('x2', String(lerp(oc.x2, nc.x2, k)));\n el.setAttribute('y2', String(lerp(oc.y2, nc.y2, k)));\n } else {\n // Directed / self-edge triangle path: interpolate the numeric tokens\n // in `d` when the command structure is stable (equal token count).\n // Otherwise leave the freshly-built `d` in place (graceful snap).\n if (!oc.nums \|\| oc.nums.length !== nc.nums.length) return;\n let i = 0;\n const d = nc.d.replace(QEGraphElement._PATH_NUM_RE,\n () => String(lerp(oc.nums[i], nc.nums[i++], k)));\n el.setAttribute('d', d);\n }\n });\n this._tweenRaf = t < 1 ? requestAnimationFrame(step) : null;\n };\n this._tweenRaf = requestAnimationFrame(step);\n }\n\n /** Serialize the current plot as a standalone SVG string (webENA P2.3). /\n toSVG(): string {\n const svg = this.svg_element.cloneNode(true) as SVGSVGElement;\n svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg');\n svg.setAttribute('xmlns:xlink', 'http://www.w3.org/1999/xlink');\n const rect = this.svg_element.getBoundingClientRect();\n if (rect.width) svg.setAttribute('width', String(Math.round(rect.width)));\n if (rect.height) svg.setAttribute('height', String(Math.round(rect.height)));\n return new XMLSerializer().serializeToString(svg);\n }\n\n /* Rasterize the current plot to a PNG data URL (webENA P2.3). `scale`\n * multiplies the pixel dimensions for a higher-resolution image. /\n toPNG(scale = 2): Promise<string> {\n const svgStr = this.toSVG();\n const rect = this.svg_element.getBoundingClientRect();\n const w = Math.max(1, Math.round(rect.width));\n const h = Math.max(1, Math.round(rect.height));\n return new Promise((resolve, reject) => {\n const blob = new Blob([svgStr], { type: 'image/svg+xml;charset=utf-8' });\n const url = URL.createObjectURL(blob);\n const img = new Image();\n img.onload = () => {\n try {\n const canvas = document.createElement('canvas');\n canvas.width = w scale;\n canvas.height = h * scale;\n const ctx = canvas.getContext('2d');\n if (!ctx) { URL.revokeObjectURL(url); reject(new Error('no 2d context')); return; }\n ctx.scale(scale, scale);\n ctx.drawImage(img, 0, 0, w, h);\n URL.revokeObjectURL(url);\n resolve(canvas.toDataURL('image/png'));\n } catch (err) { URL.revokeObjectURL(url); reject(err); }\n };\n img.onerror = (e) => { URL.revokeObjectURL(url); reject(e); };\n img.src = url;\n });\n }\n\n /** Unit points with their current graph-space coordinates. /\n getPoints(): Array<{ id: string; group?: string; set?: string; x: number; y: number }> {\n const layer = this.__children__.search('__children__', 'points') as QELayer \| undefined;\n if (!layer) return [];\n return [...layer.__data__.objects.values()]\n .filter((o: any) => o.meta?.kind === 'point')\n .map((o: any) => ({ id: o.meta?.unit ?? o.ID, group: o.meta?.group, set: o.meta?.set,\n x: o.x, y: o.y }));\n }\n\n /* Ids of unit points inside a graph-space rectangle (for drag/lasso select). /\n pointsInRect(rect: { x: number; y: number; w: number; h: number }): string[] {\n return this.getPoints()\n .filter(p => p.x >= rect.x && p.x <= rect.x + rect.w &&\n p.y >= rect.y && p.y <= rect.y + rect.h)\n .map(p => p.id);\n }\n\n // ── Host-driven highlight / selection (webENA P1.1) ─────────────────────────\n // Rendered as an overlay group so it never mutates the marks themselves, and\n // is re-applied after every render so selection survives model updates.\n private _highlight: { edges: Set<string>; nodes: Set<string> } = { edges: new Set(), nodes: new Set() };\n private _highlightGroup: SVGGElement \| null = null;\n\n /* Order-independent key so an undirected pair matches either direction. /\n private _edgeKey(a: string, b: string): string {\n return a <= b ? `${a}\u0000${b}` : `${b}\u0000${a}`;\n }\n\n /* Mark edges/nodes as highlighted. Replaces the previous selection. /\n setHighlight(sel: { edges?: Array<{ source: string; target: string }>; nodes?: Array<string> }): void {\n this._highlight.edges = new Set((sel.edges ?? []).map(e => this._edgeKey(e.source, e.target)));\n this._highlight.nodes = new Set((sel.nodes ?? []).map(String));\n this._applyHighlights();\n }\n\n /* Clear all highlighting. /\n clearHighlight(): void {\n this._highlight.edges.clear();\n this._highlight.nodes.clear();\n this._applyHighlights();\n }\n\n private _applyHighlights(): void {\n if (!this.svg_element) return;\n if (!this._highlightGroup) {\n this._highlightGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g') as SVGGElement;\n this._highlightGroup.setAttribute('data-layer-name', 'highlight');\n this._highlightGroup.setAttribute('pointer-events', 'none');\n }\n // Keep the overlay on top.\n this.svg_element.appendChild(this._highlightGroup);\n const g = this._highlightGroup;\n g.textContent = '';\n\n const extent = (this.__data__ as Graph).extremes.x_max \|\| 1;\n const HL = '#f5a623';\n const mk = (tag: string, attrs: Record<string, string \| number>) => {\n const el = document.createElementNS('http://www.w3.org/2000/svg', tag);\n for (const k in attrs) el.setAttribute(k, String(attrs[k]));\n return el;\n };\n\n // Edges — a translucent glow line between the two code-node centres.\n if (this._highlight.edges.size) {\n const xy: Record<string, { x: number; y: number }> = {};\n this.getNodes().forEach(n => { xy[n.id] = { x: n.x, y: n.y }; });\n this._highlight.edges.forEach(key => {\n const [a, b] = key.split('\u0000');\n const A = xy[a], B = xy[b];\n if (!A \|\| !B) return;\n g.appendChild(mk('line', {\n x1: A.x, y1: A.y, x2: B.x, y2: B.y,\n stroke: HL, 'stroke-width': extent 0.02, 'stroke-opacity': 0.6, 'stroke-linecap': 'round',\n }));\n });\n }\n\n // Nodes / means / points — a ring around the mark.\n this._highlight.nodes.forEach(id => {\n const el = this.svg_element.querySelector(`[data-point-id=\"${(window as any).CSS?.escape ? CSS.escape(id) : id}\"]`) as SVGElement \| null;\n if (!el) return;\n const tag = el.tagName.toLowerCase();\n let cx: number, cy: number, r: number;\n if (tag === 'rect') {\n const w = parseFloat(el.getAttribute('width') \|\| '0');\n cx = parseFloat(el.getAttribute('x') \|\| '0') + w / 2;\n cy = parseFloat(el.getAttribute('y') \|\| '0') + parseFloat(el.getAttribute('height') \|\| '0') / 2;\n r = w / 2;\n } else {\n cx = parseFloat(el.getAttribute('cx') \|\| '0');\n cy = parseFloat(el.getAttribute('cy') \|\| '0');\n r = parseFloat(el.getAttribute('r') \|\| '0');\n }\n g.appendChild(mk('circle', {\n cx, cy, r: r * 1.7 + extent * 0.004, fill: 'none', stroke: HL, 'stroke-width': extent * 0.006,\n }));\n });\n }\n\n create(): SVGElement {\n const\n svg = document.createElementNS(\"http://www.w3.org/2000/svg\", \"svg\")\n ;\n svg.classList.add(\"graph\");\n // Fill the host and keep the square ENA drawing centered (equal x/y scaling\n // preserves distances). Without this the SVG collapses to an intrinsic size\n // and pins to the left, leaving dead space in the container.\n svg.style.display = 'block';\n svg.style.width = '100%';\n svg.style.height = '100%';\n svg.setAttribute(\"preserveAspectRatio\", \"xMidYMid meet\");\n svg.setAttribute(\"viewBox\", (this.__data__ as Graph).extremes.as_viewBox());\n svg.setAttribute(\"transform\", (this.__data__ as Graph).transform.toString());\n svg.setAttribute(\"role\", \"figure\");\n svg.setAttribute(\"data-graph-size\", `${Math.min((this.__data__ as Graph).extremes.width, (this.__data__ as Graph).extremes.height)}`);\n this.svg_element = svg;\n\n // Pre-generate one arrowhead marker per palette color. Per-color markers are\n // the most reliable approach: `context-stroke` and `currentColor` inheritance\n // through SVG markers is inconsistent across browsers and shadow-DOM contexts.\n // Reference as url(#qe-arrow-RRGGBB) where RRGGBB is the hex without '#'.\n const defs = document.createElementNS('http://www.w3.org/2000/svg', 'defs');\n // Arrow dimensions in SVG user-space units (viewBox is ~4.8×4.8).\n // AW must be large enough so the body of the arrowhead is visible before it\n // disappears behind the target node circle. ~5% of the viewport (0.24 units)\n // works well. markerUnits=\"userSpaceOnUse\" keeps the size fixed regardless\n // of stroke-width, so even thin edges get a readable direction indicator.\n const AW = 0.22, AH = 0.15; // arrow length (along edge) and base width (perp)\n const makeArrow = (id: string, fill: string) => {\n const m = document.createElementNS('http://www.w3.org/2000/svg', 'marker');\n m.setAttribute('id', id);\n m.setAttribute('markerWidth', String(AW));\n m.setAttribute('markerHeight',String(AH));\n m.setAttribute('refX', String(AW)); // tip at reference point\n m.setAttribute('refY', String(AH / 2));\n m.setAttribute('orient', 'auto');\n m.setAttribute('markerUnits', 'userSpaceOnUse');\n const p = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n p.setAttribute('d', `M0,0 L0,${AH} L${AW},${AH/2} z`);\n p.setAttribute('fill', fill);\n m.appendChild(p);\n defs.appendChild(m);\n };\n // One marker per GROUP_PALETTE entry (covers all possible edge colors)\n GROUP_PALETTE.forEach(color => makeArrow(`qe-arrow-${color.slice(1)}`, color));\n svg.appendChild(defs);\n\n this.__data__.layers.forEach((layer: LayerLike) => {\n const layer_g: QELayer = new QELayer(layer as any, this.svg_element, this);\n this.__children__.push(layer_g);\n });\n\n this.__data__.__state__.setVariable(\"graph_updated\", this.__data__ );\n\n this.attach_events();\n\n return svg;\n }\n\n attach_events() {\n // Attach event for zooming\n this.svg_element.addEventListener(\"wheel\", (ev: WheelEvent) => {\n console.log(\"Wheel event: \", ev);\n ev.preventDefault();\n const delta = Math.sign(ev.deltaY);\n if (delta < 0) {\n this.zoom_level = 1.1;\n } else {\n this.zoom_level /= 1.1;\n }\n this.__data__.transform.zoom(this.zoom_level);\n this.update();\n });\n\n // Attach event for panning\n let isPanning = false;\n let startX: number, startY: number;\n\n this.svg_element.addEventListener(\"mousedown\", (ev: MouseEvent) => {\n isPanning = true;\n startX = ev.clientX;\n startY = ev.clientY;\n });\n let panAnimationFrame: number \| null = null;\n let pendingPan: { dx: number, dy: number } \| null = null;\n\n const panUpdate = () => {\n if (pendingPan) {\n this.__data__.transform.pan(pendingPan.dx, pendingPan.dy);\n this.__children__[0].svg_element.setAttribute(\"transform\", this.__data__.transform.toString());\n pendingPan = null;\n }\n panAnimationFrame = null;\n };\n\n this.svg_element.addEventListener(\"mousemove\", (ev: MouseEvent) => {\n if (!isPanning) return;\n const \n dx = ev.clientX - startX,\n dy = ev.clientY - startY\n ;\n pendingPan = { dx: dx / 100, dy: dy / 100 };\n startX = ev.clientX;\n startY = ev.clientY;\n \n if (panAnimationFrame === null) {\n panAnimationFrame = requestAnimationFrame(panUpdate);\n }\n });\n\n this.svg_element.addEventListener(\"mouseup\", (ev: MouseEvent) => {\n isPanning = false;\n });\n\n // ── Label interactions ───────────────────────────────────────────────────\n // CLICK mode: toggle label on point-clicked event\n this.svg_element.addEventListener('point-clicked', ((ev: CustomEvent) => {\n const id = ev.detail?.pointData?.ID;\n if (!id) return;\n const lbl = this._pointLabels.get(id)\n ?? this._meanLabels.get(id.replace('mean-', ''))\n ?? this._nodeLabels.get(id);\n if (lbl && lbl.displayMode === Label.DISPLAY_TYPES.CLICK) lbl.toggle();\n }) as EventListener);\n\n // AUTO mode: show/hide labels via event delegation on the SVG.\n // We look for the nearest ancestor (or the target itself) that has\n // data-point-id so the hit-area works even on complex shapes.\n const findPointId = (el: SVGElement \| null): string \| null => {\n while (el && el !== this.svg_element) {\n const id = el.getAttribute?.('data-point-id');\n if (id) return id;\n el = el.parentElement as SVGElement \| null;\n }\n return null;\n };\n\n const getAutoLabel = (id: string): QELabel \| undefined => {\n return this._pointLabels.get(id)\n ?? this._meanLabels.get(id.replace(/^mean-/, ''))\n ?? this._nodeLabels.get(id);\n };\n\n this.svg_element.addEventListener('mouseover', (ev: MouseEvent) => {\n const id = findPointId(ev.target as SVGElement);\n if (!id) return;\n const lbl = getAutoLabel(id);\n if (lbl?.displayMode === Label.DISPLAY_TYPES.AUTO) lbl.show();\n });\n\n this.svg_element.addEventListener('mouseout', (ev: MouseEvent) => {\n // Only hide when the mouse leaves the point element entirely,\n // not when it enters a child (e.g., a nested SVG element).\n const id = findPointId(ev.target as SVGElement);\n if (!id) return;\n // relatedTarget is where the mouse went — if it's still inside\n // the same point element, don't hide.\n const related = ev.relatedTarget as SVGElement \| null;\n const relatedId = findPointId(related);\n if (relatedId === id) return; // still inside the same point\n const lbl = getAutoLabel(id);\n if (lbl?.displayMode === Label.DISPLAY_TYPES.AUTO) lbl.hide();\n });\n\n // ── Public interaction events (webENA integration surface) ────────────────\n // Dispatched on the public <qe-graph> element with bubbles+composed so a\n // host app can subscribe regardless of shadow DOM. See README \"Events\".\n this._attachInteractionEvents();\n }\n\n /* Emit a namespaced CustomEvent on the public element (bubbles + composed). /\n private _emit(name: string, detail: Record<string, any>): void {\n this.dispatchEvent(new CustomEvent(name, { detail, bubbles: true, composed: true }));\n }\n\n /* Walk up from a hit element to the nearest ancestor carrying `attr`. /\n private _closestWith(el: SVGElement \| null, attr: string): SVGElement \| null {\n while (el && el !== this.svg_element) {\n if (el.getAttribute?.(attr) != null && el.hasAttribute?.(attr)) return el;\n el = el.parentElement as SVGElement \| null;\n }\n return null;\n }\n\n /* Resolve an edge hit element to a qe-edge-* detail, or null. /\n private _edgeDetail(el: SVGElement \| null): Record<string, any> \| null {\n const e = this._closestWith(el, 'data-edge-source');\n if (!e) return null;\n const d: Record<string, any> = {\n source: e.getAttribute('data-edge-source'),\n target: e.getAttribute('data-edge-target'),\n weight: parseFloat(e.getAttribute('data-edge-weight') \|\| '0'),\n directed: e.getAttribute('data-edge-directed') === 'true',\n self: e.getAttribute('data-edge-self') === 'true',\n };\n if (e.hasAttribute('data-edge-group')) d.group = e.getAttribute('data-edge-group');\n if (e.hasAttribute('data-edge-unit')) d.unit = e.getAttribute('data-edge-unit');\n return d;\n }\n\n /* Resolve a node/mean/point hit element to a qe-node-* detail, or null. /\n private _nodeDetail(el: SVGElement \| null): Record<string, any> \| null {\n const n = this._closestWith(el, 'data-point-id');\n if (!n) return null;\n const tag = n.tagName.toLowerCase();\n let x: number, y: number;\n if (tag === 'rect') {\n x = parseFloat(n.getAttribute('x') \|\| '0') + parseFloat(n.getAttribute('width') \|\| '0') / 2;\n y = parseFloat(n.getAttribute('y') \|\| '0') + parseFloat(n.getAttribute('height') \|\| '0') / 2;\n } else {\n x = parseFloat(n.getAttribute('cx') \|\| '0');\n y = parseFloat(n.getAttribute('cy') \|\| '0');\n }\n const id = n.getAttribute('data-point-id')!;\n const d: Record<string, any> = {\n id,\n kind: n.getAttribute('data-kind') \|\| 'point',\n name: n.getAttribute('data-name') \|\| id,\n x, y,\n };\n if (n.hasAttribute('data-group')) d.group = n.getAttribute('data-group');\n if (n.hasAttribute('data-unit')) d.unit = n.getAttribute('data-unit');\n return d;\n }\n\n private _attachInteractionEvents(): void {\n const svg = this.svg_element;\n\n svg.addEventListener('click', (ev: MouseEvent) => {\n const target = ev.target as SVGElement;\n const edge = this._edgeDetail(target);\n if (edge) { this._emit('qe-edge-click', { ...edge, originalEvent: ev }); return; }\n const node = this._nodeDetail(target);\n if (node) this._emit('qe-node-click', { ...node, originalEvent: ev });\n });\n\n // Hover enter/leave, tracked so we emit one unhover→hover pair per change.\n let hovered: { type: 'edge' \| 'node'; key: string } \| null = null;\n const keyOf = (t: 'edge' \| 'node', d: Record<string, any>) =>\n t === 'edge' ? `${d.source}\u0000${d.target}` : String(d.id);\n\n svg.addEventListener('mousemove', (ev: MouseEvent) => {\n const target = ev.target as SVGElement;\n const edge = this._edgeDetail(target);\n const node = edge ? null : this._nodeDetail(target);\n const next = edge ? { type: 'edge' as const, detail: edge }\n : node ? { type: 'node' as const, detail: node }\n : null;\n const nextKey = next ? keyOf(next.type, next.detail) : null;\n if (hovered && (!next \|\| hovered.key !== nextKey)) {\n this._emit(hovered.type === 'edge' ? 'qe-edge-unhover' : 'qe-node-unhover', { key: hovered.key });\n hovered = null;\n }\n if (next && (!hovered \|\| hovered.key !== nextKey)) {\n this._emit(next.type === 'edge' ? 'qe-edge-hover' : 'qe-node-hover', { ...next.detail, originalEvent: ev });\n hovered = { type: next.type, key: nextKey! };\n }\n // Opt-in built-in tooltip (P1.3 bonus): shown only when <qe-graph tooltip>.\n // The host is free to build its own from the hover events instead.\n if (this.hasAttribute('tooltip') && next) {\n this._showTooltip(this._tooltipText(next.type, next.detail), ev.clientX, ev.clientY);\n } else {\n this._hideTooltip();\n }\n });\n\n svg.addEventListener('mouseleave', () => {\n if (hovered) {\n this._emit(hovered.type === 'edge' ? 'qe-edge-unhover' : 'qe-node-unhover', { key: hovered.key });\n hovered = null;\n }\n this._hideTooltip();\n });\n }\n\n // ── Opt-in built-in tooltip ─────────────────────────────────────────────────\n private _tooltipEl: HTMLDivElement \| null = null;\n\n /* \"source – target (weight)\" for edges; the mark name for nodes/means/points. /\n private _tooltipText(type: 'edge' \| 'node', d: Record<string, any>): string {\n if (type === 'edge') {\n const w = Number(d.weight);\n const wStr = Number.isFinite(w) ? ` (${(+w.toFixed(3))})` : '';\n return `${d.source} – ${d.target}${wStr}`;\n }\n return String(d.name ?? d.id);\n }\n\n private _showTooltip(text: string, clientX: number, clientY: number): void {\n if (!this._tooltipEl) {\n const el = document.createElement('div');\n el.setAttribute('data-qe-tooltip', '');\n Object.assign(el.style, {\n position: 'fixed', zIndex: '2147483647', pointerEvents: 'none',\n background: 'rgba(20,20,20,0.92)', color: '#fff',\n font: '12px/1.4 system-ui, sans-serif', padding: '3px 7px',\n borderRadius: '4px', whiteSpace: 'nowrap',\n transform: 'translate(-50%, calc(-100% - 8px))',\n } as CSSStyleDeclaration);\n document.body.appendChild(el);\n this._tooltipEl = el;\n }\n this._tooltipEl.textContent = text;\n this._tooltipEl.style.left = `${clientX}px`;\n this._tooltipEl.style.top = `${clientY}px`;\n this._tooltipEl.style.display = 'block';\n }\n\n private _hideTooltip(): void {\n if (this._tooltipEl) this._tooltipEl.style.display = 'none';\n }\n\n draw() {\n if(!this.svg_element) {\n console.error(\"No element to draw to: \", this);\n return;\n }\n \n this.wrapper?.appendChild(this.svg_element);\n\n (this.__children__ as QELayer[]).forEach((enaLayer: QELayer) => {\n enaLayer.draw();\n });\n\n // Pixel-sized text (label-font-size, the plot title) is converted to model\n // units at the current width, so re-lay it out when the plot is resized.\n if (!this._resizeObs && typeof ResizeObserver !== 'undefined' && this.svg_element) {\n let lastW = 0;\n this._resizeObs = new ResizeObserver(entries => {\n const w = entries[0]?.contentRect.width ?? 0;\n if (w > 0 && Math.abs(w - lastW) > 0.5) {\n lastW = w;\n this.update_labels();\n this.update_axes();\n }\n });\n this._resizeObs.observe(this.svg_element);\n }\n }\n\n update() {\n // Two-pass update: first pass lays out elements and computes extremes;\n // second pass re-syncs the viewBox now that all element positions are final.\n this.update_extremes();\n this.update_layers();\n this.update_labels(); // positions labels using the freshly-computed extent\n this.update_extremes(); // re-apply viewBox after label/layer repositioning\n this.update_axes(); // axis line visibility + labels (uses final extent)\n this._applyHighlights(); // re-apply host highlight over the fresh render\n }\n\n /\n Axes (<qe-axes>): toggle the axis-line cross by presence, and draw/position\n * per-axis labels at the positive ends using the current extent. Labels are\n * cached SVG <text> nodes in the labels group; null text removes them.\n /\n update_axes(): void {\n // Show or hide the whole axis sub-tree (lines + origin) by <qe-axes> presence.\n const axesLayer = this.__children__.search('__children__', 'axes') as QELayer \| undefined;\n if (axesLayer?.svg_element) {\n (axesLayer.svg_element as SVGElement).style.display = this._showAxes ? '' : 'none';\n }\n\n const parent = this._labelsGroup;\n const extent = this.__data__.extremes.x_max;\n const { cx, cy } = this.__data__.extremes;\n if (!parent \|\| extent <= 0) return;\n\n const fontSize = extent 0.06;\n const gap = fontSize * 0.6;\n\n const place = (axis: 'x' \| 'y', text: string \| null) => {\n let el = this._axisLabelEls.get(axis);\n if (!this._showAxes \|\| text == null) { // remove when hidden / no label\n if (el) { el.remove(); this._axisLabelEls.delete(axis); }\n return;\n }\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n el.setAttribute('data-axis-label', axis);\n el.setAttribute('pointer-events', 'none');\n parent.appendChild(el);\n this._axisLabelEls.set(axis, el);\n }\n el.textContent = text;\n el.setAttribute('font-size', fontSize.toString());\n el.setAttribute('font-family', 'system-ui, sans-serif');\n el.setAttribute('font-weight', '600');\n el.setAttribute('fill', '#556');\n if (axis === 'x') {\n // At the right (+x) tip, anchored end so any-length text grows inward\n // and never clips past the viewBox edge; nudged just above the axis.\n el.setAttribute('x', (cx + extent - gap).toString());\n el.setAttribute('y', (-gap).toString());\n el.setAttribute('text-anchor', 'end');\n } else {\n // Just below the top (−y) tip, centered on the y-axis, inside the box.\n el.setAttribute('x', (gap).toString());\n el.setAttribute('y', (cy - extent + fontSize + gap).toString());\n el.setAttribute('text-anchor', 'start');\n }\n };\n\n place('x', this._axisXText);\n place('y', this._axisYText);\n\n // Magnification label, top-left inside the plot; independent of axes.\n if (this._magnifyText == null) {\n this._magnifyEl?.remove();\n this._magnifyEl = null;\n } else {\n if (!this._magnifyEl) {\n this._magnifyEl = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n this._magnifyEl.setAttribute('data-magnify-label', '');\n this._magnifyEl.setAttribute('pointer-events', 'none');\n }\n if (!this._magnifyEl.parentElement) parent.appendChild(this._magnifyEl);\n const el = this._magnifyEl;\n el.textContent = this._magnifyText;\n el.setAttribute('font-size', (fontSize * 0.85).toString());\n el.setAttribute('font-family', 'system-ui, sans-serif');\n el.setAttribute('font-style', 'italic');\n el.setAttribute('fill', '#556');\n el.setAttribute('x', (cx - extent + gap).toString());\n el.setAttribute('y', (cy - extent + fontSize + gap).toString());\n el.setAttribute('text-anchor', 'start');\n }\n\n // Plot title (qe_plot(title =)), top centre, drawn into the SVG so it is\n // part of toSVG() / toPNG() exports.\n if (!this._plotTitle) {\n this._titleEl?.remove(); this._titleEl = null;\n } else {\n if (!this._titleEl) {\n this._titleEl = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n this._titleEl.setAttribute('data-plot-title', '');\n this._titleEl.setAttribute('pointer-events', 'none');\n }\n if (!this._titleEl.parentElement) parent.appendChild(this._titleEl);\n const px = (this._labelFont.size ?? 12) * 1.35;\n const ts = px * this.unitsPerPixel();\n const t = this._titleEl;\n t.textContent = this._plotTitle;\n t.setAttribute('font-size', ts.toString());\n t.setAttribute('font-family', this._labelFont.family ?? 'system-ui, sans-serif');\n t.setAttribute('font-weight', '600');\n t.setAttribute('fill', this._labelFont.color ?? '#223');\n t.setAttribute('x', cx.toString());\n t.setAttribute('y', (cy - extent + ts * 1.1).toString());\n t.setAttribute('text-anchor', 'middle');\n }\n }\n\n update_labels(): void {\n this._nodeLabels.forEach(lbl => lbl.update());\n this._meanLabels.forEach(lbl => lbl.update());\n this._pointLabels.forEach(lbl => lbl.update());\n }\n\n update_extremes() {\n const graph = this.__data__ as Graph;\n graph.update_extremes(this._centerContent);\n if (this._rangeExtent && this._rangeExtent > 0) {\n // A centred view measures range=\"network\" from its centre, not the origin\n const { cx, cy } = graph.extremes;\n const r = this._centerContent && this._rangeMode === 'network'\n ? graph.nodeExtentFrom(cx, cy) * 1.2\n : this._rangeExtent;\n graph.extremes = new Extremes(r, r, cx, cy);\n }\n\n const svgRect = this.svg_element?.getBoundingClientRect();\n if(this.svg_element && svgRect) {\n console.log(\"SVG rect: \", svgRect);\n let w, h;\n if(svgRect.width === 0 \|\| svgRect.height === 0) {\n w = 1;\n h = 1;\n }\n else {\n w = svgRect.width;\n h = svgRect.height;\n }\n this.__data__.scale_x = 1 / (w / (4 * this.__data__.extremes.x_max));\n this.__data__.scale_y = 1 / (h / (4 * this.__data__.extremes.y_max));\n\n // this.svg_element.setAttribute(\"transform\", this.__data__.transform.toString());\n this.__children__[0].svg_element.setAttribute(\"transform\", this.__data__.transform.toString());\n\n this.svg_element.setAttribute(\"viewBox\", (this.__data__ as Graph).extremes.as_viewBox());\n\n let axisLineLayer: LayerLike \| undefined = this.__data__.layers.search(\"layers\", \"axis_lines\");\n if (axisLineLayer) {\n let \n axis_x = axisLineLayer.objects.get(\"axis-x\") as Line,\n axis_y = axisLineLayer.objects.get(\"axis-y\") as Line\n ;\n if (axis_x && axis_y) {\n const ex = this.__data__.extremes;\n axis_x.from = new Point({ ID: \"axis-x-start\", dimensions: [ex.cx - ex.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] });\n axis_x.to = new Point({ ID: \"axis-x-end\", dimensions: [ex.cx + ex.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] });\n axis_y.from = new Point({ ID: \"axis-y-start\", dimensions: [0, ex.cy - ex.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] });\n axis_y.to = new Point({ ID: \"axis-y-end\", dimensions: [0, ex.cy + ex.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] });\n }\n }\n }\n }\n\n update_layers() {\n (this.__children__ as QELayer[]).forEach((enaLayer: QELayer) => {\n enaLayer.update();\n });\n }\n}\ncustomElements.define(QEGraphElement.tagName, QEGraphElement);\n","// QEViz standalone entry point — no arbor/webr dependency.\n// Import this bundle directly from rENA or any non-arbor context.\n\nexport { QEVisualElement, vizENA } from './elements/QEVisual.js';\nexport { QEGraphElement } from './elements/QEGraph.js';\nimport { QEGraphElement as _QEGraph } from './elements/QEGraph.js';\n/** Look up a connected <qe-graph> by its `id` or `plot-group` attribute. /\nexport const getGraph = (key: string) => _QEGraph.getGraph(key);\n/* All connected <qe-graph> instances. */\nexport const getGraphs = () => _QEGraph.instances();\nexport { QENodesElement, QEMeansElement, QEPointsElement, QEEdgesElement, QETrajectoriesElement, QEAxesElement } from './elements/QEChildElements.js';\nexport { QELayer } from './elements/QELayer.js';\nexport { QEPoint } from './elements/QEPoint.js';\nexport { QELine } from './elements/QELine.js';\nexport { QETrajectory } from './elements/QETrajectory.js';\n\nexport type { ModelData, QEFrame, ONAModelData, ENAModelData, ENADataFrame } from './types/ModelData.js';\n\nexport { Graph } from './objects/Graph.js';\nexport { Edge } from './objects/Edges.js';\nexport { Trajectory } from './objects/Trajectory.js';\nexport { fitTrajectory, selectDegree, sampleCurve, nearOriginFilter, TRAJECTORY_ZERO_EPS } from './objects/polyfit.js';\nexport type { XY, DegreeSelection, TrajectoryFit } from './objects/polyfit.js';\nexport { Color, WeightedColor } from './objects/Color.js';\n\nexport { DataFrame, DataFrameRow, DataFrameColumn, DataFrameColumnType } from 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1	+ {"version":3,"file":"qeviz.umd.js","sources":["../src/types/DataFrame.ts","../src/objects/Model.ts","../src/utils/debug.ts","../src/elements/QEVisual.ts","../src/objects/Color.ts","../src/objects/Transform.ts","../src/utils/Tools.ts","../src/types/EventBus.ts","../src/objects/Layers.ts","../src/objects/PlottedObject.ts","../src/objects/Extremes.ts","../src/objects/AxisPoint.ts","../src/objects/Graph.ts","../src/elements/DrawableElement.ts","../src/objects/polyfit.ts","../src/objects/Trajectory.ts","../src/objects/Edges.ts","../src/elements/Drawable.ts","../src/objects/Sizing.ts","../src/elements/QELine.ts","../src/elements/QEPoint.ts","../src/elements/QETrajectory.ts","../src/elements/QELayer.ts","../src/elements/QELabel.ts","../src/elements/QEChildElements.ts","../src/elements/QEGraph.ts","../src/index.ts"],"sourcesContent":["export interface DataFrameRowInterface {\n get names(): string[];\n get rowName(): string \| undefined;\n get types(): DataFrameColumnType[];\n get parent(): DataFrame \| undefined;\n}\n\nexport class DataFrameRow extends Array<any> implements DataFrameRowInterface {\n #rowNumber?: number;\n #rowName?: string;\n #names: string[];\n #parent?: DataFrame;\n #classes: string[] \| undefined;\n\n constructor(names: string[], values: any[], rowName?: string, parent?: DataFrame, index?: number) {\n super(...values);\n this.#names = names;\n this.#rowName = rowName;\n this.#parent = parent;\n this.#classes = parent?.classes;\n this.#rowNumber = index;\n }\n\n get parent(): DataFrame \| undefined {\n return this.#parent;\n }\n get names(): string[] {\n return this.#names;\n }\n get rowName(): string \| undefined {\n return this.#rowName;\n }\n get types(): DataFrameColumnType[] {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this row.\");\n return this.#parent.types;\n }\n get classes(): string[] \| undefined {\n return this.#classes;\n }\n\n get rowNumber(): number \| undefined {\n return this.#rowNumber;\n }\n\n col(wh: string \| number): DataFrameColumn \| undefined {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this row.\");\n return this.#parent.col(wh);\n }\n cols(...wh: (string \| number)[]): DataFrame {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this row.\");\n return this.#parent.cols(...wh);\n }\n\n filter(predicate: (value: any, index: number, array: any[]) => boolean): any {\n console.error(\"DataFrameRow does not currently support filtering.\");\n // This method is intentionally left empty to prevent filtering on DataFrameRow.\n }\n}\n\nexport enum DataFrameColumnType {\n Character = 'character',\n Double = 'double',\n Logical = 'logical',\n Integer = 'integer'\n}\n\nexport interface DataFrameColumnInterface {\n get name(): string;\n get type(): DataFrameColumnType;\n get rowNames(): string[] \| undefined;\n}\n\nexport class DataFrameColumn extends Array<any> implements DataFrameColumnInterface {\n #name: string;\n #type: DataFrameColumnType;\n #rowNames: string[] \| undefined;\n #parent?: DataFrame;\n\n constructor(name: string, column: any, rowNames?: string[], parent?: DataFrame) {\n super(column.length);\n for (let i = 0; i < column.length; i++) {\n this[i] = column[i];\n }\n this.#name = name;\n\n if (column.type !== undefined) {\n this.#type = column.type;\n }\n // If undefined, infer type\n else {\n if (column.every((v: any) => typeof v === 'string' \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Character;\n }\n else if (column.every((v: any) => Number.isInteger(v) \|\| v === null \|\| v === undefined)) {\n // If only 1 and 0, consider as logical\n if (column.every((v: any) => v === 0 \|\| v === 1 \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Logical;\n }\n else {\n this.#type = DataFrameColumnType.Integer;\n }\n }\n else if (column.every((v: any) => typeof v === 'number' \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Double;\n }\n else if (column.every((v: any) => typeof v === 'boolean' \|\| v === null \|\| v === undefined)) {\n this.#type = DataFrameColumnType.Logical;\n }\n\n // Default to character if mixed types\n else {\n this.#type = DataFrameColumnType.Character;\n }\n }\n this.#parent = parent;\n\n if (rowNames && rowNames.length !== this.length) {\n throw new Error(\"Row names length must match the number of rows in the DataFrameColumn.\");\n }\n if (rowNames && rowNames.length > 0) {\n this.#rowNames = rowNames;\n }\n else {\n this.#rowNames = undefined;\n }\n }\n\n get name(): string {\n return this.#name;\n }\n get type(): DataFrameColumnType {\n return this.#type;\n }\n get rowNames(): string[] \| undefined {\n return this.#rowNames;\n }\n\n\n row(wh: string \| number): DataFrameRow \| undefined {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this column.\");\n return this.#parent.row(wh);\n }\n rows(...wh: (string \| number)[]): DataFrameRow[] {\n if (!this.#parent) throw new Error(\"No parent DataFrame attached to this column.\");\n return this.#parent.rows(...wh);\n }\n}\n\nexport interface DataFrameInterface {\n // Methods\n getColumnByName(name: string): DataFrameColumn \| undefined;\n getRowByIndex(index: number): any[];\n getRowByName(name: string): any[] \| undefined;\n row(wh: string \| number): any[] \| undefined;\n type(wh: string \| number): DataFrameColumnType \| undefined;\n\n get names(): string[];\n get rowNames(): string[] \| undefined;\n get types(): string[];\n\n // Properties\n nrow: number;\n ncol: number;\n}\n\nexport class DataFrame extends Array<DataFrameColumn> implements DataFrameInterface {\n #names: string[];\n #rowNames: string[] \| undefined;\n #classes: string[] \| undefined;\n\n constructor(names?: string[], colValues?: any[], rowNames?: string[], classes?: string[]) {\n if (!names \|\| !colValues) {\n colValues = [];\n names = [];\n }\n if (colValues.map( (c: any) => c.length ).every( (l: any) => l === names.length )) {\n // Transpose if needed\n const transposed: any[] = [];\n for (let i = 0; i < names.length; i++) {\n const col: any[] = [];\n for (let j = 0; j < colValues.length; j++) {\n col.push(colValues[j][i]);\n }\n transposed.push(col);\n }\n colValues = transposed;\n }\n\n super(colValues.length);\n\n colValues.forEach((col, index) => {\n if (col instanceof DataFrameColumn) {\n // If col is already a DataFrameColumn, just assign it\n this[index] = col as DataFrameColumn;\n } else {\n // Otherwise, create a new DataFrameColumn\n this[index] = new DataFrameColumn(names[index], col, rowNames, this) as DataFrameColumn;\n }\n });\n this.#names = names;\n if (rowNames && this[0] && rowNames.length !== this[0].length) {\n throw new Error(\"Row names length must match the number of rows in the DataFrame.\");\n }\n if (rowNames && rowNames.length > 0) {\n this.#rowNames = rowNames;\n }\n if (classes && classes.length !== this.length) {\n throw new Error(\"Classes length must match the number of columns in the DataFrame.\");\n }\n if (classes && classes.length > 0) {\n this.#classes = classes;\n }\n }\n\n get classes(): string[] \| undefined {\n return this.#classes;\n }\n\n getColumnByName(name: string): DataFrameColumn \| undefined {\n const idx = this.#names.indexOf(name);\n return idx >= 0 ? this[idx] : undefined;\n }\n getRowByIndex(index: number): DataFrameRow {\n if (this && this.length === 0) {\n console.warn(\"DataFrame is empty, cannot get row by index\", index);\n return new DataFrameRow(this.#names, [], undefined, this, index);\n }\n const result_vals: any[] = [];\n for (let col of this) {\n let v = col[index];\n result_vals.push(v);\n }\n return new DataFrameRow(this.#names, result_vals, this.#rowNames ? this.#rowNames[index] : undefined, this, index);\n }\n getRowByName(name: string): DataFrameRow \| undefined {\n if (!this.#rowNames) return undefined;\n\n const index = this.#rowNames.indexOf(name);\n if (index === -1) return undefined;\n return this.getRowByIndex(index);\n }\n\n get types(): DataFrameColumnType[] {\n return this.map(col => col.type);\n }\n type(wh: string \| number): DataFrameColumnType \| undefined {\n if (typeof wh === 'number') {\n return this[wh]?.type;\n }\n else if (typeof wh === 'string') {\n const col = this.getColumnByName(wh);\n return col ? col.type : undefined;\n }\n return undefined;\n }\n\n // row(wh: string \| number): DataFrameRow \| undefined {\n\n row(wh: string \| number): DataFrameRow \| undefined {\n if (typeof wh === 'number') {\n return this.getRowByIndex(wh);\n }\n else if (typeof wh === 'string') {\n return this.getRowByName(wh);\n }\n return undefined;\n }\n // rows(...wh: (string \| number)[]): DataFrame {\n rows(...wh: (string \| number)[]): DataFrameRow[] {\n // Support: rows(\"Data\"), rows(\"Data\", \"Design\"), rows([\"Data\", \"Design\"]), rows()\n let\n selectors: (string \| number)[],\n selectedRows: DataFrameRow[] = [],\n selectedRowNames: string[] \| undefined = []\n ;\n\n // No arguments: return all rows\n if (wh.length === 0) {\n if (!this[0] \|\| this.length === 0) {\n return [];\n }\n const numRows = this[0].length;\n selectedRows = Array.from({ length: numRows }, (_, i) => this.getRowByIndex(i));\n selectedRowNames = this.#rowNames;\n }\n\n else {\n // Single array argument\n if (wh.length === 1 && Array.isArray(wh[0])) {\n selectors = wh[0] as (string \| number)[];\n }\n else {\n // Rest arguments\n selectors = wh;\n }\n\n selectedRows = selectors.map((item, i: number) => {\n let r = this.row(item);\n if (this.#rowNames && r) {\n selectedRowNames?.push(this.#rowNames[i]);\n }\n return r;\n }).filter((row): row is DataFrameRow => row !== undefined);\n }\n\n // Build columns from selected rows\n // const\n // colNames = this.#names,\n // columns = colNames.map((name, colIdx) => selectedRows.map(row => row[colIdx])),\n // colObjs = colNames.map((name, idx) => new DataFrameColumn(name, { values: columns[idx], type: this[idx].type }, selectedRowNames, this))\n // ;\n\n // return new DataFrame(\n // colNames,\n // colObjs,\n // selectedRowNames\n // );\n\n return selectedRows;\n }\n\n col(wh: string \| number): DataFrameColumn \| undefined {\n if (typeof wh === 'number') {\n return this[wh];\n } else if (typeof wh === 'string') {\n return this.getColumnByName(wh);\n }\n return undefined;\n }\n\n cols(...wh: (string \| number)[]): DataFrame {\n // Support: cols(\"Data\"), cols(\"Data\", \"Design\"), cols([\"Data\", \"Design\"]), cols()\n let\n selectors: (string \| number)[],\n selectedCols: DataFrameColumn[],\n selectedNames: string[] = []\n ;\n\n // No arguments: return all columns\n if (wh.length === 0) {\n selectedCols = this.slice();\n selectedNames = this.#names;\n }\n else {\n // Single array argument\n if (wh.length === 1 && Array.isArray(wh[0])) {\n selectors = wh[0] as (string \| number)[];\n }\n // Rest arguments\n else {\n selectors = wh;\n }\n\n selectedCols = selectors.map((item) => this.col(item)).filter((col): col is DataFrameColumn => col !== undefined);\n selectedNames = selectedCols.map(col => col.name);\n }\n\n return new DataFrame(selectedNames, selectedCols, this.#rowNames);\n }\n\n subset(rows?: (string \| number)[], cols?: (string \| number)[]): DataFrame {\n const selectedCols: DataFrameColumn[] = (cols && cols.length > 0)\n ? this.cols(...cols)\n : this.slice();\n\n return new DataFrame(\n selectedCols.map(col => col.name),\n selectedCols.map(col => col.values),\n this.#rowNames\n );\n }\n\n get names(): string[] {\n return this.#names;\n }\n\n get rowNames(): string[] \| undefined {\n return this.#rowNames;\n }\n\n get nrow(): number {\n return this[0] ? this[0].length : 0;\n }\n\n get ncol(): number {\n return this.length;\n }\n}\n","import { DataFrame, DataFrameRow } from \"../types/DataFrame\";\n\n/** Internal key union for Model.setByKey /\nexport type ModelKey =\n \| \"updated\" \| \"points\" \| \"nodes\" \| \"edges\"\n \| \"dimensions\" \| \"confidence\" \| \"outlier\" \| \"groups\" \| \"trajectories\" \| \"networks\" \| \"pointsets\";\n\n/* Internal shape of the Model class — used by setByKey /\nexport interface ModelSpec {\n updated?: number;\n points: DataFrame;\n nodes: DataFrame;\n edges: DataFrame;\n dimensions: (string \| number)[];\n confidence?: DataFrame;\n outlier?: DataFrame;\n groups?: DataFrame;\n trajectories?: DataFrame;\n networks?: DataFrame;\n pointsets?: DataFrame;\n}\n\nexport class Model implements ModelSpec {\n private _updated: number \| undefined;\n private _points: DataFrame;\n private _nodes: DataFrame;\n private _edges: DataFrame;\n private _dimensions: (string \| number)[];\n private _params: any;\n private _confidence: DataFrame \| undefined;\n private _outlier: DataFrame \| undefined;\n private _groups: DataFrame \| undefined;\n private _trajectories: DataFrame \| undefined;\n private _networks: DataFrame \| undefined;\n private _pointsets: DataFrame \| undefined;\n\n // Resolved column names — set by QEVisual.setModelData() via auto-detection\n // or caller-supplied overrides. Renderers read these instead of hardcoding.\n /* ID column in the points and edges frames /\n unit_id_col: string = 'id';\n /* ID column in the nodes frame /\n node_id_col: string = 'id';\n /* Group column in the points frame (null = no grouping) /\n group_col: string \| null = null;\n /* Directed network mode — true renders arrowheads; false (default) undirected /\n directed: boolean = false;\n /* Group palette override (ModelData.palette); empty = qeviz default. /\n palette: string[] = [];\n\n constructor(o: Partial<ModelSpec> = {}) {\n this._points = o.points ?? new DataFrame();\n this._nodes = o.nodes ?? new DataFrame();\n this._edges = o.edges ?? new DataFrame();\n this._dimensions = o.dimensions ?? [];\n this._confidence = undefined;\n this._outlier = undefined;\n this._groups = undefined;\n }\n\n get updated(): number \| undefined { return this._updated; }\n set updated(v: number \| undefined) { this._updated = v; }\n\n get points(): DataFrame { return this._points; }\n set points(v: DataFrame) { this._points = v; }\n\n get nodes(): DataFrame { return this._nodes; }\n set nodes(v: DataFrame) { this._nodes = v; }\n\n get edges(): DataFrame { return this._edges; }\n set edges(v: DataFrame) { this._edges = v; }\n\n get confidence(): DataFrame \| undefined { return this._confidence; }\n set confidence(v: DataFrame \| undefined) { this._confidence = v; }\n\n get outlier(): DataFrame \| undefined { return this._outlier; }\n set outlier(v: DataFrame \| undefined) { this._outlier = v; }\n\n get groups(): DataFrame \| undefined { return this._groups; }\n set groups(v: DataFrame \| undefined) { this._groups = v; }\n\n get trajectories(): DataFrame \| undefined { return this._trajectories; }\n set trajectories(v: DataFrame \| undefined) { this._trajectories = v; }\n\n /* Explicit networks (one row per named layer, edge columns as in `edges`),\n * drawn by <qe-edges network=\"name\">. /\n get networks(): DataFrame \| undefined { return this._networks; }\n set networks(v: DataFrame \| undefined) { this._networks = v; }\n\n /* Explicit point sets (rows: set, id, x, y, group?, color?, shape?, label?),\n * drawn by <qe-points set=\"name\">. /\n get pointsets(): DataFrame \| undefined { return this._pointsets; }\n set pointsets(v: DataFrame \| undefined) { this._pointsets = v; }\n\n get dimensions(): (string \| number)[] { return this._dimensions; }\n set dimensions(v: (string \| number)[]) { this._dimensions = v; }\n\n get params(): any { return this._params; }\n set params(v: any) { this._params = v; }\n\n point(id: string): DataFrameRow \| undefined {\n return this._points.row(id);\n }\n\n setByKey<K extends keyof ModelSpec>(key: K, value: ModelSpec[K]): void {\n (this as any)[key] = value;\n }\n}\n\nexport default Model;\n","export const DEBUG: boolean = (globalThis as any).__QEVIZ_DEBUG__ === true;\n\nexport function dbg(...args: any[]): void {\n if (DEBUG) console.log(...args);\n}\n","import { Label, Point } from \"../objects/PlottedObject\";\nimport { Edge } from \"../objects/Edges\";\nimport Model, { ModelKey } from \"../objects/Model\";\nimport { DataFrame } from \"../types/DataFrame.js\";\nimport { dbg } from \"../utils/debug.js\";\nimport { ModelData } from \"../types/ModelData.js\";\n\nexport const vizENA = {\n get: (n: number) => {\n const elements = [...(document as any).querySelectorAll(\"qe-graph\")];\n if (typeof n === \"number\" && n >= 0) {\n return elements[n];\n }\n return elements;\n },\n}\n\nexport class QEVisualElement extends HTMLElement {\n static tagName = 'qe-visual';\n\n static get observedAttributes() {\n return ['updated'];\n }\n\n static styles = `\n :host { display: block; width: 100%; }\n :host(.hidden) { display: none !important; }\n / The output wrapper and the slotted graph fill the host so the plot\n stretches to its container instead of collapsing to intrinsic size. /\n div { display: block; width: 100%; height: 100%; }\n ::slotted(qe-graph) { display: block; width: 100%; height: 100%; }\n `;\n\n protected _outputElement!: HTMLElement;\n protected _isVisible: boolean = true;\n protected output: string = '';\n\n private _model: Model;\n /* Public accessor so ena-graph (and external code) can read the model. /\n get model(): Model {\n return this._model;\n }\n\n private _updated: string = '';\n get updated(): string {\n return this._updated;\n }\n set updated(val: string) {\n this._updated = val;\n this.setAttribute('updated', val);\n // Notify via CustomEvent instead of directly coupling to StateManager.\n // RQEVisualElement (and any other arbor consumer) listens for this and\n // forwards to globalStateManager.\n this.dispatchEvent(new CustomEvent('model-updated', {\n detail: this._model,\n bubbles: true,\n composed: true,\n }));\n }\n\n private _active_points: Point[] = [];\n private _points: Map<any, Point> = new Map();\n get points(): Map<any, Point> {\n return this._points;\n }\n set points(pts: Map<any, Point> \| Point[]) {\n this._points.clear();\n if (pts instanceof Map) {\n this._points = pts;\n } else if (Array.isArray(pts)) {\n pts.forEach(p => this._points.set(p.ID, p));\n }\n }\n get active_points(): Point[] {\n return Array.from(this._active_points.values());\n }\n\n private _edges: Map<any, Edge> = new Map();\n get edges(): Map<any, Edge> {\n return this._edges;\n }\n set edges(edges: Map<any, Edge> \| Edge[]) {\n this._edges.clear();\n if (edges instanceof Map) {\n this._edges = edges;\n } else if (Array.isArray(edges)) {\n this._edges = new Map();\n edges.forEach(e => this._edges.set(e.ID, e));\n }\n }\n\n private _labels: Map<any, Label> = new Map();\n get labels(): Map<any, Label> {\n return this._labels;\n }\n\n constructor() {\n super();\n\n this._model = new Model();\n\n const shadow = this.attachShadow({ mode: 'open' });\n\n const style = document.createElement('style');\n style.textContent = QEVisualElement.styles;\n shadow.appendChild(style);\n\n this._outputElement = document.createElement('div');\n shadow.appendChild(this._outputElement);\n }\n\n connectedCallback(): void {\n dbg(\"QEVisualElement connected\");\n this.render();\n }\n\n /\n Accept pre-fetched ENA model data and update the visualization.\n * Call this directly when data is available from any source —\n * rENA R package, Python package, or static JSON.\n /\n setModelData(data: ModelData): void {\n const frameKeys: ModelKey[] = ['nodes', 'edges', 'points', 'groups', 'confidence', 'outlier', 'trajectories', 'networks', 'pointsets'] as ModelKey[];\n\n // ── Step 1: ingest all frames into DataFrames ──────────────────────────\n frameKeys.forEach((name) => {\n const raw = (data as any)[name];\n if (!raw?.data?.length) return;\n\n const\n rows: any[] = raw.data,\n types: any = raw.types \|\| {},\n colNames: string[] = Object.keys(rows[0]),\n colValues: any[][] = rows.map((v: any) => Object.values(v)),\n classes: string[] = colNames.map(col => (types[col] ?? 'character') as string);\n\n // Determine which column is the row-identifier (stored as DataFrame.rowName).\n // The caller can supply overrides; otherwise we auto-detect.\n let idCol: string \| undefined;\n if (name === 'networks') {\n idCol = 'name'; // one row per explicit network layer\n } else if (name === 'pointsets') {\n idCol = 'id'; // point id within its set\n } else if (name === 'nodes') {\n idCol = data.node_id_col\n ?? colNames.find(c => (types[c] ?? 'character') === 'character');\n } else if (name === 'edges' \|\| name === 'points' \|\| name === 'trajectories') {\n idCol = data.id_col\n ?? colNames.find(c => (types[c] ?? 'character') === 'character');\n } else {\n // groups / confidence / outlier: first character column is the group id\n idCol = data.group_col\n ?? colNames.find(c => (types[c] ?? 'character') === 'character');\n }\n\n const removalCol = idCol ? colNames.indexOf(idCol) : 0;\n const rowNames = colValues.map((v: any) => String(v[removalCol]));\n this._model.setByKey(name, new DataFrame(colNames, colValues, rowNames, classes));\n });\n\n // ── Step 2: ingest scalar fields ─────────────────────────────────────\n if (data.updated !== undefined) this._model.setByKey('updated', data.updated);\n if (data.directed !== undefined) this._model.directed = data.directed;\n if (Array.isArray((data as any).palette)) this._model.palette = (data as any).palette.map(String);\n\n // ── Step 3: resolve and store column names on the model ───────────────\n // These are read by QEGraph at render time instead of hardcoded strings.\n\n // node id col — first character column in nodes, or override\n const nodesDF = this._model.nodes;\n this._model.node_id_col = data.node_id_col\n ?? nodesDF?.names?.find(n => nodesDF.col(n)?.type === 'character')\n ?? 'id';\n\n // unit id col — first character column in points, or override\n const pointsDF = this._model.points;\n this._model.unit_id_col = data.id_col\n ?? pointsDF?.names?.find(n => pointsDF.col(n)?.type === 'character')\n ?? 'id';\n\n // group col — caller override, or first non-unit-id character col in points\n const unitId = this._model.unit_id_col;\n this._model.group_col = data.group_col\n ?? pointsDF?.names?.find(n => n !== unitId && pointsDF.col(n)?.type === 'character')\n ?? null;\n\n // ── Step 4: auto-detect dimension (x/y) columns from nodes ───────────\n // Numeric columns that aren't the node id. Caller can override via\n // x_col / y_col but those are passed in ModelData for the renderer to use\n // directly; here we just set model.dimensions as the default.\n if (nodesDF?.names?.length) {\n const nodeId = this._model.node_id_col;\n const xColOvr = data.x_col;\n const yColOvr = data.y_col;\n if (xColOvr && yColOvr) {\n this._model.dimensions = [xColOvr, yColOvr];\n } else {\n const numCols = nodesDF.names.filter(n => {\n if (n === nodeId) return false;\n const col = nodesDF.col(n);\n return col && col.type !== 'character' && col.type !== 'logical';\n });\n if (numCols.length >= 2) {\n this._model.dimensions = [xColOvr ?? numCols[0], yColOvr ?? numCols[1]];\n }\n }\n }\n\n this.updated = this._model.updated !== undefined ? String(this._model.updated) : String(Date.now());\n dbg(\"Model updated via setModelData:\", this.updated);\n this.render();\n }\n\n /\n Base implementation is a no-op. Subclasses (e.g. RQEVisualElement) override\n * this to fetch data from a backend and call setModelData().\n /\n async calculate(): Promise<void> {}\n\n render(): void {\n if (!this._isVisible) {\n this.classList.add('hidden');\n } else {\n this.classList.remove('hidden');\n }\n\n if (this._model?.updated !== undefined && this._model.updated !== null) {\n this._outputElement.innerHTML = `${this.output}<slot></slot>`;\n } else {\n this._outputElement.innerHTML = \"Define the model on the left.\";\n }\n }\n}\ncustomElements.define(QEVisualElement.tagName, QEVisualElement);\n\nexport default QEVisualElement;\n","export class Color {\n base: string;\n\n constructor(base: Color \| string) {\n this.base = typeof base === \"string\" ? base : base.base;\n\n // Return a Proxy to allow 0-based indexing for r, g, b\n return new Proxy(this, {\n get(target, prop) {\n if (typeof prop === \"string\" && /^[0-2]$/.test(prop)) {\n const { r, g, b } = Color.parseColor(target.base);\n return [r, g, b][Number(prop)];\n }\n return (target as any)[prop];\n }\n });\n }\n\n toString(): string {\n return this.base;\n }\n\n setBase(base: string): void {\n this.base = base;\n }\n\n static parseColor(color: string): { r: number; g: number; b: number } {\n const c = String(color).trim();\n // \"#RRGGBB\" (fast path), \"#RGB\", \"#RRGGBBAA\" (alpha dropped)\n if (/^#[0-9a-f]{6}([0-9a-f]{2})?$/i.test(c)) {\n const n = parseInt(c.slice(1, 7), 16);\n return { r: (n >> 16) & 255, g: (n >> 8) & 255, b: n & 255 };\n }\n if (/^#[0-9a-f]{3}$/i.test(c)) {\n const [r, g, b] = [1, 2, 3].map(i => parseInt(c[i] + c[i], 16));\n return { r, g, b };\n }\n const m = c.match(/^rgba?\\(\\s([\\d.]+)[,\\s]+([\\d.]+)[,\\s]+([\\d.]+)/i);\n if (m) return { r: Math.round(+m[1]), g: Math.round(+m[2]), b: Math.round(+m[3]) };\n // Anything else CSS understands (\"red\", \"steelblue\", hsl(), …), as the\n // adapters pass colour names through: let the browser resolve it.\n const resolved = Color.resolveCss(c);\n if (resolved) return Color.parseColor(resolved);\n throw new Error(`Unsupported color format: ${color}`);\n }\n\n private static _ctx: CanvasRenderingContext2D \| null \| undefined;\n private static _cssCache = new Map<string, string \| null>();\n\n /** A CSS colour as \"#rrggbb\" / \"rgba(...)\", or null if it isn't one. /\n static resolveCss(color: string): string \| null {\n if (Color._cssCache.has(color)) return Color._cssCache.get(color)!;\n if (Color._ctx === undefined) {\n Color._ctx = typeof document !== 'undefined'\n ? document.createElement('canvas').getContext('2d') : null;\n }\n let out: string \| null = null;\n const ctx = Color._ctx;\n if (ctx) {\n // An invalid value leaves fillStyle unchanged, so test against two sentinels.\n ctx.fillStyle = '#000000'; ctx.fillStyle = color; const a = ctx.fillStyle;\n ctx.fillStyle = '#ffffff'; ctx.fillStyle = color; const b = ctx.fillStyle;\n if (a === b) out = String(a);\n }\n Color._cssCache.set(color, out);\n return out;\n }\n\n static rgb(r: number, g: number, b: number): string {\n return `rgb(${r}, ${g}, ${b})`;\n }\n}\n\nexport class WeightedColor extends Color {\n weight: number;\n /* Optional alpha; defaults to `weight` (saturation and alpha together). /\n alpha: number \| undefined;\n\n constructor(base: Color \| string, weight: number, alpha?: number) {\n super(base);\n this.weight = weight;\n this.alpha = alpha;\n }\n\n // Parse hex → HSV (h in [0, 360), s/v in [0, 1]).\n static toHSV(hex: string): { h: number; s: number; v: number } {\n const { r, g, b } = Color.parseColor(hex);\n const rn = r / 255, gn = g / 255, bn = b / 255;\n const max = Math.max(rn, gn, bn), min = Math.min(rn, gn, bn);\n const d = max - min;\n const v = max;\n const s = max === 0 ? 0 : d / max;\n let h = 0;\n if (d > 0) {\n switch (max) {\n case rn: h = ((gn - bn) / d + (gn < bn ? 6 : 0)) / 6; break;\n case gn: h = ((bn - rn) / d + 2) / 6; break;\n default: h = ((rn - gn) / d + 4) / 6;\n }\n }\n return { h: h 360, s, v };\n }\n\n // Convert HSV + alpha → rgba() CSS string.\n static hsvToRgba(h: number, s: number, v: number, a: number): string {\n const c = v * s;\n const x = c * (1 - Math.abs((h / 60) % 2 - 1));\n const m = v - c;\n let r = 0, g = 0, b = 0;\n if (h < 60) { r = c; g = x; b = 0; }\n else if (h < 120) { r = x; g = c; b = 0; }\n else if (h < 180) { r = 0; g = c; b = x; }\n else if (h < 240) { r = 0; g = x; b = c; }\n else if (h < 300) { r = x; g = 0; b = c; }\n else { r = c; g = 0; b = x; }\n return `rgba(${Math.round((r + m) * 255)},${Math.round((g + m) * 255)},${Math.round((b + m) * 255)},${a.toFixed(4)})`;\n }\n\n // Returns rgba(...) matching rENA's edge-color convention (ena.plot.network):\n // • hue and value (brightness) are preserved from the base color\n // • HSV saturation is set to \|weight\| directly (0 = grey, 1 = fully vivid)\n // • alpha is also set to \|weight\|\n //\n // rENA converts the input color to HSV, replaces the S component with the\n // normalized edge weight, and additionally sets plotly element opacity to the\n // same value. Working in HSV (not HSL) is essential: palette colors like\n // #EE6677 have HSL lightness ≈ 67%, so 100% HSL saturation still looks\n // washed-out, whereas HSV value ≈ 0.93 gives the expected vivid output.\n toString(): string {\n const { h, v } = WeightedColor.toHSV(this.base);\n const w = Math.min(1, Math.abs(this.weight));\n const a = this.alpha === undefined ? w : Math.min(1, Math.max(0, this.alpha));\n return WeightedColor.hsvToRgba(h, w, v, a);\n }\n}","export class Transform {\n private _values: number[] = [1, 0, 0, 1, 0, 0];\n private _keys: string[] = [\"a\", \"b\", \"c\", \"d\", \"e\", \"f\"];\n\n get values() {\n return this._values;\n }\n set values(vals: number[]) {\n if (vals && vals.length === 6) {\n this._values = vals;\n }\n }\n get keys() {\n return this._keys;\n }\n set keys(vals: string[]) {\n if (vals && vals.length === 6) {\n this._keys = vals;\n }\n }\n\n constructor(vals: number[] \| null = null) {\n if (vals) {\n this.values = vals;\n }\n }\n\n toString() {\n let matrix_str = this.keys.map((k, i) => this.values[i]).join(\" \")\n ;\n\n return `matrix(${matrix_str})`;\n }\n\n toMatrix() {\n return Object.fromEntries(this._keys.map((k, i) => [k, this._values[i]]));\n }\n\n toArray() {\n return this._values;\n }\n\n set(wh: string, val: number) {\n if (val !== 0.0075 && val !== 0) {\n this._values[this._keys.findIndex(k => k === wh)] = val;\n }\n }\n get(wh: string) {\n return this._values[this._keys.findIndex(k => k === wh)];\n }\n\n scale(a: number, d: number = a) {\n this.a = a;\n this.d = d;\n }\n\n zoom(z: number) {\n this.a = z;\n this.d = z;\n }\n\n pan(x: number, y: number) {\n this.e = this.e + x;\n this.f = this.f + y;\n }\n\n set a(x: number) { this.set(\"a\", x); }\n set b(x: number) { this.set(\"b\", x); }\n set c(x: number) { this.set(\"c\", x); }\n set d(x: number) { this.set(\"d\", x); }\n set e(x: number) { this.set(\"e\", x); }\n set f(x: number) { this.set(\"f\", x); }\n\n get a() { return this.get(\"a\"); }\n get b() { return this.get(\"b\"); }\n get c() { return this.get(\"c\"); }\n get d() { return this.get(\"d\"); }\n get e() { return this.get(\"e\"); }\n get f() { return this.get(\"f\"); }\n}","// const __ = {\n// matrix_string: (matrix) => {\n// let matrix_str = ['a','b','c','d','e','f'].map( l => matrix[l] ).join(\" \")\n// return `matrix(${matrix_str})`\n// },\n// isArray: (obj) => {\n// return typeof Array.isArray === \"function\" ? Array.isArray(obj) :\n// (obj && typeof obj === \"object\" && obj.constructor.name === \"Array\");\n// },\n// recurse: (obj, opt, iterator) => {\n// function recurse(obj, i, parent = null) {\n// if (__.isArray(obj)) {\n// for (const [i, o] of obj.entries()) {\n// recurse(o, i, parent);\n// }\n// } else {\n// iterator(obj, i, parent);\n// if (obj && __.isArray(obj[opt.children])) {\n// for (const [i, o] of obj[opt.children].entries()) {\n// recurse(o, i, obj);\n// }\n// }\n// }\n// }\n\n// recurse(obj);\n// },\n// geom: {\n// point: {\n// // source https://github.com/HarryStevens/geometric/\n// translate: (point, angle, distance) => {\n// const r = __.geom.angle.torad(angle);\n// return [point[0] + distance * Math.cos(r), point[1] + distance * Math.sin(r)];\n// },\n\n// // source https://github.com/HarryStevens/geometric/\n// rotate: (point, angle, origin) => {\n\n// // See: https://en.wikipedia.org/wiki/Cartesian_coordinate_system#Rotation\n// function rotate(point, angle){\n// return [\n// (point[0] * Math.cos(angle)) - point[1] * Math.sin(angle),\n// (point[0] * Math.sin(angle)) + point[1] * Math.cos(angle)\n// ];\n// }\n\n// const r = __.geom.angle.torad(angle);\n\n// if (!origin \|\| (origin[0] === 0 && origin[1] === 0)){\n// return rotate(point, r);\n// }\n// else {\n// // See: https://math.stackexchange.com/questions/1964905/rotation-around-non-zero-point\n// const p0 = point.map((c, i) => c - origin[i]);\n// const rotated = rotate(p0, r);\n// return rotated.map((c, i) => c + origin[i]);\n// }\n// }\n// },\n// line: {\n// slope: (p1, p2) => {\n// let\n// m = (p2[1] - p1[1])/(p2[0] - p1[0]),\n// n = p1[0] - m * p1[0]\n// ;\n// return m;\n// },\n// intercept: (p1, p2) => {\n// let\n// m = __.geom.line.slope(p1, p2),\n// n = p1[1] - m * p1[0]\n// ;\n// return n;\n// },\n// slope_intercept: (p1, p2) => {\n// return {\n// slope: __.geom.line.slope(p1, p2),\n// intercept: __.geom.line.intercept(p1, p2)\n// };\n// },\n// midpoint: (p1, p2, w = 0.5) => {\n// if(Array.isArray(p1[0])) {\n// p2 = (p1[1]);\n// p1 = (p1[0]);\n// }\n// return [0, 1].map( i => (parseFloat(p1[i]) + parseFloat(p2[i])) * w );\n// },\n// length: (p1, p2) => {\n// if(Array.isArray(p1[0])) {\n// p2 = p1[1];\n// p1 = p1[0];\n// }\n// return Math.sqrt([0, 1].map( i => Math.pow(p2[i] - p1[i], 2) ).reduce( (a,b) => a + b, 0))\n// },\n// interpolate: (line) => {\n// // source https://github.com/HarryStevens/geometric/\n// return t =>\n// t === 0 ?\n// line[0] :\n// t === 1 ?\n// line[1] :\n// __.geom.point.translate(line[0], __.geom.angle.line(line), __.geom.line.length(line) * t)\n// ;\n// },\n// point_along: (line, distance = 0) => {\n// let\n// len = __.geom.line.length(line),\n// ratio = distance / len,\n// Xt = ((1 - ratio) * line[0][0] + (ratio * line[1][0])),\n// Yt = ((1 - ratio) * line[0][1] + (ratio * line[1][1]))\n// ;\n// return [Xt, Yt];\n// },\n// rotate: (line, by = [0, 0]) => {\n// let\n// translated = [line[1][0] - by[0], line[1][1] - by[1]],\n// rotated = [-(translated[1]), translated[0]],\n// rotated_reflection = [-(rotated[0]), -(rotated[1])],\n// untranslated = [rotated[0] + by[0], rotated[1] + by[1]],\n// untranslated2 = [rotated_reflection[0] + by[0], rotated_reflection[1] + by[1]]\n// ;\n// return [untranslated, untranslated2];\n// },\n// rotate2: (line, fixed, angle = 90) => {\n// let\n// line_si = __.geom.line.slope_intercept(line[0], line[1]),\n// P = [0, line_si.intercept],\n// Q = [1, line_si.slope + line_si.intercept]\n// ;\n// line = [P, Q];\n\n// let\n// xx = [line[0][0], line[1][0]],\n// yy = [line[0][1], line[1][1]],\n// x_fixed = fixed[0],\n// y_fixed = fixed[1],\n// angle_rad = -2 * Math.PI * angle/360,\n// xx_new = xx.map( (x, i) => (x - x_fixed) * Math.cos(angle_rad) - (yy[i] - y_fixed) * Math.sin(angle_rad) + x_fixed ),\n// yy_new = yy.map( (y, i) => (xx[i] - x_fixed) * Math.sin(angle_rad) - (y - y_fixed) * Math.cos(angle_rad) + y_fixed ),\n// object_new = [\n// [xx_new[0], yy_new[0]],\n// [xx_new[1], yy_new[1]]\n// ]\n// ;\n\n// return(object_new);\n// },\n// intersection: (lineA, lineB) => {\n// const\n// [[x1, y1], [x2, y2]] = lineA,\n// [[x3, y3], [x4, y4]] = lineB,\n// D = ( (x1 - x2) * (y3 - y4) ) - ( (y1 - y2) * (x3 - x4) ),\n// num1 = ( ((x1 * y2) - (y1 * x2)) * (x3 - x4) ) -\n// ( (x1 - x2) * ((x3 * y4) - (y3 * x4)) ),\n// num2 = ( ((x1 * y2) - (y1 * x2)) * (y3 - y4) ) -\n// ( (y1 - y2) * ((x3 * y4) - (y3 * x4)) )\n// ;\n// return [num1 / D, num2 / D];\n// },\n// intersect_circle(line, circle_xy, circle_r) {\n// let { slope: m, intercept: n } = __.geom.line.slope_intercept(line[0], line[1]);\n// let\n// a = 1 + Math.pow(m,2),\n// b = 2 * m * n - 2 * circle_xy[1] * m - 2 * circle_xy[0],\n// c = Math.pow(circle_xy[0], 2) + Math.pow(n, 2) + Math.pow(circle_xy[1], 2) - 2 * circle_xy[1] * n - Math.pow(circle_r, 2),\n// int\n// ;\n// if (Math.sqrt( Math.pow(b, 2) - (4 * a * c)) >= 0) {\n// let\n// x1 = (-b + Math.sqrt( Math.pow(b, 2) - (4 * a * c)))/(2 * a),\n// x2 = (-b - Math.sqrt( Math.pow(b, 2) - (4 * a * c)))/(2 * a),\n// y1 = m * x1 + n,\n// y2 = m * x2 + n\n// ;\n// int = [[x1, y1], [x2, y2]];\n// }\n// else {\n// int = \"The line and the circumference do not intersect\"\n// }\n// return(int)\n// }\n// },\n// angle: {\n// torad: (a) => a / 180 * Math.PI,\n// todeg: (a) => a * 180 / Math.PI,\n// line: (line) => {\n// // source https://github.com/HarryStevens/geometric/\n// return __.geom.angle.todeg(\n// Math.atan2(line[1][1] - line[0][1], line[1][0] - line[0][0])\n// );\n// }\n// }\n// },\n// object: {\n// proxy(obj, handler, deep = false) {\n// if(deep === false) {\n// return new Proxy(obj, handler);\n// }\n// else {\n// if (typeof obj !== 'object' \|\| obj === null) {\n// return obj;\n// }\n\n// for (const key in obj) {\n// if (obj.hasOwnProperty(key)) {\n// obj[key] = __.object.proxy(obj[key], handler, deep);\n// }\n// }\n\n// return new Proxy(obj, handler);\n// }\n// },\n// handler: {\n// set: function(target, property, value) {\n// target[property] = value;\n// window.dispatchEvent(__.event(\"settingUpdate\", this, { target, property, value }))\n\n// return true;\n// },\n// get: function(target, property) {\n// return target[property];\n// }\n// },\n// get: (obj, key) => {\n// const parts = key.split(\".\");\n// let current = obj;\n// for (const part of parts) {\n// if (current && typeof current === \"object\" && current.hasOwnProperty(part)) {\n// current = current[part];\n// }\n// else {\n// return undefined;\n// }\n// }\n// return current;\n// },\n// set: (obj, key, value) => {\n// const parts = key.split(\".\");\n// let current = obj,\n// i\n// ;\n\n// for (i = 0; i < parts.length - 1; i++) {\n// const part = parts[i];\n// if (current && typeof current === \"object\") {\n// if (!current.hasOwnProperty(part)) {\n// current[part] = {};\n// }\n// current = current[part];\n// }\n// else {\n// return false;\n// }\n// }\n\n// if (current && typeof current === \"object\") {\n// current[parts[i]] = value;\n// return true;\n// }\n// else {\n// return false;\n// }\n// }\n// },\n// array: {\n// unique: (x) => [...new Set(x)],\n// divide: (a, b) => {\n// let ret;\n\n// if(Array.isArray(a)) {\n// if(Array.isArray(b)) {\n// if(a.length === b.length) {\n// ret = a.map( (a_,i) => a_ / b[i] )\n// }\n// else {\n// console.error(\"If both are arrays, they must be equal length.\")\n// }\n// }\n// else {\n// ret = a.map( a_ => a_ / b );\n// }\n// }\n// else {\n// ret = a / b;\n// }\n\n// return(ret);\n// },\n// multiply: (a, b) => {\n// let ret;\n\n// if(Array.isArray(a)) {\n// if(Array.isArray(b)) {\n// if(a.length === b.length) {\n// ret = a.map( (a_,i) => a_ * b[i] )\n// }\n// else {\n// console.error(\"If both are arrays, they must be equal length.\")\n// }\n// }\n// else {\n// ret = a.map( a_ => a_ * b );\n// }\n// }\n// else {\n// ret = a * b;\n// }\n\n// return(ret);\n// },\n// subtract: (a, b) => {\n// let ret;\n\n// if(Array.isArray(a)) {\n// if(Array.isArray(b)) {\n// if(a.length === b.length) {\n// ret = a.map( (a_,i) => a_ - b[i] )\n// }\n// else {\n// console.error(\"If both are arrays, they must be equal length.\")\n// }\n// }\n// else {\n// ret = a.map( a_ => a_ - b );\n// }\n// }\n// else {\n// ret = a - b;\n// }\n\n// return(ret);\n// },\n// shift: () => {\n// return Array.from(a, (b, i) => a[i + 1]);\n// }\n// },\n// math: {\n// sum: (a) => a.reduce( (a,b) => a + b, 0),\n// mean: (a) => __.math.sum(a) / a.length,\n// round: (a, b) => {\n// const factor = Math.pow(10, b);\n// return Math.round(a * factor) / factor;\n// }\n// },\n// event: (nm, elm, data) => {\n// return new CustomEvent(nm, {\n// bubbles: true,\n// cancelable: true,\n// detail: {\n// element: elm,\n// data: data \|\| (elm ? elm.__data__ : undefined)\n// }\n// })\n// },\n// hash: {\n// parts: () => location.hash.replace(/#/,'').split(/\\//).filter(a => a).map(a => a.split(/:/)),\n// exists: (x) => __.hash.parts().flat().findIndex(a => a === x) >= 0\n// },\n// url: {\n// parse: (l = window.location) => {\n// },\n// query: {\n// parse: (l = window.location.search) =>\n// Object.fromEntries(l.replace(/^\\?/,'').split(/&/).map( i => i.split(/=/) ))\n// ,\n// keys: (l = window.location.search) =>\n// l.replace(/^\\?/,'').split(/&/).map( i => i.split(/=/)[0] )\n// ,\n// has: (k, l = window.location.search) =>\n// __.url.query.keys(l).findIndex(i => i == k) >= 0\n// }\n// }\n// };\n\nexport namespace Tools {\n export namespace Matrix {\n export function matrixString(matrix: Record<string, number>): string {\n const matrixStr = ['a', 'b', 'c', 'd', 'e', 'f'].map(l => matrix[l]).join(' ');\n return `matrix(${matrixStr})`;\n }\n }\n\n export namespace Geometry {\n export namespace Point {\n export function translate(point: [number, number], angle: number, distance: number): [number, number] {\n const r = Angle.toRad(angle);\n return [point[0] + distance * Math.cos(r), point[1] + distance * Math.sin(r)];\n }\n\n export function rotate(point: [number, number], angle: number, origin?: [number, number]): [number, number] {\n const r = Angle.toRad(angle);\n\n function rotatePoint(p: [number, number], a: number): [number, number] {\n return [\n p[0] * Math.cos(a) - p[1] * Math.sin(a),\n p[0] * Math.sin(a) + p[1] * Math.cos(a),\n ];\n }\n\n if (!origin \|\| (origin[0] === 0 && origin[1] === 0)) {\n return rotatePoint(point, r);\n } else {\n const p0 = point.map((c, i) => c - origin[i]) as [number, number];\n const rotated = rotatePoint(p0, r);\n return rotated.map((c, i) => c + origin[i]) as [number, number];\n }\n }\n }\n\n export namespace Line {\n export function slope(p1: [number, number], p2: [number, number]): number {\n return (p2[1] - p1[1]) / (p2[0] - p1[0]);\n }\n export function intercept(p1: [number, number], p2: [number, number]): number {\n const m = slope(p1, p2);\n return p1[1] - m * p1[0];\n }\n export function slopeIntercept(p1: [number, number], p2: [number, number]): { slope: number; intercept: number } {\n return {\n slope: slope(p1, p2),\n intercept: intercept(p1, p2),\n };\n }\n export function point_along(line: [[number, number], [number, number]], distance: number = 0): [number, number] {\n const ratio = distance;\n const Xt = ((1 - ratio) * line[0][0] + (ratio * line[1][0]));\n const Yt = ((1 - ratio) * line[0][1] + (ratio * line[1][1]));\n return [Xt, Yt];\n }\n export function midpoint(p1: [number, number], p2: [number, number], w = 0.5): [number, number] {\n if (Array.isArray(p1[0])) {\n p2 = (p1[1] as any);\n p1 = (p1[0] as any);\n }\n\n return [0, 1].map(i => (parseFloat(p1[i] as any) + parseFloat(p2[i] as any)) * w) as [number, number];\n }\n export function length(\n p1: [number, number] \| [[number, number], [number, number]],\n p2?: [number, number]\n ): number {\n if (Array.isArray((p1 as any)[0])) {\n p2 = (p1 as [[number, number], [number, number]])[1];\n p1 = (p1 as [[number, number], [number, number]])[0];\n }\n return Math.sqrt(\n [0, 1].map(i => Math.pow((p2 as [number, number])[i] - (p1 as [number, number])[i], 2)).reduce((a, b) => a + b, 0)\n );\n }\n export function rotate(\n line: [[number, number], [number, number]],\n by: [number, number] = [0, 0]\n ): [[number, number], [number, number]] {\n const translated: [number, number] = [\n line[1][0] - by[0],\n line[1][1] - by[1]\n ];\n const rotated: [number, number] = [\n -translated[1],\n translated[0]\n ];\n const rotated_reflection: [number, number] = [\n -rotated[0],\n -rotated[1]\n ];\n const untranslated: [number, number] = [\n rotated[0] + by[0],\n rotated[1] + by[1]\n ];\n const untranslated2: [number, number] = [\n rotated_reflection[0] + by[0],\n rotated_reflection[1] + by[1]\n ];\n return [untranslated, untranslated2];\n }\n export function rotate2(\n line: [[number, number], [number, number]],\n fixed: [number, number],\n angle: number = 90\n ): [[number, number], [number, number]] {\n // Calculate slope and intercept\n const m = Tools.Geometry.Line.slope(line[0], line[1]);\n const n = Tools.Geometry.Line.intercept(line[0], line[1]);\n const P: [number, number] = [0, n];\n const Q: [number, number] = [1, m + n];\n line = [P, Q];\n\n const xx = [line[0][0], line[1][0]];\n const yy = [line[0][1], line[1][1]];\n const x_fixed = fixed[0];\n const y_fixed = fixed[1];\n const angle_rad = -2 * Math.PI * angle / 360;\n const xx_new = xx.map((x, i) =>\n (x - x_fixed) * Math.cos(angle_rad) - (yy[i] - y_fixed) * Math.sin(angle_rad) + x_fixed\n );\n const yy_new = yy.map((y, i) =>\n (xx[i] - x_fixed) * Math.sin(angle_rad) - (y - y_fixed) * Math.cos(angle_rad) + y_fixed\n );\n const object_new: [[number, number], [number, number]] = [\n [xx_new[0], yy_new[0]],\n [xx_new[1], yy_new[1]]\n ];\n\n return object_new;\n }\n export function intersection(\n lineA: [[number, number], [number, number]],\n lineB: [[number, number], [number, number]]\n ): [number, number] {\n const\n [[x1, y1], [x2, y2]] = lineA,\n [[x3, y3], [x4, y4]] = lineB,\n D = ((x1 - x2) * (y3 - y4)) - ((y1 - y2) * (x3 - x4)),\n num1 = (((x1 * y2) - (y1 * x2)) * (x3 - x4)) -\n ((x1 - x2) * ((x3 * y4) - (y3 * x4))),\n num2 = (((x1 * y2) - (y1 * x2)) * (y3 - y4)) -\n ((y1 - y2) * ((x3 * y4) - (y3 * x4)));\n return [num1 / D, num2 / D];\n }\n export function intersect_circle(line: [[number, number], [number, number]], circle_xy: [number, number], circle_r: number): [[number, number], [number, number]] {\n let { slope: m, intercept: n } = Tools.Geometry.Line.slopeIntercept(line[0], line[1]);\n let\n a = 1 + Math.pow(m, 2),\n b = 2 * m * n - 2 * circle_xy[1] * m - 2 * circle_xy[0],\n c = Math.pow(circle_xy[0], 2) + Math.pow(n, 2) + Math.pow(circle_xy[1], 2) - 2 * circle_xy[1] * n - Math.pow(circle_r, 2),\n int: [[number, number], [number, number]] = [[Infinity, Infinity], [Infinity, Infinity]]\n ;\n\n if (Math.sqrt(Math.pow(b, 2) - (4 * a * c)) >= 0) {\n let\n x1 = (-b + Math.sqrt(Math.pow(b, 2) - (4 * a * c))) / (2 * a),\n x2 = (-b - Math.sqrt(Math.pow(b, 2) - (4 * a * c))) / (2 * a),\n y1 = m * x1 + n,\n y2 = m * x2 + n\n ;\n int = [[x1, y1], [x2, y2]];\n }\n else {\n console.error(\"The line and the circumference do not intersect\");\n }\n\n return (int)\n }\n export function interpolate(line: [[number, number], [number, number]]): (t: number) => [number, number] {\n // source https://github.com/HarryStevens/geometric/\n return t =>\n t === 0 ?\n line[0] :\n t === 1 ?\n line[1] :\n Tools.Geometry.Point.translate(line[0], Tools.Geometry.Angle.line(line), Tools.Geometry.Line.length(line) * t)\n ;\n }\n }\n\n export namespace Angle {\n export function toRad(angle: number): number {\n return (angle / 180) * Math.PI;\n }\n\n export function toDeg(angle: number): number {\n return (angle * 180) / Math.PI;\n }\n // source https://github.com/HarryStevens/geometric/\n export function line(line: [[number, number], [number, number]]): number {\n if (line.length !== 2 \|\| !Array.isArray(line[0]) \|\| !Array.isArray(line[1]) \|\| line[0].length !== 2 \|\| line[1].length !== 2) {\n throw new Error('Invalid line format. Expected [[x1, y1], [x2, y2]].');\n }\n //console.log(\"line: \", line)\n return Tools.Geometry.Angle.toDeg(\n Math.atan2(line[1][1] - line[0][1], line[1][0] - line[0][0])\n );\n }\n }\n }\n\n export namespace ArrayTools {\n export function unique<T>(arr: T[]): T[] {\n return [...new Set(arr)];\n }\n\n export function divide(a: number \| number[], b: number \| number[]): number \| number[] {\n if (Array.isArray(a)) {\n if (Array.isArray(b)) {\n if (a.length !== b.length) throw new Error('Arrays must be of equal length');\n return a.map((val, i) => val / b[i]);\n }\n return a.map(val => val / (b as number));\n }\n return (a as number) / (b as number);\n }\n\n export function isArray(obj: any): boolean {\n return typeof Array.isArray === \"function\" ? Array.isArray(obj) :\n (obj && typeof obj === \"object\" && obj.constructor.name === \"Array\");\n }\n }\n\n export namespace Mathematics {\n export function sum(arr: number[]): number {\n return arr.reduce((a, b) => a + b, 0);\n }\n\n export function mean(arr: number[]): number {\n return sum(arr) / arr.length;\n }\n\n export function round(value: number, decimals: number): number {\n const factor = Math.pow(10, decimals);\n return Math.round(value * factor) / factor;\n }\n }\n\n export namespace Events {\n export function createEvent(name: string, element?: HTMLElement, data?: any): CustomEvent {\n return new CustomEvent(name, {\n bubbles: true,\n cancelable: true,\n detail: {\n element,\n data: data \|\| (element ? (element as any).__data__ : undefined),\n },\n });\n }\n }\n\n export namespace Hash {\n export function parts(): string[][] {\n return location.hash\n .replace(/#/, '')\n .split(/\\//)\n .filter(a => a)\n .map(a => a.split(/:/));\n }\n\n export function exists(key: string): boolean {\n return parts().flat().findIndex(a => a === key) >= 0;\n }\n }\n\n\n export namespace Objects {\n export function proxy<T extends object>(obj: T, handler: ProxyHandler<any>, deep = false): T {\n if (!deep) {\n return new Proxy(obj, handler);\n } else {\n if (typeof obj !== 'object' \|\| obj === null) {\n return obj;\n }\n\n for (const key in obj) {\n if (Object.prototype.hasOwnProperty.call(obj, key)) {\n (obj as any)[key] = proxy((obj as any)[key], handler, deep);\n }\n }\n\n return new Proxy(obj, handler);\n }\n }\n\n export const handler: ProxyHandler<any> = {\n set(target, property, value) {\n target[property] = value;\n window.dispatchEvent(\n Tools.Events.createEvent(\"settingUpdate\", window as any, { target, property, value })\n );\n return true;\n },\n get(target, property) {\n return target[property];\n }\n };\n\n export function get(obj: any, key: string): any {\n const parts = key.split(\".\");\n let current = obj;\n for (const part of parts) {\n if (current && typeof current === \"object\" && Object.prototype.hasOwnProperty.call(current, part)) {\n current = current[part];\n } else {\n return undefined;\n }\n }\n return current;\n }\n\n export function set(obj: any, key: string, value: any): boolean {\n const parts = key.split(\".\");\n let current = obj;\n let i: number;\n\n for (i = 0; i < parts.length - 1; i++) {\n const part = parts[i];\n if (current && typeof current === \"object\") {\n if (!Object.prototype.hasOwnProperty.call(current, part)) {\n current[part] = {};\n }\n current = current[part];\n } else {\n return false;\n }\n }\n\n if (current && typeof current === \"object\") {\n current[parts[i]] = value;\n return true;\n } else {\n return false;\n }\n }\n }\n\n export namespace URL {\n export function parse(location: Location = window.location): Record<string, string> {\n return Object.fromEntries(new URLSearchParams(location.search));\n }\n\n export namespace Query {\n export function parse(location: string = window.location.search): Record<string, string> {\n return Object.fromEntries(\n location.replace(/^\\?/, '').split(/&/).map(i => i.split(/=/))\n );\n }\n\n export function keys(location: string = window.location.search): string[] {\n return location.replace(/^\\?/, '').split(/&/).map(i => i.split(/=/)[0]);\n }\n\n export function has(key: string, location: string = window.location.search): boolean {\n return keys(location).findIndex(i => i === key) >= 0;\n }\n }\n }\n}\n\n","export type EventBusListener = (details: { key: string, newValue: any, oldValue: any }) => any;\n\n/*\n Minimal local pub/sub used by vizena Graph and Layer objects.\n * Has the same API surface as arbor's StateManager but carries no R/arbor deps.\n /\nexport class EventBus {\n private _state: Map<string, any> = new Map();\n private listeners: Map<string, Map<string, Set<EventBusListener>>> = new Map();\n\n get state(): Map<string, any> {\n return this._state;\n }\n\n hasVariable(key: string): boolean {\n return this._state.has(key);\n }\n\n getVariable(key: string): any {\n return this._state.get(key);\n }\n\n setVariable(key: string, value: any, options?: { lazy?: boolean }): void {\n const oldValue = this._state.get(key);\n this._state.set(key, value);\n if (!options?.lazy) {\n this.notifyListeners(key, value, oldValue);\n }\n }\n\n addListener(key: string, type: string, listener: EventBusListener): void {\n if (!this.listeners.has(key)) this.listeners.set(key, new Map());\n const typeMap = this.listeners.get(key)!;\n if (!typeMap.has(type)) typeMap.set(type, new Set());\n typeMap.get(type)!.add(listener);\n }\n\n removeListener(key: string, type: string, listener: EventBusListener): void {\n this.listeners.get(key)?.get(type)?.delete(listener);\n }\n\n getListeners(key: string, type: string): EventBusListener[] {\n return Array.from(this.listeners.get(key)?.get(type) ?? []);\n }\n\n notifyListeners(key: string, newValue: any, oldValue: any): void {\n const typeMap = this.listeners.get(key);\n if (!typeMap) return;\n for (const set of typeMap.values()) {\n set.forEach((listener) => {\n if (typeof listener === 'function') {\n listener({ key, newValue, oldValue });\n } else if (typeof (listener as any).calculate === 'function') {\n (listener as any).calculate.call(listener, { key, newValue, oldValue });\n }\n });\n }\n }\n}\n","import { Transform } from \"./Transform.js\";\nimport { Tools } from \"../utils/Tools.js\";\nconst { ArrayTools } = Tools;\nimport { Graph } from \"./Graph.js\";\nimport { PlottedObject } from \"./PlottedObject.js\";\nimport { EventBus as StateManager } from \"../types/EventBus.js\";\n\nexport type LayerLike = {\n name?: string;\n layers?: LayerArray;\n [key: string]: any;\n};\n\nexport class LayerArray extends Array<LayerLike> {\n constructor(...args: any[]) {\n super(...args);\n }\n\n search(key: string, name: string): LayerLike \| undefined {\n let found: LayerLike \| undefined;\n\n function fn(a: LayerLike): LayerLike \| undefined {\n return a.name === name ? a : undefined;\n }\n\n function recurse(obj: any, i?: number, parent: any = null): LayerLike \| undefined {\n if (ArrayTools.isArray(obj)) {\n for (const [i, o] of obj.entries()) {\n found = recurse(o, i, parent);\n if (found) {\n return found;\n }\n }\n } else {\n found = fn(obj);\n if (!found) {\n if (obj && ArrayTools.isArray(obj[key])) {\n for (const [i, o] of obj[key].entries()) {\n found = recurse(o, i, obj);\n if (found) {\n return found;\n }\n }\n }\n } else {\n return found;\n }\n }\n return found;\n }\n\n return recurse(this);\n }\n\n flatten(): LayerLike[] {\n return this.reduce<LayerLike[]>((a, l: LayerLike) => {\n a.push(l);\n if (l.layers && Array.isArray(l.layers)) {\n a.push(...l.layers);\n }\n return a;\n }, []);\n }\n \n recurse(\n key: string,\n callback: (layer: LayerLike, parent?: LayerLike \| null, depth?: number) => any, \n parent: LayerLike \| null = null, \n depth: number = 0\n ): any {\n let results: any[] = new LayerArray();\n for (const layer of this) {\n let result = callback(layer, parent, depth);\n \n if (layer[key] && Array.isArray(layer[key])) {\n let r = new LayerArray(...layer[key]).recurse(key, callback, layer, depth + 1);\n if (r !== undefined) {\n results.push(...r);\n }\n }\n\n results.push(result);\n }\n console.log(\"Recurse results: \", results);\n return results;\n }\n}\n\nexport class Layer {\n __state__: StateManager = new StateManager();\n\n name: string;\n ID: string;\n scale_x: number = 1;\n scale_y: number = 1;\n tabindex?: number;\n _transform: Transform;\n scale_objects: boolean = true;\n layers: LayerArray = new LayerArray();\n objects: Map<string, PlottedObject> = new Map();\n parent?: Layer \| Graph;\n visible: boolean = true;\n\n constructor(ID: string, o: any, parent?: Graph \| Layer) {\n this.ID = ID;\n this.name = o.name \|\| `layer-${ID}`;\n this.tabindex = o.tabindex;\n this.parent = parent;\n this._transform = new Transform();\n\n parent?.__state__.addListener(\"graph_updated\", \"live\", ({ key, newValue, oldValue }) => {\n // console.log(`Graph updated, updating layer: ${this.name}`);\n });\n \n parent?.__state__.addListener(`graph_updated_${this.name}`, \"live\", ({ key, newValue, oldValue }) => {\n // console.log(`Graph updated, updating layer: ${this.name}, Key: ${key}`, \"New Value: \", newValue, \"Old Value: \", oldValue);\n this.objects = newValue;\n this.__state__.setVariable(`layer_updated`, this );\n });\n }\n\n get transform(): Transform {\n return this._transform;\n }\n set transform(t: Transform) {\n this._transform = t;\n }\n}","import { Transform } from './Transform';\nimport { Color } from './Color';\nimport { Edge } from './Edges';\nimport { DataFrameRow } from '../types/DataFrame';\n\nexport type DimensionType = DimensionVector \| DataFrameRow \| number[];\n\nexport interface DimensionVectorInterface extends Array<number> {\n\n [index: number]: number;\n flipped: boolean;\n flip(): DimensionVector;\n get names(): string[];\n get(wh: string \| number): number \| undefined;\n}\nexport class DimensionVector extends Array<number> implements DimensionVectorInterface {\n #flipped: boolean = false;\n #names: string[] \| undefined;\n\n constructor(...args: number[]) {\n super(arguments.length);\n for (let i = 0; i < args.length; i++) {\n this[i] = args[i];\n }\n this.#flipped = false;\n }\n\n static fromArray(arr: DataFrameRow): DimensionVector {\n const vec = new DimensionVector();\n arr.forEach((v, i) => {\n vec.push(v);\n });\n vec.#names = arr.names;\n\n return vec;\n }\n\n flip(): DimensionVector {\n this.#flipped = !this.#flipped;\n for (let i = 0; i < this.length; i++) {\n this[i] = -this[i];\n }\n return this;\n }\n\n get(wh: string \| number): number \| undefined {\n if (typeof wh === 'number') {\n return this[wh];\n } else if (this.#names && this.#names.includes(wh)) {\n return this[this.#names.indexOf(wh)];\n } else {\n return undefined;\n }\n }\n\n get flipped(): boolean {\n return this.#flipped;\n }\n\n get names(): string[] {\n if (this.#names) {\n return this.#names;\n } else {\n return this.map((_, i) => `V${i + 1}`);\n }\n }\n}\n\nexport interface PlottedObjectOptions {\n ID: string;\n dimensions?: DimensionVector;\n x?: number \| number[];\n y?: number \| number[];\n size: number \| 0;\n color: Color;\n highlight: Color \| null;\n shape?: any;\n active: boolean;\n meta: any;\n\n [key: string]: any;\n}\n\nexport class PlottedObject implements PlottedObjectOptions {\n private readonly _original: PlottedObjectOptions;\n private readonly _dimensions: DimensionVector;\n\n ID: string;\n scale_x: number = 1;\n scale_y: number = 1;\n scale_size: number = 0.05;\n active: boolean = false;\n visible: boolean = false;\n highlighting: boolean = false;\n meta: any = {};\n \n _transform: Transform;\n _x: any = 0;\n _y: any = 0;\n _color: Color;\n _highlight: Color;\n _highlight_default: Color = new Color('#000000');\n _size: number = 0;\n\n shape?: any;\n\n // graph: Graph;\n parent: any;\n\n get dimensions(): DimensionVector {\n return this._dimensions;\n }\n\n get color(): Color {\n return (\n // This was expecting hightight to be an object with a color property\n // but now it is just a Color object, so we can simplify this.\n (this.highlighting && this._highlight) ? this._highlight : this._color\n );\n }\n set color(c: Color) {\n this._color = c;\n }\n get highlight(): Color {\n return this._highlight \|\| this._highlight_default;\n }\n set highlight(h: Color) {\n this._highlight = h;\n }\n\n get size(): number {\n return this._size;\n }\n set size(s: number) {\n this._size = s;\n }\n\n get original(): PlottedObjectOptions {\n return this._original;\n }\n\n get x() {\n return this._x; // this.graph.x_mirror();\n }\n get y() {\n return this._y; // * this.graph.y_mirror();\n }\n set x(x_: any) { this._x = x_; }\n set y(y_: any) { this._y = y_; }\n dimension(wh: string \| number): number \| undefined {\n return this._dimensions.get(wh);\n }\n\n get transform() { return this._transform; }\n set transform(t: any) { this._transform = t; }\n\n constructor(dimensions: DimensionType, o: PlottedObjectOptions) {\n this.ID = o.ID;\n // this.graph = graph;\n this._transform = new Transform();\n\n // If dimensions is already a DimensionVector, use it directly\n if (dimensions instanceof DimensionVector) {\n this._dimensions = dimensions;\n }\n else if (dimensions instanceof DataFrameRow) {\n // If dimensions is a DataFrameRow, convert it to a DimensionVector\n this._dimensions = DimensionVector.fromArray(dimensions);\n }\n\n // If dimensions is an array, convert it to a DimensionVector\n else if (Array.isArray(dimensions)) {\n this._dimensions = new DimensionVector(...dimensions);\n }\n\n // Else is a warning and fallback to a default DimensionVector\n else {\n console.warn(\"Invalid dimensions provided, using default DimensionVector(0, 0)\");\n this._dimensions = new DimensionVector(0, 0);\n }\n\n // make a copy of the object to avoid mutating the original\n let data: PlottedObjectOptions = { ...o };\n\n // keep the original data for reference\n this._original = { ...data };\n\n this.ID = data.ID;\n this.x = data.x \|\| this._dimensions[0];\n this.y = data.y \|\| this._dimensions[1];\n this._size = data.size \|\| 1;\n this._color = data.color \|\| new Color('#000000');\n this.active = data.active \|\| false;\n this.shape = data.shape \|\| null;\n this.meta = data.meta \|\| {};\n\n this._highlight = this._highlight_default;\n if (data.highlight) {\n this._highlight = data.highlight;\n }\n // else if (graph && graph.options && graph.options[this.constructor.name.toUpperCase()]) {\n // this._highlight = graph.options[this.constructor.name.toUpperCase()].highlight;\n // }\n }\n}\n\nexport interface LineOptions extends PlottedObjectOptions {\n x1: number \| string;\n y1: number \| string;\n x2: number \| string;\n y2: number \| string;\n width?: number;\n color: Color;\n shape: string \| null;\n [key: string]: any;\n}\n\nexport class Line extends PlottedObject {\n from: Point;\n to: Point;\n width?: number;\n _color!: Color;\n shape!: string;\n\n // constructor(x: LineOptions) {\n // super([], x);\n // // const data = Object.assign({}, x);\n // const { x1, y1, x2, y2, width, color, shape } = x;\n\n // // console.log(\"Line constructor data:\", data);\n // // console.warn(\" this was using `meta` but it is deprecated now - should be using `original` instead\");\n // // this.meta = Object.keys(data)\n // // .filter(k => ['ID', 'x1', 'y1', 'x2', 'y2', 'size', 'color'].indexOf(k) < 0)\n // // .reduce((n: any, k: string) => { n[k] = data[k]; return n; }, {});\n\n // this.x1 = parseFloat(x1 as string);\n // this.y1 = parseFloat(y1 as string);\n // this.x2 = parseFloat(x2 as string);\n // this.y2 = parseFloat(y2 as string);\n // this.width = width;\n // this._color = color \|\| new Color('#000000');\n // this.shape = shape \|\| 'line';\n // }\n\n constructor(data: DataFrameRow \| any, from: Point, to: Point) {\n // let\n // // dimensions: DimensionType = data.classes.map( (c: string, i: number) => c === \"ena.co.occurrence\" ? data[i] : -1).filter(a => a !== -1),\n // // meta: any = data.classes.map( (c: string, i: number) => c === \"ena.metadata\" ? [data.names[i], data[i]] : null).filter(a => a !== null).reduce((n: any, c: any) => { n[c[0]] = c[1]; return n; }, {}),\n // // ID: string = data.rowName \|\| `point-${Math.random().toString(36).substring(2, 9)}`\n // ;\n\n super([], {} as any);\n\n this.from = from;\n this.to = to;\n }\n\n get line(): [[number, number], [number, number]] {\n return [[this.from.x, this.from.y], [this.to.x, this.to.y]];\n }\n get midpoint(): [number, number] {\n return [\n (this.from.x + this.to.x) / 2,\n (this.from.y + this.to.y) / 2\n ];\n }\n get length(): number {\n return Math.sqrt(\n Math.pow(this.to.x - this.from.x, 2) +\n Math.pow(this.to.y - this.from.y, 2)\n );\n }\n get color(): Color { return this._color; }\n set color(c: Color) { this._color = c; }\n}\n\nexport interface PointOptions extends PlottedObjectOptions {\n shape?: string;\n label?: string;\n [key: string]: any;\n}\n\nexport class Point extends PlottedObject {\n static SHAPES = { CIRCLE: 'circle', SQUARE: 'rect' };\n\n private _label: Label \| undefined;\n edges: Map<any, Edge> = new Map();\n shape: string = Point.SHAPES.CIRCLE;\n\n // constructor(dimensions: DimensionType, o: PointOptions) { //, graph?: any) {\n // super(dimensions, o);\n // this.active = o.active \|\| false;\n // this.visible = o.visible \|\| false;\n // this.size = o.size \|\| 1;\n // this.color = o.color \|\| new Color('#000000');\n // this.shape = o.shape ? o.shape : \"circle\";\n // this.scale_size = 2;\n // this._x = dimensions[0];\n // this._y = dimensions[1];\n // this.label = new Label(this.ID, this);\n // }\n constructor(data: DataFrameRow \| any) {\n let\n dimensions: DimensionType \| undefined, // = data.classes.map( (c, i) => (c === \"ena.co.occurrence\" \|\| c === \"ena.dimension\") ? data[i] : -1).filter(a => a !== -1),\n meta: any, // = data.classes.map( (c, i) => c === \"ena.metadata\" ? [data.names[i], data[i]] : null).filter(a => a !== null).reduce((n: any, c: any) => { n[c[0]] = c[1]; return n; }, {}),\n ID: string // = data.rowName \|\| `point-${Math.random().toString(36).substring(2, 9)}`\n ;\n\n if(data) {\n if(data instanceof DataFrameRow) {\n dimensions = data.classes?.map( (c, i) => (c === \"ena.co.occurrence\" \|\| c === \"ena.dimension\") ? data[i] : -1).filter(a => a !== -1);\n meta = data.classes?.map( (c, i) => c === \"ena.metadata\" ? [data.names[i], data[i]] : null).filter(a => a !== null).reduce((n: any, c: any) => { n[c[0]] = c[1]; return n; }, {});\n ID = data.rowName \|\| `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n else if(typeof data === \"object\") {\n dimensions = data.dimensions \|\| [];\n meta = data.meta \|\| {};\n ID = data.ID \|\| `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n else {\n console.warn(\"Invalid data provided for Point, using default values\");\n dimensions = [];\n meta = {};\n ID = `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n }\n else {\n dimensions = [];\n meta = {};\n ID = `point-${Math.random().toString(36).substring(2, 9)}`;\n }\n\n super(dimensions ?? [], { meta, ID } as any);\n }\n\n set label(l: Label \| undefined) {\n this._label = l;\n }\n get label(): Label \| undefined {\n return this._label;\n }\n get x(): number {\n // const dims = this.graph.options.GRAPH.dimensions;\n // const _ = this.meta[dims[0]];\n // const mult = 1;\n // return parseFloat(_) * mult;\n return this._x;\n }\n get y(): number {\n // const dims = this.graph.options.GRAPH.dimensions;\n // const _ = this.meta[dims[1]];\n // const mult = 1;\n // return parseFloat(_) * mult;\n return this._y;\n }\n set x(x_: number) { this._x = parseFloat(x_ as any); }\n set y(y_: number) { this._y = parseFloat(y_ as any); }\n}\n\nexport class ConfidenceInterval extends PlottedObject {\n width?: number;\n z: number = 1.959964;\n // meta: any;\n\n private _mean: any;\n\n constructor(mean: any) {\n super(mean.dimensions, mean);\n this.ID = \"mean_ci_\" + mean.ID;\n this._mean = mean;\n }\n\n get line(): [[number, number], [number, number]] {\n // x1, y1, x2, y2 should be defined on mean or this\n return [\n [this._mean.x1, this._mean.y1],\n [this._mean.x2, this._mean.y2]\n ];\n }\n get variance(): [number, number] {\n const points = [...this._mean.points.values()];\n return [\n points.length > 1 ? points.map(p => Math.pow(p.x - this._mean.x, 2)).reduce((a, b) => a + b, 0) / (points.length - 1) : 0,\n points.length > 1 ? points.map(p => Math.pow(p.y - this._mean.y, 2)).reduce((a, b) => a + b, 0) / (points.length - 1) : 0\n ];\n }\n get std(): [number, number] {\n return this.variance.map(Math.sqrt) as [number, number];\n }\n get value(): [number, number] {\n const pointsSize = this._mean.points.size;\n return this.std.map(s => this.z * (s / Math.sqrt(pointsSize))) as [number, number];\n }\n get length(): number {\n const [a, b] = this.line;\n return Math.sqrt(Math.pow(b[0] - a[0], 2) + Math.pow(b[1] - a[1], 2));\n }\n\n get path(): string {\n const x_ = this._mean.x;\n const y_ = this._mean.y;\n const v = this.value;\n const x = v[0];\n const y = v[1];\n const xl = x_ - x;\n const xr = x_ + x;\n const yt = y_ - y;\n const yb = y_ + y;\n return `M${xl},${yt} ${xr},${yt} ${xr},${yb} ${xl},${yb}z`;\n }\n}\n\nexport class Label extends PlottedObject {\n object: PlottedObject;\n _visible: boolean = false;\n text: string;\n offset: number = 0;\n dragging?: boolean;\n\n constructor(txt: string, object: PlottedObject) {\n // super(object.ID);\n super(object.dimensions, object);\n this.text = txt;\n this.ID = object.ID;\n this.object = object;\n this.x = this.dimensions[0]; //object.x;\n this.y = this.dimensions[1]; //object.y;\n this.offset = object.size \|\| 0;\n this.size = this.offset / 4;\n this.visible = false;\n\n this._transform.set(\"e\", 1); // this.object.size * this.graph.SIZE_EFFECT * 2);\n this._transform.set(\"f\", 1); // this.object.size * this.graph.SIZE_EFFECT * 2);\n }\n\n get x(): number {\n return parseFloat(this._x);\n }\n get y(): number {\n return parseFloat(this._y);\n }\n set x(x_: number) { this._x = x_; }\n set y(y_: number) { this._y = y_; }\n\n get transform(): Transform {\n console.warn(\"transform is disabled - need updated reference for the graph options\")\n // if (\n // !this.dragging &&\n // this.graph.options[this.object.constructor.name.toUpperCase()].labelposition === Label.POSITION.OBJECT\n // ) {\n // const s = this.object.size;\n // const effect = 1; // this.graph.object.SIZE_EFFECT\n // this._transform.set(\"e\", s * effect / 2 / this._transform.a);\n // this._transform.set(\"f\", s * effect / 2 / this._transform.a);\n // } else if (\n // !this.dragging &&\n // this.graph.options[this.object.constructor.name.toUpperCase()].labelposition === Label.POSITION.STATIC\n // ) {\n // const eVal = this.graph.extremes[this.graph.options.LABEL.position[1] as keyof typeof this.graph.extremes];\n // const fVal = this.graph.extremes[this.graph.options.LABEL.position[0] as keyof typeof this.graph.extremes];\n // this._transform.set(\"e\", typeof eVal === \"number\" ? eVal : 0);\n // this._transform.set(\"f\", typeof fVal === \"number\" ? fVal : 0);\n // }\n return this._transform;\n }\n set transform(t: Transform) { this._transform = t; }\n\n static DISPLAY_TYPES = { OFF: 0, AUTO: 1, CLICK: 2, ON: 3 };\n static HIGHLIGHT = { OFF: 0, ON: 2 };\n static POSITION = { OBJECT: 1, STATIC: 2, CONTAINER: 3, CUSTOM: 4 };\n}\n","\nclass Extremes {\n x_max: number;\n y_max: number;\n // _point_max?: Point;\n // _node_max?: Point;\n\n /** Centre of the view; (0, 0) — the ENA origin — unless centred on the content /\n cx: number;\n cy: number;\n\n constructor(x: number, y: number, cx: number = 0, cy: number = 0) { //, n?: Point, p?: Point) {\n this.x_max = x;\n this.y_max = y;\n this.cx = cx;\n this.cy = cy;\n // this._point_max = p;\n // this._node_max = n;\n }\n as_viewBox(p: number = 1.2): string {\n let x = this.x_max p;\n let y = this.y_max * p;\n return (`${this.cx - x} ${this.cy - y} ${x * 2} ${y * 2}`);\n }\n\n // get point_max(): Point {\n // return this._point_max \|\| { x: 1, y: 1 };\n // }\n // get node_max(): Point {\n // return this._node_max \|\| { x: 1, y: 1 };\n // }\n\n get height(): number {\n return this.y_max * 2;\n } \n get width(): number {\n return this.x_max * 2;\n }\n get top(): number {\n return this.y_max * -1;\n }\n get bottom(): number {\n return this.y_max;\n }\n get left(): number {\n return this.x_max * -1;\n }\n get right(): number {\n return this.x_max;\n }\n}\n\nexport { Extremes };","import { DimensionVector, PlottedObject } from \"./PlottedObject\";\n\nexport class AxisPoint extends PlottedObject {\n\n constructor(dimensions: DimensionVector, o: any) {\n super(dimensions, o);\n\n this.visible = true;\n\n this.size = o.size;\n }\n\n set size(s: number) {\n this._size = s;\n }\n get size(): number {\n return this._size;\n }\n\n get x(): number {\n return this._x;\n }\n get y(): number {\n return this._y;\n }\n set x(x_: number) { this._x = x_; }\n set y(y_: number) { this._y = y_; }\n\n get transform() {\n return this._transform;\n }\n}","import { Color } from \"./Color\";\nimport { Layer, LayerArray, LayerLike } from \"./Layers\";\nimport { DimensionVector, Label, Line, Point } from \"./PlottedObject\";\nimport { Transform } from \"./Transform\";\nimport { Extremes } from \"./Extremes\";\nimport { Node } from \"./Points\";\nimport { Edge } from \"./Edges\";\nimport { AxisPoint } from \"./AxisPoint\";\nimport { DataFrame, DataFrameRow } from \"../types/DataFrame\";\nimport { EventBus as StateManager } from \"../types/EventBus\";\n\nexport let DefaultGraphOptions = {\n GRAPH: {\n ratio: 1,\n x_max: 1,\n y_max: 1,\n selector: \"body\",\n width: 1,\n height: 1,\n axes: true,\n SIZE_EFFECT: 1,\n dimensions: [ 0, 1 ]\n },\n NODE: {\n size: 1,\n highlight: {\n color: 'yellow',\n labels: Label.DISPLAY_TYPES.ON,\n },\n labels: Label.DISPLAY_TYPES.ON,\n labelposition: Label.POSITION.OBJECT\n },\n POINT: {\n active: 2,\n size: 0.05,\n color: \"#000\",\n shape: Point.SHAPES.CIRCLE,\n labels: Label.DISPLAY_TYPES.AUTO,\n labelposition: Label.POSITION.OBJECT\n },\n MEAN: {\n shape: Point.SHAPES.SQUARE,\n labels: Label.DISPLAY_TYPES.AUTO,\n },\n LABEL: {\n highlight: Label.HIGHLIGHT.OFF,\n position: ['top', 'left'],\n container: \"#label-container\"\n },\n EDGE: {\n multiplier: 1\n }\n};\n\nexport class Graph {\n __state__: StateManager = new StateManager();\n\n name: string = \"unnamed-graph\";\n origin: AxisPoint \| undefined = undefined;\n\n options: typeof DefaultGraphOptions;\n\n points: Map<string, Point \| AxisPoint> = new Map();\n nodes: Map<string, Node> = new Map();\n edges: Map<string, Edge> = new Map();\n trajectories: Map<string, any> = new Map();\n labels: Map<string, Label> = new Map();\n transform: Transform = new Transform();\n\n scale_x: number = 1;\n scale_y: number = 1;\n\n _extremes!: Extremes;\n SIZE_EFFECT: number = 1;\n _mirror_y: boolean = true;\n _mirror_x: boolean = false;\n\n layers: LayerArray;\n _layers: LayerArray = new LayerArray(\n { name: \"graph\", tabindex: 0, layers: [\n { \n name: \"axes\",\n layers: [\n { \n name: \"axis_lines\", tabindex: 0, layers: [], \n objects: [\n\n ]\n },\n { \n name: \"axis_labels\", tabindex: 0, layers: [], objects: []\n },\n {\n name: \"axis_points\", \n tabindex: 0, \n layers: [], \n objects: [\n this.origin\n ]\n }\n ]\n },\n\n {\n name: \"network\",\n layers: [\n { name: \"edges\", layers: [], tabindex: 0 },\n { name: \"nodes\", layers: [], tabindex: 0 },\n { name: \"edgenodes\", layers: [], tabindex: 0 },\n ]\n },\n { name: \"trajectories\", layers: [], tabindex: 0 },\n { name: \"points\", layers: [], tabindex: 0 },\n\n { name: \"labels\", layers: [], tabindex: 0 },\n ] },\n );\n\n constructor(\n options: typeof DefaultGraphOptions = { ...DefaultGraphOptions }\n ) {\n this.options = options;\n \n this.origin = new AxisPoint(\n new DimensionVector(0, 0),\n {\n ID: \"origin\",\n x: 0, y: 0,\n size: 0,\n meta: {},\n graph: this,\n color: new Color(\"#FFFFFF\"),\n highlight: new Color(\"#FFFFFF\"),\n active: false\n }\n );\n\n let layer_id = 1;\n function buildLayerTree(layerData: any, parent: Layer \| null, graph: Graph): Layer {\n const new_layer = new Layer(`${layer_id}`, layerData, graph);\n layer_id += 1;\n new_layer.parent = parent \|\| undefined;\n if (layerData.layers && Array.isArray(layerData.layers)) {\n new_layer.layers = new LayerArray(...layerData.layers.map((child: any) => buildLayerTree(child, new_layer, graph)));\n }\n return new_layer;\n }\n\n this.layers = new LayerArray(...this._layers.map((l: any) => buildLayerTree(l, null, this)));\n\n let axisPointLayer: LayerLike \| undefined = this.layers.search(\"layers\", \"axis_points\");\n if (axisPointLayer) {\n axisPointLayer.objects.set(this.origin.ID, this.origin);\n }\n \n let axisLineLayer: LayerLike \| undefined = this.layers.search(\"layers\", \"axis_lines\");\n if (axisLineLayer) {\n let extremes = this.extremes \|\| new Extremes(1, 1);\n let axis_x = new Line(\n {}, \n new Point({ ID: \"axis-x-start\", dimensions: [-extremes.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] }), \n new Point({ ID: \"axis-x-end\", dimensions: [extremes.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] })\n );\n axis_x.ID = \"axis-x\";\n axisLineLayer.objects.set(axis_x.ID, axis_x);\n let axis_y = new Line(\n {}, \n new Point({ ID: \"axis-y-start\", dimensions: [0, -extremes.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] }),\n new Point({ ID: \"axis-y-end\", dimensions: [0, extremes.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] })\n );\n axis_y.ID = \"axis-y\";\n axisLineLayer.objects.set(axis_y.ID, axis_y);\n console.log(\"Added axis lines to layer: \", axisLineLayer);\n }\n\n // Define extremes based on options\n this.extremes = new Extremes(options.GRAPH.x_max, options.GRAPH.y_max);\n }\n\n set extremes(e: Extremes) {\n this._extremes = e;\n }\n get extremes(): Extremes {\n return this._extremes;\n }\n get mirror_x(): boolean {\n return this._mirror_x;\n }\n set mirror_x(m: boolean) {\n this._mirror_x = m;\n }\n get mirror_y(): boolean {\n return this._mirror_y;\n }\n set mirror_y(m: boolean) {\n this._mirror_y = m;\n }\n\n x_mirror(): number {\n return (this.mirror_x ? -1 : 1);\n }\n y_mirror(): number {\n return (this.mirror_y ? -1 : 1);\n }\n\n add_point(p: DataFrameRow) {\n const point: Point = new Point(p);\n this.points.set(point.ID, point);\n\n // if (g_.options.POINT && g_.options.POINT.label) {\n // p.label = new Label(p.meta[g_.options.POINT.label], p, g_);\n // g_.labels.set(p.label.ID, p.label);\n // }\n // g_.points.set(p.ID, p);\n // const pointsLayer = g_.layers.search(\"layers\", \"points\");\n // if (pointsLayer) {\n // pointsLayer.objects.push(p);\n // }\n // g_.update_extremes();\n }\n add_points(ps: DataFrame) {\n let g_ = this;\n ps.rows().forEach((p: DataFrameRow) => {\n g_.add_point(p);\n });\n }\n\n add_nodes(ns: any[]) {\n let\n g_ = this\n ;\n\n ns.forEach((new_node) => {\n // if (g_.options.NODE && g_.options.NODE.label) {\n // new_node.label = new Label(new_node.meta[g_.options.NODE.label], new_node, g_);\n new_node.label = new Label(new_node.ID, new_node);\n g_.labels.set(new_node.label.ID, new_node.label);\n // }\n g_.nodes.set(new_node.ID, new_node);\n const nodesLayer = g_.layers.search(\"layers\", \"nodes\");\n if (nodesLayer) {\n nodesLayer.objects.push(new_node);\n }\n });\n g_.update_extremes();\n }\n add_edge(e: any, from?: any, to?: any) {\n let g_ = this;\n g_.edges.set(e.ID, e);\n\n this.add_nodes([from \|\| e.from, to \|\| e.to]);\n\n return (e);\n }\n add_edges(es: any[]) {\n let added = es.map(e => this.add_edge(e));\n const edgesLayer = this.layers.search(\"layers\", \"edges\");\n if (edgesLayer) {\n edgesLayer.objects.push(...added);\n }\n return (added);\n }\n\n /*\n The visible extent: 1.3 × the farthest point or node. Centred on the\n * origin (the ENA convention: (0, 0) is the mean of the points), or with\n * `centerContent`, on the middle of the points' and nodes' bounding box, so\n * a network that sits off to one side of the origin fills the plot.\n /\n update_extremes(centerContent: boolean = false) {\n // let\n // dim1 = this.options.GRAPH.dimensions[0],\n // dim2 = this.options.GRAPH.dimensions[1],\n // // Get all points and nodes to calculate extremes\n // all_points = [...this.points.values(), ...this.nodes.values()].flat(),\n // x_max = Math.max(...all_points.map((p: PlottedObject) => Math.abs(p.dimension(dim1) \|\| 0))),\n // y_max = Math.max(...all_points.map((p: PlottedObject) => Math.abs(p.dimension(dim2) \|\| 0))),\n // max = Math.max(x_max, y_max)\n // ;\n // this.extremes = new Extremes(Math.ceil(max), Math.ceil(max), { x: 1, y: 1 }, { x: 1, y: 1 });\n\n const search_layers = [\n this.layers.search(\"layers\", \"points\"),\n this.layers.search(\"layers\", \"nodes\")\n ].filter((l): l is LayerLike => l !== undefined);\n if (search_layers.length === 0) {\n this.extremes = new Extremes(1, 1);\n }\n else {\n // Bound = largest \|x\|/\|y\| across points and nodes, plus a modest margin\n // for peripheral node labels. The previous Math.ceil() snapped this up to\n // the next integer, which — for ENA's small coordinate ranges (≈1–2) —\n // left the network floating in a lot of dead space. Keep the raw value so\n // the drawing fills the canvas.\n let minX = Infinity, maxX = -Infinity, minY = Infinity, maxY = -Infinity;\n search_layers.forEach(l => l.objects.forEach((o: any) => {\n if (Number.isFinite(o.x)) { minX = Math.min(minX, o.x); maxX = Math.max(maxX, o.x); }\n if (Number.isFinite(o.y)) { minY = Math.min(minY, o.y); maxY = Math.max(maxY, o.y); }\n }));\n const found = Number.isFinite(minX) && Number.isFinite(minY);\n const cx = centerContent && found ? (minX + maxX) / 2 : 0;\n const cy = centerContent && found ? (minY + maxY) / 2 : 0;\n const content_max = found\n ? Math.max(Math.abs(minX - cx), Math.abs(maxX - cx), Math.abs(minY - cy), Math.abs(maxY - cy))\n : 0;\n const found_max = (content_max > 0 ? content_max : 1) 1.3;\n this.extremes = new Extremes(found_max, found_max, cx, cy);\n }\n }\n\n /** Farthest node from (cx, cy), on either axis /\n nodeExtentFrom(cx: number, cy: number): number {\n const nodes = this.layers.search(\"layers\", \"nodes\");\n let max = 0;\n nodes?.objects.forEach((o: any) => {\n if (Number.isFinite(o.x) && Number.isFinite(o.y)) max = Math.max(max, Math.abs(o.x - cx), Math.abs(o.y - cy));\n });\n return max;\n }\n\n base_point_size(scale = 8): number {\n let minDim = Math.min(this.extremes.x_max, this.extremes.y_max);\n let n = this.points.size + this.nodes.size;\n return Math.min(1, minDim / (Math.sqrt(n) scale));\n }\n}\n","import { Graph } from \"../objects/Graph\";\nimport { Layer } from \"../objects/Layers\";\nimport { PlottedObject } from \"../objects/PlottedObject\";\n\nexport abstract class DrawableElement extends HTMLElement {\n \n static style: string = `\n :host {\n max-width: 100%;\n display: block;\n }\n .wrapper {\n height: 100%;\n display: flex;\n justify-content: center;\n }\n `;\n\n element: Element \| null = null;\n object: PlottedObject \| Graph \| Layer \| null = null;\n\n get wrapper() {\n const\n element = this,\n shadow = element.shadowRoot,\n wrapper = shadow?.querySelector(\".wrapper\")\n ;\n return wrapper;\n }\n\n constructor() {\n super();\n\n const\n element = this,\n shadow = element.attachShadow({ mode: 'open' }),\n style = document.createElement('style'),\n wrapper = document.createElement('div')\n ;\n\n style.textContent = (this.constructor as any).style;\n shadow.appendChild(style);\n\n wrapper.setAttribute('class', 'wrapper');\n shadow.appendChild(wrapper);\n }\n}","// Pure, DOM-free polynomial trajectory fitting.\n//\n// Ported from `ena.plot.trajectory()` in the ETM Explorer (RescuShell) R kit:\n// - near-origin filtering of the fit set (points at the cumulative origin are\n// drawn but excluded from the fit),\n// - `loocv_2d` degree selection (joint 2D leave-one-out CV via the hat-matrix\n// shortcut), with a `fixed` escape hatch,\n// - least-squares polynomial fit solved by QR for numerical parity with R's\n// `lm(y ~ poly(t, deg))`.\n//\n// Leverages and residuals depend only on the column space of the design, so a\n// raw monomial basis solved by QR reproduces R's selected degree and fitted\n// curve to floating-point tolerance despite R using orthogonal `poly()`.\n\n/** Near-origin tolerance; hardcoded to match the R kit's `zero_eps` default. /\nexport const TRAJECTORY_ZERO_EPS = 1e-8;\n\nexport interface XY {\n x: number;\n y: number;\n}\n\nexport type DegreeSelection = 'loocv_2d' \| 'fixed';\n\nexport interface TrajectoryFit {\n degree: number;\n coeffsX: number[];\n coeffsY: number[];\n}\n\n/* Drop near-origin points (both coords within eps of 0) from the fit set. /\nexport function nearOriginFilter(pts: XY[], eps: number = TRAJECTORY_ZERO_EPS): XY[] {\n return pts.filter(p => Math.abs(p.x) > eps \|\| Math.abs(p.y) > eps);\n}\n\n/* Evenly spaced parameter t in [0,1] by index — matches R's seq(0,1,length.out=n). /\nfunction normalizedT(n: number): number[] {\n if (n <= 0) return [];\n if (n === 1) return [0];\n const t = new Array(n);\n for (let i = 0; i < n; i++) t[i] = i / (n - 1);\n return t;\n}\n\n/* Vandermonde design [1, t, t^2, ..., t^deg], n×(deg+1). /\nfunction design(t: number[], degree: number): number[][] {\n return t.map(ti => {\n const row = new Array(degree + 1);\n let p = 1;\n for (let k = 0; k <= degree; k++) {\n row[k] = p;\n p = ti;\n }\n return row;\n });\n}\n\n/*\n Modified Gram-Schmidt QR. `A` is n×m (n >= m). Returns Q (n×m, orthonormal\n * columns) and R (m×m upper triangular). More stable than raw normal equations,\n * matching what R's `lm` does internally.\n /\nfunction qr(A: number[][]): { Q: number[][]; R: number[][] } {\n const n = A.length;\n const m = A[0].length;\n const Q = A.map(row => row.slice());\n const R = Array.from({ length: m }, () => new Array(m).fill(0));\n for (let j = 0; j < m; j++) {\n let norm = 0;\n for (let i = 0; i < n; i++) norm += Q[i][j] Q[i][j];\n norm = Math.sqrt(norm);\n R[j][j] = norm;\n if (norm > 1e-300) {\n for (let i = 0; i < n; i++) Q[i][j] /= norm;\n }\n for (let k = j + 1; k < m; k++) {\n let dot = 0;\n for (let i = 0; i < n; i++) dot += Q[i][j] * Q[i][k];\n R[j][k] = dot;\n for (let i = 0; i < n; i++) Q[i][k] -= dot * Q[i][j];\n }\n }\n return { Q, R };\n}\n\n/** Qᵀy (length m). /\nfunction qtY(Q: number[][], y: number[]): number[] {\n const n = Q.length;\n const m = Q[0].length;\n const out = new Array(m).fill(0);\n for (let j = 0; j < m; j++) {\n let s = 0;\n for (let i = 0; i < n; i++) s += Q[i][j] y[i];\n out[j] = s;\n }\n return out;\n}\n\n/** Back-substitution for R c = b, R upper triangular m×m. /\nfunction backSolve(R: number[][], b: number[]): number[] {\n const m = b.length;\n const c = new Array(m).fill(0);\n for (let i = m - 1; i >= 0; i--) {\n let s = b[i];\n for (let j = i + 1; j < m; j++) s -= R[i][j] c[j];\n c[i] = Math.abs(R[i][i]) > 1e-12 ? s / R[i][i] : 0;\n }\n return c;\n}\n\n/** Leverages h_ii = sum_j Q[i][j]^2 (diagonal of the hat matrix). /\nfunction leverages(Q: number[][]): number[] {\n return Q.map(row => {\n let s = 0;\n for (let j = 0; j < row.length; j++) s += row[j] row[j];\n return s;\n });\n}\n\n/** Least-squares monomial coefficients for y ~ poly(t, degree). /\nfunction fitCoeffs(t: number[], y: number[], degree: number): number[] {\n const X = design(t, degree);\n const { Q, R } = qr(X);\n return backSolve(R, qtY(Q, y));\n}\n\n/* Evaluate a monomial polynomial (ascending coeffs) at t. /\nexport function evalPoly(coeffs: number[], t: number): number {\n let v = 0;\n let p = 1;\n for (let k = 0; k < coeffs.length; k++) {\n v += coeffs[k] p;\n p = t;\n }\n return v;\n}\n\n/\n Joint 2D leave-one-out CV PRESS for a candidate degree. x(t) and y(t) share\n * one design (hence one hat matrix), so LOO residuals are e_i / (1 - h_ii).\n * Returns Infinity for a degenerate (saturated) fit so it is never selected.\n /\nfunction loocv2d(t: number[], x: number[], y: number[], degree: number): number {\n const X = design(t, degree);\n const { Q, R } = qr(X);\n const h = leverages(Q);\n const cx = backSolve(R, qtY(Q, x));\n const cy = backSolve(R, qtY(Q, y));\n let press = 0;\n for (let i = 0; i < t.length; i++) {\n const denom = 1 - h[i];\n if (denom <= 0) return Infinity;\n const ex = x[i] - evalPoly(cx, t[i]);\n const ey = y[i] - evalPoly(cy, t[i]);\n press += (ex / denom) * 2 + (ey / denom) 2;\n }\n return press;\n}\n\n/\n * Select a degree in 1..min(maxDegree, n-1). For `loocv_2d`, minimises the joint\n * 2D LOOCV PRESS; ties resolve to the smallest degree (matching R's which.min).\n * For `fixed`, or when there are too few points to run CV, returns the cap.\n /\nexport function selectDegree(fitPts: XY[], maxDegree: number, mode: DegreeSelection): number {\n const n = fitPts.length;\n const cap = Math.min(Math.max(1, Math.floor(maxDegree)), Math.max(1, n - 1));\n if (mode === 'fixed' \|\| n < 3) return cap;\n const t = normalizedT(n);\n const x = fitPts.map(p => p.x);\n const y = fitPts.map(p => p.y);\n let best = 1;\n let bestVal = Infinity;\n for (let deg = 1; deg <= cap; deg++) {\n const v = loocv2d(t, x, y, deg);\n if (v < bestVal) {\n bestVal = v;\n best = deg;\n }\n }\n return best;\n}\n\n/\n Fit a trajectory polynomial. The near-origin filter is applied to both the\n * per-frame points and the (optional) full-trajectory `selectionSet`. The degree\n * is chosen on `selectionSet` when given — so it stays constant as a playhead\n * scrubs a growing prefix — then clamped to what the current frame can support,\n * and the coefficients are re-fit on the current frame's points.\n \n Returns null when fewer than three non-origin points are available (matching\n * the R kit's n_fit < 3 guard); callers should fall back to raw steps.\n /\nexport function fitTrajectory(\n activePts: XY[],\n opts: { maxDegree: number; degreeSelection: DegreeSelection; selectionSet?: XY[] \| null }\n): TrajectoryFit \| null {\n const fitPts = nearOriginFilter(activePts);\n if (fitPts.length < 3) return null;\n\n const selBasis = opts.selectionSet ? nearOriginFilter(opts.selectionSet) : fitPts;\n const basis = selBasis.length >= 3 ? selBasis : fitPts;\n let degree = selectDegree(basis, opts.maxDegree, opts.degreeSelection);\n\n // A growing playhead prefix may hold fewer points than the held degree needs.\n degree = Math.min(degree, Math.max(1, fitPts.length - 1));\n\n const t = normalizedT(fitPts.length);\n const coeffsX = fitCoeffs(t, fitPts.map(p => p.x), degree);\n const coeffsY = fitCoeffs(t, fitPts.map(p => p.y), degree);\n return { degree, coeffsX, coeffsY };\n}\n\n/* Sample the fitted curve at steps+1 evenly spaced points over t in [0,1]. /\nexport function sampleCurve(fit: TrajectoryFit, steps = 100): XY[] {\n const out: XY[] = [];\n for (let s = 0; s <= steps; s++) {\n const t = s / steps;\n out.push({ x: evalPoly(fit.coeffsX, t), y: evalPoly(fit.coeffsY, t) });\n }\n return out;\n}\n","import { PlottedObject, PlottedObjectOptions, Point } from './PlottedObject';\nimport { Color } from './Color';\nimport { DegreeSelection, fitTrajectory, sampleCurve } from './polyfit';\n\nexport interface TrajectoryOptions {\n ID?: string;\n unitId?: string;\n points?: Point[] \| { x: number; y: number; time?: number; label?: string }[];\n color?: Color \| string;\n smooth?: 'none' \| 'poly' \| 'spline';\n maxDegree?: number;\n degreeSelection?: DegreeSelection;\n polyCoeffsX?: number[];\n polyCoeffsY?: number[];\n currentTime?: number;\n showPoints?: boolean;\n showTips?: boolean;\n lineStyle?: 'uniform' \| 'tapered';\n strokeWidth?: number;\n strokeWidthRange?: [number, number];\n opacityRange?: [number, number];\n size?: number;\n active?: boolean;\n meta?: any;\n [key: string]: any;\n}\n\nconst TRAJECTORY_CURVE_STEPS = 100;\n\nexport class Trajectory extends PlottedObject {\n readonly _typeName: string = 'Trajectory';\n trajPoints: Point[] = [];\n smooth: 'none' \| 'poly' \| 'spline' = 'none';\n maxDegree: number = 3;\n degreeSelection: DegreeSelection = 'loocv_2d';\n /* Degree chosen at the most recent fit; -1 until a poly curve is built. /\n selectedDegree: number = -1;\n polyCoeffsX: number[] = [];\n polyCoeffsY: number[] = [];\n currentTime: number = Infinity;\n showPoints: boolean = true;\n showTips: boolean = true;\n lineStyle: 'uniform' \| 'tapered' = 'uniform';\n strokeWidth: number = 2;\n strokeWidthRange: [number, number] = [1, 6];\n opacityRange: [number, number] = [0.3, 1];\n\n constructor(options: TrajectoryOptions = {}) {\n const defaultColor = options.color instanceof Color ? options.color : new Color(typeof options.color === 'string' ? options.color : '#000000');\n super([], {\n ID: options.ID \|\| `traj-${Math.random().toString(36).substring(2, 9)}`,\n size: options.size \|\| 1,\n color: defaultColor,\n highlight: null,\n active: options.active \|\| false,\n meta: options.meta \|\| {},\n ...options\n } as PlottedObjectOptions);\n\n this.smooth = options.smooth \|\| 'none';\n this.maxDegree = options.maxDegree !== undefined ? options.maxDegree : 3;\n this.degreeSelection = options.degreeSelection \|\| 'loocv_2d';\n this.polyCoeffsX = options.polyCoeffsX \|\| [];\n this.polyCoeffsY = options.polyCoeffsY \|\| [];\n this.currentTime = options.currentTime !== undefined ? options.currentTime : Infinity;\n this.showPoints = options.showPoints !== undefined ? options.showPoints : true;\n this.showTips = options.showTips !== undefined ? options.showTips : true;\n this.lineStyle = options.lineStyle \|\| 'uniform';\n this.strokeWidth = options.strokeWidth \|\| 2;\n this.strokeWidthRange = options.strokeWidthRange \|\| [1, 6];\n this.opacityRange = options.opacityRange \|\| [0.3, 1];\n\n if (options.points && Array.isArray(options.points)) {\n this.trajPoints = options.points.map(p => {\n if (p instanceof Point) return p;\n const pt = new Point({ dimensions: [p.x, p.y], meta: { time: p.time, label: p.label } });\n pt.x = p.x;\n pt.y = p.y;\n return pt;\n });\n }\n }\n\n get activePoints(): Point[] {\n if (this.currentTime === Infinity) {\n return this.trajPoints;\n }\n return this.trajPoints.filter(p => {\n const t = (p.meta && typeof p.meta.time === 'number') ? p.meta.time : 0;\n return t <= this.currentTime;\n });\n }\n\n get path(): string {\n return this.pathPoints.reduce((acc, pt, idx) => {\n return idx === 0 ? `M${pt.x},${pt.y}` : `${acc} L${pt.x},${pt.y}`;\n }, '');\n }\n\n get pathPoints(): Array<{ x: number; y: number }> {\n const pts = this.activePoints;\n if (pts.length < 2) return [];\n\n if (this.smooth === 'poly') {\n // Precomputed coefficients override the fit (caller-supplied curve).\n if (this.polyCoeffsX.length > 0 && this.polyCoeffsY.length > 0) {\n return sampleCurve(\n { degree: this.polyCoeffsX.length - 1, coeffsX: this.polyCoeffsX, coeffsY: this.polyCoeffsY },\n TRAJECTORY_CURVE_STEPS\n );\n }\n\n // Select the degree on the full trajectory so it stays constant while a\n // playhead scrubs a growing prefix; fit coefficients on the visible frame.\n const fit = fitTrajectory(\n pts.map(p => ({ x: p.x, y: p.y })),\n {\n maxDegree: this.maxDegree,\n degreeSelection: this.degreeSelection,\n selectionSet: this.trajPoints.map(p => ({ x: p.x, y: p.y }))\n }\n );\n if (fit) {\n this.selectedDegree = fit.degree;\n return sampleCurve(fit, TRAJECTORY_CURVE_STEPS);\n }\n // Too few non-origin points to fit — fall back to raw steps below.\n }\n\n return pts.map(pt => ({ x: pt.x, y: pt.y }));\n }\n}\n","import { PlottedObject, Line, PlottedObjectOptions } from './PlottedObject.js';\nimport { Node } from './Points.js';\nimport { Color, WeightedColor } from './Color.js';\nimport { Tools } from '../utils/Tools.js';\nimport { DataFrameRow } from '../types/DataFrame.js';\n\n// Placeholder for zoom level, should be defined in the context of the application\nconst zoom_level = 1;\n\nexport class Edge extends Line {\n declare from: Node;\n declare to: Node;\n _totalweight: number = 0;\n _weight: number;\n declare _color: WeightedColor;\n\n constructor(data: DataFrameRow \| any, from: Node, to: Node, weight: number = 0) {\n super(data, from, to);\n this._weight = weight;\n }\n\n get base_color(): Color { return this._color };\n get color(): WeightedColor {\n const base = this._color \|\| new Color(\"#000000\");\n return new WeightedColor(base, Math.abs(this.weight));\n }\n set color(c: Color) { this._color = c as any; }\n\n base_weight() { return this._weight };\n get weight() {\n // let w = Array.isArray(this.#weight) ? this.#weight.reduce( (a, b) => a - b, 0) : this.#weight;\n let w = Array.isArray(this._weight) ? (this._weight[0] - this._weight[1]) : this._weight;\n return w; // this.graph.options.EDGE.multiplier\n }\n set weight(w) {\n this._weight = w;\n }\n\n get totalweight(): number {\n return this.weight;\n }\n set totalweight(w: number) {\n this._totalweight = w;\n }\n}\n\nexport class SubtractedEdges extends Edge {\n edge_one: Edge;\n edge_two: Edge;\n\n #weight: number;\n #color: WeightedColor;\n\n constructor(e1: Edge, e2: Edge) {\n super(e1, e1.from, e1.to);\n\n this.edge_one = e1;\n this.edge_two = e2;\n\n this.#weight = this.edge_one.weight - this.edge_two.weight;\n\n let\n color_type_fn: new (color: Color \| string, weight: number) => WeightedColor = this.edge_one.color.constructor as any,\n color: string = this.edge_one.color.base\n ;\n if (this.weight > 0) {\n color = this.edge_one.color.base;\n }\n else {\n color = this.edge_two.color.base;\n }\n\n this.#color = new color_type_fn(color, this.#weight);\n }\n\n get weight() {\n return this.#weight;\n }\n set weight(w) {\n this.#weight = w;\n }\n\n get color() {\n return this.#color;\n }\n set color(c) {\n this.#color = c;\n }\n}\n\nexport class MeanEdge extends Edge {\n edges: Set<Edge> = new Set<Edge>();\n\n constructor(o: any) {\n super(o, o.from, o.to);\n\n this.visible = true;\n // this.meta = o.meta \|\| { ID: this.ID };\n }\n\n // get weight() { return __.math.mean([...this.edges.values()].map( e => e.weight )) * this.graph.options.EDGE.multiplier; }\n get weight() {\n let wt = Tools.Mathematics.mean([...this.edges.values()].map((e: Edge) => e.weight)) * 1;\n return wt;\n }\n set weight(w) { this._weight = w; }\n\n get path() {\n return `M${this.from.x} ${this.from.y} L${this.to.x} ${this.to.y}z`;\n }\n\n get totalweight() {\n return Array.from(this.edges).reduce((acc, edge) => acc + edge.totalweight, 0);\n }\n}\n\nexport class EdgeArrow extends PlottedObject {\n #edge;\n\n constructor(edge: PlottedObjectOptions) {\n super(edge.dimensions \|\| [], edge);\n this.#edge = edge;\n }\n\n get edge() {\n return this.#edge;\n }\n\n get path(): string {\n /*\n \n * mid_int0 nock_int0\n * --------------------------------- <- edge of arrow from midpoint to base_pt0\n * / /\n * / /\n * / /\n * / /\n * / /\n * / /\n * <-- edge node head--> * * * <-- nock ---> edge midpoint this way ---->\n * \\ ^-mid \|\n * \\ \| \\ \|\n * \\ \| \\ \| <---- showing line from nock to edge used to find\n * \\ \| \\ \| intersection with edge\n * \\\| \\\|\n * --------------------------------- <- edge of arrow from midpoint to base_pt1\n * mid_int1---^ ^----nock_int1\n \n /\n // Pure vector geometry on the tapered edge: T = target (wide end, base\n // points B0/B1), A = apex. The chevron sits 20% of the way from T toward\n // A, but its length follows the triangle's local width (≈ a constant\n // shape) rather than a fixed share of the edge length — on long, thin\n // edges the old fractional sizing stretched it into a sliver. (The old\n // slope-intercept intersections also misbehaved on near-vertical edges.)\n const _this = this.#edge;\n const T: [number, number] = [_this.to.x, _this.to.y];\n const A: [number, number] = _this.from_point;\n const [B0, B1] = _this.base_pts as [[number, number], [number, number]];\n const L = Math.hypot(A[0] - T[0], A[1] - T[1]);\n const W = Math.hypot(B0[0] - B1[0], B0[1] - B1[1]);\n if (!(L > 0) \|\| !(W > 0)) return '';\n const u = [(A[0] - T[0]) / L, (A[1] - T[1]) / L]; // along the edge, T → A\n const b = Math.hypot(B0[0] - T[0], B0[1] - T[1]);\n const v = [(B0[0] - T[0]) / b, (B0[1] - T[1]) / b]; // across, toward B0\n const halfW = (d: number) => (W / 2) * Math.max(0, 1 - d / L);\n const at = (d: number, s: number) => `${T[0] + u[0] * d + v[0] * s} ${T[1] + u[1] * d + v[1] * s}`;\n\n const dh = 0.2 * L; // head\n const c = Math.min(0.15 * L, 0.8 * 2 * halfW(dh)); // length ≈ local width\n const dm = dh + c / 2, dn = dh + c; // notch, back\n const p = `M${at(dh, 0)} L${at(dm, halfW(dm))} L${at(dn, halfW(dn))} ` +\n `L${at(dm, 0)} L${at(dn, -halfW(dn))} L${at(dm, -halfW(dm))}z`;\n return p;\n }\n}\n\nexport enum EdgeDirection {\n FROM = 'from',\n TO = 'to'\n}\n\nexport class TaperedEdge extends Edge {\n // base_pts = [];\n _path: string = '';\n // Arrowheads are off by default — the tapered triangle shape already\n // communicates direction. Enabling #with_arrow currently throws because\n // EdgeArrow.constructor passes the edge as the lone super() arg.\n #with_arrow = false;\n #arrow;\n\n _directions: EdgeDirection[] = [EdgeDirection.FROM, EdgeDirection.TO];\n towards: EdgeDirection = EdgeDirection.TO;\n\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n\n if (this.#with_arrow === true) {\n this.#arrow = new EdgeArrow(this);\n }\n }\n\n get path(): string {\n return `M${this.from.x} ${this.from.y} L${this.base_pts[0].join(' ')} L${this.base_pts[1].join(' ')}z`;\n }\n static calculate_base_points(edg: TaperedEdge): [[number, number], [number, number]] {\n // Find the two endpoints of the tapered edge based on its `towards` direction.\n const top: EdgeDirection = edg.towards;\n const base: EdgeDirection = edg._directions.find(d => d !== edg.towards) as EdgeDirection;\n\n const bx = edg[base].x, by = edg[base].y;\n const tx = edg[top].x, ty = edg[top].y;\n const dx = tx - bx, dy = ty - by;\n const L = Math.hypot(dx, dy);\n\n // Degenerate: zero-length edge or unset weight — collapse to a point at `top`.\n const wt = (edg.weight ?? 0) * zoom_level;\n if (L === 0 \|\| !isFinite(wt) \|\| wt === 0) {\n return [[tx, ty], [tx, ty]];\n }\n\n // Unit perpendicular to the edge direction; offset both sides by wt/2.\n // Pure vector math here avoids the slope-intercept form used by\n // Tools.Geometry, which produces NaN for vertical edges and ill-conditioned\n // values for horizontal ones.\n const px = -dy / L, py = dx / L;\n const halfW = wt / 2;\n return [\n [tx + px * halfW, ty + py * halfW],\n [tx - px * halfW, ty - py * halfW],\n ];\n }\n get base_pts() {\n return TaperedEdge.calculate_base_points(this);\n }\n get arrow() {\n return this.#arrow;\n }\n get with_arrow() {\n return this.#with_arrow;\n }\n get from_point() {\n return [this.from.x, this.from.y];\n }\n}\n\nexport class TaperedMidpointEdge extends TaperedEdge {\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n }\n\n get path(): string {\n return `M${this.midpoint[0]} ${this.midpoint[1]} L${this.base_pts[0].join(' ')} L${this.base_pts[1].join(' ')}z`;\n }\n get from_point(): [number, number] {\n return this.midpoint;\n }\n}\n\nexport class TaperedWeightedMidpointEdge extends TaperedEdge {\n // Preserve the original data weight so that QELine.update()'s\n // `edge.weight = sw * 4` (which sets _weight for display sizing) doesn't\n // corrupt the midpoint calculation.\n private _dataWeight: number = 0;\n\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n this._totalweight = data.totalweight ?? 0;\n this._dataWeight = data.weight ?? this._weight;\n }\n\n get weighted_midpoint(): [number, number] {\n return Tools.Geometry.Line.interpolate(this.line)(1 - (this._dataWeight / this._totalweight));\n }\n\n get base_pts(): [[number, number], [number, number]] {\n return TaperedEdge.calculate_base_points(this);\n }\n\n static build_path(edg: TaperedWeightedMidpointEdge \| MeanTaperedWeightedMidpointEdge): string {\n if (edg._totalweight > 0) {\n let p = `M${edg.weighted_midpoint[0]} ${edg.weighted_midpoint[1]} L${edg.base_pts[0].join(' ')} L${edg.base_pts[1].join(' ')}z`;\n\n return p\n }\n else {\n console.error(\"TaperedWeightedMidpointEdge: No totalweight, returning empty path\");\n return '';\n }\n }\n get path(): string {\n return TaperedWeightedMidpointEdge.build_path(this);\n }\n\n get from_point() {\n return this.weighted_midpoint;\n }\n}\n\nexport class MeanNodeEdge extends MeanEdge {\n constructor(o: any) {\n super(o);\n }\n get path() {\n return NodeEdge.build_path(this.weight, [...this.edges.values()][0].to)\n }\n get weight() {\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.weight)) * 1;\n }\n set weight(w) { this._weight = w; }\n}\n\nexport class MeanTaperedEdge extends MeanEdge {\n #with_arrow = true;\n #arrow;\n\n constructor(o: PlottedObjectOptions) {\n super(o);\n\n if (this.#with_arrow === true) {\n this.#arrow = new EdgeArrow(this);\n }\n }\n\n get with_arrow() {\n return this.#with_arrow;\n }\n get arrow() {\n return this.#arrow;\n }\n get from_point() {\n return [this.from.x, this.from.y];\n }\n}\n\nexport class MeanTaperedMidpointEdge extends MeanTaperedEdge {\n constructor(o: PlottedObjectOptions) {\n super(o);\n }\n\n get base_pts(): [[number, number], [number, number]] {\n const\n top = EdgeDirection.TO,\n base = EdgeDirection.FROM\n ;\n\n let\n edge_line: [[number, number], [number, number]] = [[this[base].x, this[base].y], [this[top].x, this[top].y]],\n perp_line = Tools.Geometry.Line.rotate2(edge_line, edge_line[1], 90),\n ints = Tools.Geometry.Line.intersect_circle(perp_line, edge_line[1], this.weight / 2)\n ;\n\n return ints;\n }\n get path(): string {\n return `M${this.midpoint[0]} ${this.midpoint[1]} L${this.base_pts[0].join(' ')} L${this.base_pts[1].join(' ')}z`;\n }\n get weight(): number {\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.weight)) * 1;\n }\n set weight(w) { this._weight = w; }\n}\n\nexport class MeanTaperedWeightedMidpointEdge extends MeanTaperedEdge {\n constructor(o: PlottedObjectOptions) {\n super(o);\n }\n\n get totalweight(): number {\n // debugger;\n // console.error(\"THIS NEEDS THE MEAN WEIGHT OF ITS COUNTERPART (FROM -> TO -- TO --> FROM)\")\n // or does the mean of the edges.totalweight equal to the same?\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.totalweight));\n }\n\n get weighted_midpoint() {\n // console.log(\"Weighted: \", this.weight, this.totalweight)\n return Tools.Geometry.Line.interpolate(this.line)(1 - (this.weight / this.totalweight))\n }\n\n get base_pts() {\n const\n top = EdgeDirection.TO, //this.#directions[this.#directions.findIndex( d => d === this.towards )],\n base = EdgeDirection.FROM //this.#directions[this.#directions.findIndex( d => d !== this.towards )]\n ;\n\n let\n edge_line: [[number, number], [number, number]] = [[this[base].x, this[base].y], [this[top].x, this[top].y]],\n perp_line = Tools.Geometry.Line.rotate2(edge_line, edge_line[1], 90),\n ints = Tools.Geometry.Line.intersect_circle(perp_line, edge_line[1], this.weight / 2)\n ;\n\n return ints;\n }\n\n get path() {\n let p = TaperedWeightedMidpointEdge.build_path(this)\n // console.log(\"Static p: \", p);\n return p;\n }\n get weight() {\n return Tools.Mathematics.mean([...this.edges.values()].map(e => e.weight)) * 1;\n }\n set weight(w) { this._weight = w; }\n}\n\nexport class NodeEdge extends Edge {\n\n constructor(data: any, from: Node, to: Node) {\n super(data, from, to);\n }\n\n static build_path(weight: number, to: Node) {\n let\n R = weight / 2,\n CX = to.x - R,\n R2 = R * 2,\n p = `M ${CX}, ${to.y} a ${R},${R} 0 1,0 ${R2},0 a ${R},${R} 0 1,0 -${R2},0`\n ;\n\n return p;\n }\n\n get path() {\n let wt = this.weight * zoom_level; //this.graph.get_graphs()[0].object.SIZE_EFFECT;\n return NodeEdge.build_path(wt, this.to);\n }\n}\n","import { PlottedObject } from \"../objects/PlottedObject\";\nimport { QEArray, } from \"./QELayer\";\nimport { QEGraphElement } from \"./QEGraph\";\n\nexport abstract class Drawable {\n abstract create(): SVGElement;\n \n svg_element: SVGElement;\n\n constructor(\n public __data__: PlottedObject, \n public parent: SVGElement, \n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray()\n ) {\n this.svg_element = this.create();\n }\n\n get_size() {\n return this.__data__.size;\n }\n\n draw() {\n this.parent?.appendChild(this.svg_element);\n }\n\n update(elem: SVGElement, animate = true) {\n // this.update(elem);\n }\n\n animateSVGAttribute(elem: SVGElement, attr: string, to: number) {\n const from = parseFloat(elem.getAttribute(attr) \|\| '0');\n if (from === to) return;\n\n const duration = 5000;\n const start = performance.now();\n function animate(now: number) {\n const t = Math.min(1, (now - start) / duration);\n const value = from + (to - from) * t;\n elem.setAttribute(attr, value.toString());\n if (t < 1) requestAnimationFrame(animate);\n else elem.setAttribute(attr, to.toString());\n }\n requestAnimationFrame(animate);\n }\n}\n","// Shared mark-size and colour rules, sizes in units of the coordinate extent.\n//\n// Width follows webENA: absolute, raw weight × a constant (`edge-width`, as a\n// fraction of the plot width), so equal weights draw equally wide in graphs of\n// the same size. That one width-per-weight drives undirected strokes, the\n// wide ends of directed edges, self-connection dots, and code nodes (whose\n// diameter is the sum of their edges' widths).\n//\n// Colour follows webENA's ramps (saturation 0.25–1, opacity 0.3–1), but the\n// rescaling range is taken across the whole model rather than per network.\n\n/** Default `<qe-graph edge-width>`: the width of an edge of weight 1 as a\n * fraction of the plot width. Width is absolute — raw weight × this — as in\n * webENA, so equal weights get equal widths in graphs of the same size. /\nexport const DEFAULT_EDGE_WIDTH = 0.04;\n\n/* webENA's colour ramps: non-zero weights are rescaled linearly from the\n * reference [min, max] onto these saturation and opacity ranges. /\nexport const SATURATION_RANGE: [number, number] = [0.25, 1];\nexport const OPACITY_RANGE: [number, number] = [0.3, 1];\n\n/* Linear map of \|w\| from [lo, hi] onto `range`; 0 stays 0 (not drawn). /\nexport function rampFor(w: number, lo: number, hi: number, range: [number, number]): number {\n const a = Math.abs(w);\n if (!(a > 0)) return 0;\n if (!(hi > lo)) return range[1];\n const t = Math.min(1, Math.max(0, (a - lo) / (hi - lo)));\n return range[0] + t (range[1] - range[0]);\n}\n\n/** Edge stroke width for edges drawn outside the network rule (fallback). /\nexport const EDGE_WIDTH_PER_EXTENT = 0.011;\n\n/* On-screen width (CSS px) of the outline drawn around directed (tapered)\n * edges so long, thin triangles stay legible along their whole length. /\nexport const TAPERED_OUTLINE_PX = 0.75;\n\n/* Direction chevrons on directed edges: RGB multiplier applied to the\n * (opaque, white-flattened) edge colour, and the white halo's on-screen\n * width in CSS px. /\nexport const CHEVRON_DARKEN = 0.8;\nexport const CHEVRON_HALO_PX = 0.75;\n\n/* Point radius per unit of `size` (QEPoint). /\nexport const POINT_RADIUS_PER_EXTENT = 0.006;\n\n/* `size` for a code node with no drawn edges: a tiny dot that still marks\n * where the code sits (hide it with <qe-nodes unconnected=\"hide\">). /\nexport const UNCONNECTED_NODE_SIZE = 0.6;\n\n/* Width per unit of weight in extent units (plot width = 2 × extent). /\nexport function widthPerWeight(edgeWidth: number): number {\n return 2 edgeWidth;\n}\n\n/** QEPoint `size` for a node whose diameter equals the summed widths of its\n * edges, `weightSum × widthFrac` (both in extent units). /\nexport function nodeSizeForEdges(weightSum: number, widthFrac: number): number {\n return (weightSum widthFrac) / (2 * POINT_RADIUS_PER_EXTENT);\n}\n","import { Line } from \"../objects/PlottedObject\";\nimport { NodeEdge, TaperedEdge, EdgeArrow } from \"../objects/Edges\";\nimport { Color, WeightedColor } from \"../objects/Color\";\nimport { Drawable } from \"./Drawable\";\nimport { QEArray, QEElement } from \"./QELayer\";\nimport { QEGraphElement } from \"./QEGraph\";\nimport { CHEVRON_DARKEN, CHEVRON_HALO_PX, EDGE_WIDTH_PER_EXTENT, TAPERED_OUTLINE_PX } from \"../objects/Sizing\";\n\n/** Composite an rgba() colour over white, returning an opaque rgb(). /\nfunction flattenOnWhite(col: string): string {\n const m = /rgba?\$([^)]+)\$/.exec(col);\n if (!m) return col;\n const [r, g, b, a = 1] = m[1].split(',').map(Number);\n const f = (c: number) => Math.round(255 + (c - 255) a);\n return `rgb(${f(r)},${f(g)},${f(b)})`;\n}\n\n/** Scale an rgba()/rgb() colour's RGB channels by `k` (alpha unchanged). /\nfunction darkenRgba(col: string, k: number): string {\n const m = /rgba?\$([^)]+)\$/.exec(col);\n if (!m) return col;\n const [r, g, b, a = 1] = m[1].split(',').map(Number);\n return `rgba(${Math.round(r k)},${Math.round(g * k)},${Math.round(b * k)},${a})`;\n}\n\nexport class QELine extends Drawable implements QEElement {\n __name__: string = \"unnamed-line\";\n // Optional second element for the direction-indicator chevron on directed edges.\n private _arrow_el: SVGPathElement \| null = null;\n // Invisible wide companion line giving thin undirected edges a clickable/\n // hoverable hit target for the qe-edge-* interaction events.\n private _hit_el: SVGLineElement \| null = null;\n\n /** Stamp edge identity onto an element so <qe-graph> delegation can resolve\n * qe-edge-* events. No-op for non-edges (e.g. axis lines). /\n private _stampEdge(el: SVGElement): void {\n const meta = (this.__data__ as any).meta ?? {};\n if (!meta.isMeanEdge) return;\n el.setAttribute('data-edge-source', String(meta.source ?? ''));\n el.setAttribute('data-edge-target', String(meta.target ?? ''));\n el.setAttribute('data-edge-weight', String(meta.weight ?? 0));\n el.setAttribute('data-edge-directed', meta.isDirected ? 'true' : 'false');\n if (meta.isSelf) el.setAttribute('data-edge-self', 'true');\n if (meta.group != null) el.setAttribute('data-edge-group', String(meta.group));\n if (meta.unit != null) el.setAttribute('data-edge-unit', String(meta.unit));\n }\n\n constructor(\n public __data__: Line,\n public parent: SVGElement,\n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray(),\n ) {\n super(__data__, parent, graph, __children__);\n\n this.svg_element = this.create();\n }\n\n create() {\n if (this.__data__ instanceof NodeEdge) {\n // Self-connection: filled circle inside the node, sized by weight.\n const path = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n path.setAttribute('fill', this.__data__.color.toString());\n path.setAttribute('stroke', 'none');\n this.svg_element = path;\n return path;\n }\n\n if (this.__data__ instanceof TaperedEdge) {\n // Directed edges render as filled triangles via TaperedEdge.path.\n // A second SVG path is reserved for the direction-indicator chevron;\n // it is populated lazily in update() once meta.isDirected is known.\n const path = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n path.setAttribute('fill', this.__data__.color.toString());\n path.setAttribute('stroke', 'none');\n this.svg_element = path;\n return path;\n }\n\n const line = document.createElementNS('http://www.w3.org/2000/svg', 'line');\n line.setAttribute('x1', this.__data__.from.x.toString());\n line.setAttribute('y1', this.__data__.from.y.toString());\n line.setAttribute('x2', this.__data__.to.x.toString());\n line.setAttribute('y2', this.__data__.to.y.toString());\n line.setAttribute('stroke-width', this.get_size().toString());\n line.setAttribute('stroke', this.__data__.color.toString());\n\n this.svg_element = line;\n return line;\n }\n\n update() {\n if (!this.svg_element) {\n this.create();\n }\n if (!this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n\n const extent = (this.graph.__data__ as any).extremes?.x_max ?? 1;\n const meta = (this.__data__ as any).meta ?? {};\n\n if (meta.isMeanEdge) {\n this._stampEdge(this.svg_element);\n const weight = typeof meta.weight === 'number' ? meta.weight : 0;\n const maxW = typeof meta.maxWeight === 'number' ? meta.maxWeight : 1;\n const opacity = typeof meta.opacity === 'number' ? meta.opacity : Math.min(1, weight / (maxW \|\| 1));\n // Target ≈ multiplier×5 in plotly-px to match rENA (ena.plot.network\n // default: multiplier=5, width = raw_weight × 5). For a ±2.66-extent\n // coordinate space rendered at ~460px, 1 data-unit ≈ 86px, so\n // rENA's max stroke (0.47 × 5 ≈ 2.4px) ≈ 0.028 data units.\n // Factor 0.011 × extent(2.66) × 1.0 ≈ 0.029 → ~2.5px at 86px/unit.\n // Width = weight × the plot's shared width-per-weight (objects/Sizing.ts);\n // the fallback keeps edges visible if an edge arrives without one.\n const ext = extent > 0 ? extent : 1;\n const sw = typeof meta.widthFrac === 'number'\n ? ext meta.widthFrac * weight\n : ext * EDGE_WIDTH_PER_EXTENT * (weight / (maxW \|\| 1));\n\n // Build a WeightedColor from the stored base color + normalized weight so\n // that toString() produces hsla(h, sw%, l%, w) — matching the Web ENA\n // convention of scaling both saturation and alpha together with weight.\n const baseColor = (this.__data__ as any)._color \|\| new Color('#000000');\n // Saturation and opacity come from the graph's colour ramps\n // (<qe-edges color-scale>); older edges carry only opacity.\n const saturation = typeof meta.saturation === 'number' ? meta.saturation : opacity;\n const edgeColor = new WeightedColor(baseColor, saturation, opacity).toString();\n\n if (this.__data__ instanceof NodeEdge) {\n // Diameter = the self weight's width (same width-per-weight as edges\n // and nodes), matching ona. The node's diameter includes this self\n // weight, so the dot always fits inside it. Computed here because the\n // live extent is not known when the edge objects are built.\n (this.__data__ as NodeEdge).weight = sw;\n (this.svg_element as SVGPathElement).setAttribute('d', (this.__data__ as NodeEdge).path);\n this.svg_element.setAttribute('fill', edgeColor);\n this.svg_element.setAttribute('stroke', 'none');\n } else if (this.__data__ instanceof TaperedEdge) {\n // TaperedEdge.path uses .weight as the total base width (the wide end,\n // at the target node); node sizes sum these base widths.\n (this.__data__ as TaperedEdge).weight = sw;\n (this.svg_element as SVGPathElement).setAttribute('d', (this.__data__ as TaperedEdge).path);\n this.svg_element.setAttribute('fill', edgeColor);\n // Hairline outline (constant on-screen width, same weighted colour as\n // the fill). A long, thin triangle tapers below a pixel for most of its\n // length; the outline keeps the whole connection legible without\n // changing its width or colour encoding (ona draws a similar halo).\n this.svg_element.setAttribute('stroke', edgeColor);\n this.svg_element.setAttribute('stroke-width', String(TAPERED_OUTLINE_PX));\n this.svg_element.setAttribute('vector-effect', 'non-scaling-stroke');\n this.svg_element.setAttribute('stroke-linejoin', 'round');\n\n // ── Direction-indicator chevron ──────────────────────────────────────\n // For directed mean edges, overlay an EdgeArrow chevron filled with a\n // more-opaque/saturated version of the edge colour. Rendered over the\n // semi-transparent triangle body, the fully-opaque fill reads as a\n // visibly darker notch that indicates the direction without introducing\n // a foreign colour.\n if (meta.isDirected) {\n try {\n const arrow = new EdgeArrow(this.__data__ as any);\n const arrowPath = arrow.path;\n // Discard degenerate paths that contain NaN or Infinity (geometry\n // collapsed — zero-length edge, parallel lines, etc.).\n if (arrowPath && !arrowPath.includes('NaN') && !arrowPath.includes('Infinity')) {\n if (!this._arrow_el) {\n this._arrow_el = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n this._arrow_el.setAttribute('stroke', 'none');\n }\n if (!this._arrow_el.parentElement) {\n this.parent.appendChild(this._arrow_el);\n }\n this._arrow_el.setAttribute('d', arrowPath);\n // As ona draws arrows: the edge's weighted colour flattened onto\n // white (\"fake alpha\", so it is opaque and weak edges still get\n // lighter chevrons), then darkened — plus ona's optional white\n // halo, at a constant on-screen width, so it stands out from the\n // triangle it sits on.\n this._arrow_el.setAttribute('fill', darkenRgba(flattenOnWhite(edgeColor), CHEVRON_DARKEN));\n this._arrow_el.setAttribute('stroke', '#ffffff');\n this._arrow_el.setAttribute('stroke-width', String(CHEVRON_HALO_PX));\n this._arrow_el.setAttribute('vector-effect', 'non-scaling-stroke');\n this._arrow_el.setAttribute('stroke-linejoin', 'round');\n }\n } catch (_) {\n // EdgeArrow geometry degenerates for very short or zero-weight edges —\n // silently skip rather than crashing the render loop.\n }\n }\n } else {\n // Regular undirected edge\n const x1 = this.__data__.from.x, y1 = this.__data__.from.y;\n const x2 = this.__data__.to.x, y2 = this.__data__.to.y;\n (this.svg_element as SVGLineElement).setAttribute('x1', x1.toString());\n (this.svg_element as SVGLineElement).setAttribute('y1', y1.toString());\n (this.svg_element as SVGLineElement).setAttribute('x2', x2.toString());\n (this.svg_element as SVGLineElement).setAttribute('y2', y2.toString());\n this.svg_element.setAttribute('stroke-width', sw.toString());\n this.svg_element.setAttribute('stroke', edgeColor);\n this.svg_element.setAttribute('pointer-events', 'stroke');\n this.svg_element.removeAttribute('marker-end');\n\n // Transparent wide hit target so thin edges are clickable/hoverable.\n // Sized to a comfortable minimum regardless of the visible stroke width.\n if (!this._hit_el) {\n this._hit_el = document.createElementNS('http://www.w3.org/2000/svg', 'line');\n this._hit_el.setAttribute('stroke', 'transparent');\n this._hit_el.setAttribute('stroke-linecap', 'round');\n this._hit_el.setAttribute('pointer-events', 'stroke');\n }\n if (!this._hit_el.parentElement) this.parent.appendChild(this._hit_el);\n this._hit_el.setAttribute('x1', x1.toString());\n this._hit_el.setAttribute('y1', y1.toString());\n this._hit_el.setAttribute('x2', x2.toString());\n this._hit_el.setAttribute('y2', y2.toString());\n this._hit_el.setAttribute('stroke-width', Math.max(sw, extent 0.03).toString());\n this._stampEdge(this._hit_el);\n }\n } else {\n // Thin axis lines: ~0.4% of coordinate extent\n (this.svg_element as SVGLineElement).setAttribute('x1', this.__data__.from.x.toString());\n (this.svg_element as SVGLineElement).setAttribute('y1', this.__data__.from.y.toString());\n (this.svg_element as SVGLineElement).setAttribute('x2', this.__data__.to.x.toString());\n (this.svg_element as SVGLineElement).setAttribute('y2', this.__data__.to.y.toString());\n const sw = (extent > 0 ? extent : 1) * 0.004 * this.get_size();\n this.svg_element.setAttribute('stroke-width', sw.toString());\n this.svg_element.setAttribute('stroke-opacity', '1');\n this.svg_element.setAttribute('stroke', this.__data__.color.toString());\n }\n }\n\n draw() {\n if (this._hit_el) this.parent?.appendChild(this._hit_el);\n this.parent?.appendChild(this.svg_element);\n if (this._arrow_el) {\n this.parent?.appendChild(this._arrow_el);\n }\n }\n}\n","import { PlottedObject } from \"../objects/PlottedObject\";\nimport { Drawable } from \"./Drawable\";\nimport { QEArray, QEElement } from \"./QELayer\";\nimport { QEGraphElement } from \"./QEGraph\";\nimport { POINT_RADIUS_PER_EXTENT } from \"../objects/Sizing\";\n\nexport class QEPoint extends Drawable implements QEElement {\n __name__: string = \"unnamed-point\";\n\n constructor(\n public __data__: PlottedObject,\n public parent: SVGElement,\n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray(),\n ) {\n super(__data__, parent, graph, __children__);\n\n this.svg_element = this.create();\n }\n\n get x() {\n return this.__data__.dimensions[this.graph.__data__.options.GRAPH.dimensions[0]];\n }\n get y() {\n return this.__data__.dimensions[this.graph.__data__.options.GRAPH.dimensions[1]];\n }\n\n get isSquare(): boolean {\n return (this.__data__ as any).shape === 'rect';\n }\n\n /** \"circle\" (default) \| \"rect\" \| \"triangle\" \| \"diamond\". /\n get shapeKind(): 'circle' \| 'rect' \| 'triangle' \| 'diamond' {\n const s = (this.__data__ as any).shape;\n return s === 'rect' \|\| s === 'square' ? 'rect'\n : s === 'triangle' \|\| s === 'diamond' ? s : 'circle';\n }\n\n /* SVG tag for the current shape. /\n private get tag(): string {\n const k = this.shapeKind;\n return k === 'circle' ? 'circle' : k === 'rect' ? 'rect' : 'path';\n }\n\n /* Position / size the element for its shape (r = half-size). /\n private setGeometry(el: SVGElement, r: number): void {\n const x = this.x, y = this.y;\n switch (this.shapeKind) {\n case 'rect':\n el.setAttribute('x', (x - r).toString()); el.setAttribute('y', (y - r).toString());\n el.setAttribute('width', (r 2).toString()); el.setAttribute('height', (r * 2).toString());\n break;\n case 'triangle': {\n // Equilateral, pointing up (SVG y-down), centred on the point.\n const h = r * 1.15;\n el.setAttribute('d', `M${x} ${y - h} L${x + h * 0.866} ${y + h * 0.5} L${x - h * 0.866} ${y + h * 0.5}Z`);\n break;\n }\n case 'diamond':\n el.setAttribute('d', `M${x} ${y - r * 1.2} L${x + r} ${y} L${x} ${y + r * 1.2} L${x - r} ${y}Z`);\n break;\n default:\n el.setAttribute('cx', x.toString()); el.setAttribute('cy', y.toString());\n el.setAttribute('r', r.toString());\n }\n }\n\n /** Half-side length for squares / radius for circles, in SVG user units.\n * Factor 0.006 keeps code-node diameters in the same visual range as rENA\n * (≈ 1–2 % of the coordinate half-extent for a typical ENA network).\n /\n computeRadius(): number {\n const r = this.baseRadius();\n // Optional ceiling (user units): group means are capped to their CI box so\n // a tight interval is never hidden under the marker.\n const cap = (this.__data__ as any).meta?.maxRadius;\n return typeof cap === 'number' && cap > 0 ? Math.min(r, cap) : r;\n }\n\n private baseRadius(): number {\n const extent = (this.graph.__data__.extremes.x_max) \|\| 1;\n const sizeScale = (this.__data__ as any).meta?.sizeScale ?? 1;\n // Fixed-on-screen mode (webENA size decoupling): keep a constant pixel size\n // regardless of data extent / container size / wheel-zoom, by converting a\n // target px into user units via the current px-per-unit and zoom. Otherwise\n // size scales with the coordinate space (default — nodes/edges do the same).\n if ((this.__data__ as any).meta?.fixedSize) {\n const rect = (this.graph.svg_element as SVGSVGElement)?.getBoundingClientRect?.();\n const zoom = (this.graph as any).zoom_level \|\| 1;\n const pxPerUnit = rect && rect.width > 0 ? rect.width / (2 extent) : 1;\n const targetPx = this.__data__.size * 2 * sizeScale; // size 2.5 → 5px radius\n return (targetPx / pxPerUnit) / zoom;\n }\n return extent * POINT_RADIUS_PER_EXTENT * this.__data__.size * sizeScale;\n }\n\n /** Optional halo stroke (e.g. white outline on unit points to separate\n * overlapping dots in dense clusters). Width scales with the dot so it holds\n * up at any zoom. No-op unless the object requests it via meta.stroke. /\n private applyStroke(el: SVGElement): void {\n const stroke = (this.__data__ as any).meta?.stroke;\n if (!stroke) return;\n el.setAttribute('stroke', stroke);\n el.setAttribute('stroke-width', (this.computeRadius() 0.22).toString());\n }\n\n create() {\n const el = document.createElementNS('http://www.w3.org/2000/svg', this.tag) as SVGElement;\n\n el.setAttribute('data-point-id', this.__data__.ID);\n // Identity for <qe-graph> delegation → qe-node-* interaction events.\n const meta = (this.__data__ as any).meta ?? {};\n if (meta.kind) el.setAttribute('data-kind', meta.kind);\n if (meta.name != null) el.setAttribute('data-name', String(meta.name));\n if (meta.group != null) el.setAttribute('data-group', String(meta.group));\n if (meta.unit != null) el.setAttribute('data-unit', String(meta.unit));\n el.setAttribute('fill', this.__data__.color.toString());\n this.applyStroke(el);\n\n this.setGeometry(el, this.computeRadius());\n\n this.svg_element = el;\n\n el.addEventListener('click', () => {\n // Note: do NOT stopPropagation — the click must bubble to <qe-graph>'s\n // delegation so it can emit the public qe-node-click event.\n this.__data__.active = !this.__data__.active;\n this.update();\n\n const pointEvent = new CustomEvent('point-clicked', {\n detail: { pointData: this.__data__ },\n bubbles: true, composed: true\n });\n this.svg_element.dispatchEvent(pointEvent);\n });\n\n el.addEventListener('mouseover', () => {\n // Do not stopPropagation — the parent SVG uses mouseover delegation\n // to show AUTO-mode labels. The fill is already set; this handler is\n // retained as a hook for future hover-highlight logic.\n });\n\n return el;\n }\n\n update() {\n if (!this.svg_element) {\n (this.parent as any).__data__.__children__.push(this.create());\n }\n if (!this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n\n this.svg_element.setAttribute('fill', this.__data__.color.toString());\n this.applyStroke(this.svg_element);\n this.setGeometry(this.svg_element, this.computeRadius());\n }\n\n draw() {\n this.parent?.appendChild(this.svg_element);\n }\n}\n","import { Trajectory } from '../objects/Trajectory';\nimport { Drawable } from './Drawable';\nimport { QEArray, QEElement } from './QELayer';\nimport { QEGraphElement } from './QEGraph';\n\nexport class QETrajectory extends Drawable implements QEElement {\n __name__: string = 'trajectory';\n private _path_el: SVGPathElement \| null = null;\n private _segments_group: SVGGElement \| null = null;\n private _tip_el: SVGCircleElement \| null = null;\n private _points_group: SVGGElement \| null = null;\n\n constructor(\n public __data__: Trajectory,\n public parent: SVGElement,\n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray()\n ) {\n super(__data__, parent, graph, __children__);\n this.svg_element = this.create();\n }\n\n // Trajectory styling is specified in display pixels, while SVG paths use\n // graph coordinates. Convert at render time so marks stay legible at any scale.\n private graphUnitsForPixels(pixels: number): number {\n const extent = this.graph.__data__.extremes.x_max \|\| 1;\n const width = this.graph.svg_element?.getBoundingClientRect().width \|\| 0;\n return width > 0 ? pixels * (2 * extent / width) : pixels * extent * 0.006;\n }\n\n create() {\n const group = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n group.setAttribute('class', 'qe-trajectory-group');\n\n const path = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n path.setAttribute('fill', 'none');\n path.setAttribute('stroke', this.__data__.color.toString());\n path.setAttribute('stroke-width', this.graphUnitsForPixels(this.__data__.strokeWidth).toString());\n group.appendChild(path);\n this._path_el = path;\n\n const segmentsGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n segmentsGroup.setAttribute('class', 'qe-trajectory-segments');\n group.appendChild(segmentsGroup);\n this._segments_group = segmentsGroup;\n\n const pointsGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n pointsGroup.setAttribute('class', 'qe-trajectory-points');\n group.appendChild(pointsGroup);\n this._points_group = pointsGroup;\n\n if (this.__data__.showTips) {\n const tip = document.createElementNS('http://www.w3.org/2000/svg', 'circle');\n tip.setAttribute('fill', this.__data__.color.toString());\n tip.setAttribute('r', this.graphUnitsForPixels(4).toString());\n tip.setAttribute('stroke', '#ffffff');\n tip.setAttribute('stroke-width', this.graphUnitsForPixels(1.5).toString());\n group.appendChild(tip);\n this._tip_el = tip;\n }\n\n this.svg_element = group;\n return group;\n }\n\n update() {\n if (!this.svg_element) {\n this.create();\n }\n if (!this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n\n const dStr = this.__data__.path;\n if (this._path_el) {\n this._path_el.setAttribute('d', dStr);\n this._path_el.setAttribute('stroke', this.__data__.color.toString());\n this._path_el.setAttribute('stroke-width', this.graphUnitsForPixels(this.__data__.strokeWidth).toString());\n this._path_el.style.display = this.__data__.lineStyle === 'tapered' ? 'none' : 'block';\n }\n\n if (this._segments_group) {\n this._segments_group.innerHTML = '';\n if (this.__data__.lineStyle === 'tapered') {\n const pathPts = this.__data__.pathPoints;\n const nSegments = pathPts.length - 1;\n const [minWidth, maxWidth] = this.__data__.strokeWidthRange;\n const [minOpacity, maxOpacity] = this.__data__.opacityRange;\n\n for (let i = 0; i < nSegments; i++) {\n const start = pathPts[i];\n const end = pathPts[i + 1];\n const progress = nSegments <= 1 ? 1 : i / (nSegments - 1);\n const width = minWidth + (maxWidth - minWidth) * progress;\n const opacity = minOpacity + (maxOpacity - minOpacity) * progress;\n const segment = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n\n segment.setAttribute('d', `M${start.x},${start.y} L${end.x},${end.y}`);\n segment.setAttribute('fill', 'none');\n segment.setAttribute('stroke', this.__data__.color.toString());\n segment.setAttribute('stroke-linecap', 'round');\n segment.setAttribute('stroke-linejoin', 'round');\n segment.setAttribute('stroke-width', this.graphUnitsForPixels(width).toString());\n segment.setAttribute('opacity', opacity.toString());\n this._segments_group.appendChild(segment);\n }\n this._segments_group.style.display = 'block';\n } else {\n this._segments_group.style.display = 'none';\n }\n }\n\n const pts = this.__data__.activePoints;\n\n if (this._points_group) {\n if (this.__data__.showPoints && pts.length > 0) {\n this._points_group.innerHTML = '';\n pts.forEach(pt => {\n const dot = document.createElementNS('http://www.w3.org/2000/svg', 'circle');\n dot.setAttribute('cx', pt.x.toString());\n dot.setAttribute('cy', pt.y.toString());\n dot.setAttribute('r', this.graphUnitsForPixels(2.5).toString());\n dot.setAttribute('fill', this.__data__.color.toString());\n dot.setAttribute('opacity', '0.7');\n this._points_group?.appendChild(dot);\n });\n this._points_group.style.display = 'block';\n } else {\n this._points_group.style.display = 'none';\n }\n }\n\n if (this._tip_el && this.__data__.showTips) {\n if (pts.length > 0) {\n const lastPt = pts[pts.length - 1];\n this._tip_el.setAttribute('cx', lastPt.x.toString());\n this._tip_el.setAttribute('cy', lastPt.y.toString());\n this._tip_el.setAttribute('fill', this.__data__.color.toString());\n this._tip_el.setAttribute('r', this.graphUnitsForPixels(4).toString());\n this._tip_el.setAttribute('stroke-width', this.graphUnitsForPixels(1.5).toString());\n this._tip_el.style.display = 'block';\n } else {\n this._tip_el.style.display = 'none';\n }\n }\n }\n\n draw() {\n if (this.svg_element && !this.svg_element.parentElement) {\n this.parent.appendChild(this.svg_element);\n }\n this.update();\n }\n}\n","import { Tools } from \"../utils/Tools\";\nimport { Graph } from \"../objects/Graph\";\nimport { Layer, LayerLike } from \"../objects/Layers\";\nimport { PlottedObject, Point } from \"../objects/PlottedObject\";\nimport { Trajectory } from \"../objects/Trajectory\";\nimport { QELine } from \"./QELine\";\nimport { QEPoint } from \"./QEPoint\";\nimport { QETrajectory } from \"./QETrajectory\";\nimport { QEGraphElement } from \"./QEGraph\";\n\n\nconst { ArrayTools } = Tools;\nexport class QEArray extends Array<any> {\n constructor(...args: any[]) {\n super(...args);\n }\n\n search(key: string, name: string): LayerLike \| undefined {\n let found: LayerLike \| undefined;\n\n function fn(a: LayerLike): LayerLike \| undefined {\n return a.name === name ? a : undefined;\n }\n\n function recurse(obj: any, i?: number, parent: any = null): LayerLike \| undefined {\n if (ArrayTools.isArray(obj)) {\n for (const [i, o] of obj.entries()) {\n found = recurse(o, i, parent);\n if (found) {\n return found;\n }\n }\n } else {\n found = fn(obj);\n if (!found) {\n if (obj && ArrayTools.isArray(obj[key])) {\n for (const [i, o] of obj[key].entries()) {\n found = recurse(o, i, obj);\n if (found) {\n return found;\n }\n }\n }\n } else {\n return found;\n }\n }\n return found;\n }\n\n return recurse(this);\n }\n\n flatten(): LayerLike[] {\n return this.reduce<LayerLike[]>((a, l: LayerLike) => {\n a.push(l);\n if (l.layers && Array.isArray(l.layers)) {\n a.push(...l.layers);\n }\n return a;\n }, []);\n }\n}\n\nexport interface QEElement {\n svg_element: SVGElement;\n graph: QEGraphElement;\n parent: SVGElement \| null;\n __name__: string;\n __data__: Graph \| PlottedObject \| LayerLike;\n __children__: QEArray;\n draw(): void;\n update(): void;\n}\n\nconst\n QEElementConstructors: Record<string, new (d: any, p: SVGElement, g: QEGraphElement) => QEElement> =\n {\n \"AxisPoint\": QEPoint,\n \"AxisLine\": QELine,\n \"Point\": QEPoint,\n \"Line\": QELine,\n \"Edge\": QELine,\n \"TaperedEdge\": QELine,\n \"TaperedWeightedMidpointEdge\": QELine,\n \"NodeEdge\": QELine,\n \"Trajectory\": QETrajectory,\n }\n;\n\nexport class QELayer implements QEElement {\n static tagName = 'g';\n\n svg_element: SVGElement; \n __name__: string;\n\n constructor(\n public __data__: Layer, \n public parent: SVGElement, \n public graph: QEGraphElement,\n public __children__: QEArray = new QEArray(),\n ) {\n this.__name__ = __data__.name \|\| \"unnamed-layer\";\n\n __data__.__state__.addListener(`layer_updated`, \"live\", ({ key, newValue, oldValue } : any) => {\n const childId = (child: QEElement) => (child.__data__ as PlottedObject)?.ID;\n\n const removing = this.__children__.filter((child: QEElement) =>\n !newValue.objects.has(childId(child))\n );\n const updating = this.__children__.filter((child: QEElement) =>\n newValue.objects.has(childId(child))\n );\n const adding = [...newValue.objects.values()].filter((obj: PlottedObject) =>\n !this.__children__.some((child: QEElement) => childId(child) === obj.ID)\n );\n\n adding.forEach((obj: PlottedObject) => {\n const obj_name = (obj as any)._typeName \|\| obj.constructor.name;\n let constructor = QEElementConstructors[obj_name];\n if (!constructor) {\n if (obj instanceof Trajectory) constructor = QETrajectory;\n else if (obj instanceof Point) constructor = QEPoint;\n else constructor = QELine;\n }\n const ena_element: QEElement = new constructor(obj, this.svg_element, this.graph);\n this.__children__.push(ena_element);\n });\n\n updating.forEach((child: QEElement) => {\n // Pull the new PlottedObject from the updated layer data so that any\n // changed properties (e.g. weight, color, meta flags) are picked up by\n // the child's update() call.\n const newData = newValue.objects.get(childId(child)) as PlottedObject;\n if (newData) (child as any).__data__ = newData;\n child.update();\n });\n\n removing.forEach((child: QEElement) => {\n if (child.svg_element.parentElement) {\n child.svg_element.parentElement.removeChild(child.svg_element);\n }\n const idx = this.__children__.indexOf(child);\n if (idx >= 0) this.__children__.splice(idx, 1);\n });\n\n this.update();\n });\n\n this.svg_element = this.create();\n }\n\n get name() {\n return this.__name__;\n }\n\n create(): SVGElement {\n if(!this.__data__) {\n throw new Error(\"Layer is null\");\n }\n let layer: Layer = this.__data__ as Layer;\n this.svg_element = document.createElementNS(\"http://www.w3.org/2000/svg\", QELayer.tagName);\n this.svg_element.setAttribute('data-layer-name', layer.name);\n this.svg_element.setAttribute('data-layer-id', layer.ID);\n\n (this.svg_element as any).__data__ = layer;\n\n this.svg_element.classList.add('ena-layer');\n\n if(this.__data__.layers && this.__data__.layers.length > 0) {\n this.__data__.layers.forEach((sublayer: LayerLike) => {\n const layer_g: QELayer = new QELayer(sublayer as any, this.svg_element, this.graph);\n this.__children__.push(layer_g);\n });\n }\n\n return this.svg_element;\n }\n\n update() {\n if(!this.__data__) {\n throw new Error(\"Layer is null\");\n }\n\n if(this.__data__.visible) {\n // Update layer properties here\n if(this.parent.nodeName.toLowerCase() === \"svg\") {\n // Compute the transform string based on the size of the parent SVG elemet. \n // -- a circle with radius 1 should be scaled to the size of the parent SVG element, \n // so that as the graph is zoomed in and out, the circle scales with it.\n // this.svg_element.style.transform = `scale(${this.parent.clientWidth / 100}, ${this.parent.clientHeight / 100})`;\n }\n\n // Update sublayers\n this.__children__.forEach((child: QEElement) => {\n child.update();\n });\n\n if(this.__data__.scale_objects === true) {\n if(this.__name__ === \"points\") {\n // this.svg_element.setAttribute('transform', `\n // scale(${this.graph.__data__.scale_x}, ${this.graph.__data__.scale_y})\n // `);\n }\n }\n else {\n // this.svg_element.setAttribute('transform', `scale(${this.graph.x_mirror()}, ${this.graph.y_mirror()})`); \n }\n }\n }\n\n draw(): void {\n this.parent?.appendChild(this.svg_element);\n\n this.__children__.forEach((child: QEElement) => {\n child.draw();\n });\n }\n\n add(child: QEElement) {\n this.__children__.push(child);\n }\n}","import { Label, Point } from \"../objects/PlottedObject\";\nimport { QEGraphElement } from \"./QEGraph\";\n\n/*\n SVG <text> drawable for a single ENA label.\n \n ── Display modes (Label.DISPLAY_TYPES) ──────────────────────────────────────\n * OFF (0) — never shown\n * AUTO (1) — shown on mouseover of the associated point, hidden on mouseout\n * CLICK (2) — toggled by clicking the associated point\n * ON (3) — always shown\n \n ── Position modes (Label.POSITION) ─────────────────────────────────────────\n * OBJECT (1) — offset near the point (quadrant-aware, default)\n * STATIC (2) — centered directly on the point (no offset; label overlaps point)\n * CONTAINER (3) — projected to the viewBox boundary in the point's direction;\n * useful for code-node labels that appear at the outer ring\n * CUSTOM (4) — caller provides explicit (customX, customY) coordinates\n /\nexport class QELabel {\n svg_element: SVGTextElement;\n private _visible: boolean = false;\n // Drag offset (graph-space units) and pin state for host-repositionable labels.\n private _offsetX = 0;\n private _offsetY = 0;\n pinned = false;\n\n constructor(\n public readonly text: string,\n public readonly point: Point,\n public readonly parent: SVGElement,\n public readonly graph: QEGraphElement,\n public readonly displayMode: number = Label.DISPLAY_TYPES.ON,\n public readonly position: number = Label.POSITION.OBJECT,\n public customX?: number,\n public customY?: number,\n ) {\n this.svg_element = this._create();\n\n // Set initial visibility without calling update() yet.\n // The QEGraphElement calls update_labels() after update_extremes() so that\n // the first real positioning uses the correct graph extent, not the default 1.\n if (displayMode === Label.DISPLAY_TYPES.ON) {\n this._visible = true;\n this.svg_element.setAttribute('display', 'block');\n } else {\n this._visible = false;\n this.svg_element.setAttribute('display', 'none');\n }\n }\n\n private _create(): SVGTextElement {\n const el = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n el.textContent = this.text;\n el.setAttribute('data-label-for', this.point.ID);\n el.setAttribute('pointer-events', 'auto'); // draggable\n el.style.cursor = 'grab';\n this._attachDrag(el);\n this.parent.appendChild(el);\n return el;\n }\n\n /* Drag to reposition; pins the label open and emits qe-label-move on drop. /\n private _attachDrag(el: SVGTextElement): void {\n el.addEventListener('mousedown', (ev: MouseEvent) => {\n ev.preventDefault();\n ev.stopPropagation(); // don't start a graph pan\n const svg = el.ownerSVGElement;\n if (!svg) return;\n const toUser = (cx: number, cy: number) => {\n const p = svg.createSVGPoint(); p.x = cx; p.y = cy;\n const m = svg.getScreenCTM();\n return m ? p.matrixTransform(m.inverse()) : ({ x: 0, y: 0 } as DOMPoint);\n };\n const start = toUser(ev.clientX, ev.clientY);\n const baseX = this._offsetX, baseY = this._offsetY;\n el.style.cursor = 'grabbing';\n\n const onMove = (e: MouseEvent) => {\n const p = toUser(e.clientX, e.clientY);\n this._offsetX = baseX + (p.x - start.x);\n this._offsetY = baseY + (p.y - start.y);\n this.pinned = true; // keep it shown once moved\n this._visible = true;\n this.svg_element.setAttribute('display', 'block');\n this.update();\n };\n const onUp = () => {\n document.removeEventListener('mousemove', onMove);\n document.removeEventListener('mouseup', onUp);\n el.style.cursor = 'grab';\n // Public event so the host can persist / mirror across coordinated plots.\n this.graph.dispatchEvent(new CustomEvent('qe-label-move', {\n detail: { id: this.point.ID, transform: { x: this._offsetX, y: this._offsetY } },\n bubbles: true, composed: true,\n }));\n };\n document.addEventListener('mousemove', onMove);\n document.addEventListener('mouseup', onUp);\n });\n }\n\n /\n Recompute position and font-size from current graph extents.\n * No-ops when the label is hidden (AUTO/CLICK modes while not hovered/clicked).\n /\n update(): void {\n if (!this._visible) return;\n\n const extent = this.graph.__data__.extremes.x_max;\n if (extent <= 0) return; // graph not initialised yet\n\n // qe_labels(font_size =) is in CSS pixels (constant on screen); default\n // scales with the plot extent.\n const font = (this.graph as any)._labelFont ?? {};\n const fontSize = font.size ? font.size (this.graph as any).unitsPerPixel() : extent * 0.06;\n const offset = fontSize * 1.2;\n\n let x: number, y: number, anchor: string;\n\n switch (this.position) {\n\n case Label.POSITION.STATIC: {\n // Centered on the point — label sits at exactly the point's coordinates.\n // Useful when the caller wants to control offset manually via customX/Y.\n x = this.point.x;\n y = this.point.y - offset * 0.3;\n anchor = 'middle';\n break;\n }\n\n case Label.POSITION.CONTAINER: {\n // Project from the view's centre (the origin, unless center=\"content\")\n // through the point onto the viewBox boundary. Labels ring the outer\n // edge of the plot, one per code/group direction.\n const { cx, cy } = this.graph.__data__.extremes;\n const px = this.point.x - cx;\n const py = this.point.y - cy;\n const dist = Math.sqrt(px * px + py * py) \|\| 1;\n const scale = (extent * 0.93) / dist;\n x = cx + px * scale;\n y = cy + py * scale - offset * 0.3;\n anchor = px >= 0 ? 'start' : 'end';\n break;\n }\n\n case Label.POSITION.CUSTOM: {\n // Caller-provided coordinates; fall back to OBJECT behaviour if unset.\n if (this.customX != null && this.customY != null) {\n x = this.customX;\n y = this.customY;\n anchor = 'start';\n break;\n }\n // fall through to OBJECT\n }\n\n default:\n case Label.POSITION.OBJECT: {\n // Quadrant-aware offset: push label away from origin.\n const dx = this.point.x >= 0 ? offset : -offset;\n anchor = this.point.x >= 0 ? 'start' : 'end';\n x = this.point.x + dx;\n y = this.point.y - offset * 0.4;\n break;\n }\n }\n\n this.svg_element.setAttribute('x', x.toString());\n this.svg_element.setAttribute('y', y.toString());\n // Host drag offset (graph-space units) composes on top of the computed spot.\n if (this._offsetX \|\| this._offsetY) {\n this.svg_element.setAttribute('transform', `translate(${this._offsetX}, ${this._offsetY})`);\n }\n this.svg_element.setAttribute('font-size', fontSize.toString());\n this.svg_element.setAttribute('font-family', font.family ?? 'system-ui, sans-serif');\n this.svg_element.setAttribute('font-weight', '500');\n this.svg_element.setAttribute('text-anchor', anchor);\n this.svg_element.setAttribute('fill', font.color ?? this.point.color?.toString() ?? '#333333');\n }\n\n /** Make the label visible and position it immediately. /\n show(): void {\n this._visible = true;\n this.svg_element.setAttribute('display', 'block');\n this.update();\n }\n\n hide(): void {\n if (this.pinned) return; // a dragged/pinned label stays visible\n this._visible = false;\n this.svg_element.setAttribute('display', 'none');\n }\n\n toggle(): void {\n this._visible ? this.hide() : this.show();\n }\n\n get visible(): boolean { return this._visible; }\n\n remove(): void {\n this.svg_element.remove();\n }\n}\n","/\n Declarative child layer elements for <qe-graph>.\n \n Each element is an inert configuration holder — no shadow DOM, no rendering\n * logic. <qe-graph> reads their presence and attributes via querySelector() to\n * configure each rendering layer.\n \n Presence = the layer is rendered.\n * Absence = the layer is hidden. (Code-node positions come from the\n * model and anchor the coordinate space whether or not\n * <qe-nodes> is present; the element only controls drawing.)\n \n HTML authoring example:\n \n <qe-graph width=\"100%\" height=\"440\">\n * <qe-nodes label=\"on\"></qe-nodes>\n * <qe-means groups=\"FirstGame,SecondGame\" confidence></qe-means>\n * <qe-points label=\"auto\"></qe-points>\n * <qe-edges group=\"FirstGame\" compare=\"SecondGame\"></qe-edges>\n * </qe-graph>\n /\n\n/\n <qe-nodes> — renders the code nodes.\n * Presence = draw nodes; absence = hide them (positions still set the extent).\n * A node's diameter equals the summed widths of its drawn edges: every edge\n * touching it (undirected), or the wide ends of the edges directed at it,\n * including its self-connection (directed / ONA).\n \n Attributes:\n * label \"on\" \| \"off\" \| \"click\" \| \"auto\" (default \"on\")\n * unconnected \"dot\" (default) — nodes with no drawn edges show as a tiny\n * dot; \"hide\" — hide them (and their labels).\n /\nexport class QENodesElement extends HTMLElement {\n static tagName = 'qe-nodes' as const;\n}\n\n/\n <qe-means> — renders group mean markers and optional CI boxes.\n * Presence = show means; absence = hide means.\n \n Attributes:\n * groups Comma-separated group names to show. Omit for all groups.\n * confidence Boolean — show 95% CI rectangles.\n * label \"on\" \| \"off\" \| \"click\" \| \"auto\" (default \"on\")\n * fixed-size Boolean — keep mean markers a constant on-screen pixel size\n * regardless of data extent, container size, or zoom (default:\n * markers scale with the coordinate space, like nodes and edges).\n /\nexport class QEMeansElement extends HTMLElement {\n static tagName = 'qe-means' as const;\n}\n\n/\n <qe-points> — renders individual unit scatter dots.\n * Presence = show unit points; absence = hide unit points.\n \n Attributes:\n * label \"on\" \| \"off\" \| \"click\" \| \"auto\" (default \"auto\")\n * size Numeric dot size (default 2.5), relative to the code-node size.\n * fixed-size Boolean — keep unit dots a constant on-screen pixel size\n * regardless of data extent, container size, or zoom (default:\n * dots scale with the coordinate space, like nodes and edges).\n /\nexport class QEPointsElement extends HTMLElement {\n static tagName = 'qe-points' as const;\n}\n\n/\n <qe-edges> — renders an edge network.\n * Presence = draw edges; absence = no edge network.\n \n Attributes:\n * group Group name whose mean network to draw.\n * unit Individual unit ID whose personal network to draw\n * (e.g. \"FirstGame::steven z\"). Mutually exclusive with `group`.\n * compare Second group to subtract (group − compare).\n * also Second group to overlay alongside `group`.\n * scale Reference node weight for mark sizes — the node drawn at\n * <qe-graph mark-size> × the plot width (edge widths follow):\n * \"model\" (default) — the largest node among the model's\n * group-mean networks, so separate plots of\n * one model are comparable;\n * \"plot\" — this plot's own largest node;\n * <number> — a fixed node weight.\n * magnify Multiply this plot's edge widths and node sizes (not colour),\n * e.g. to read a faint subtraction. Whenever the attribute is\n * present — any value, including \"1\" — the plot is labelled\n * \"(scaled N.Nx)\", so exported plots state their scaling.\n * color-scale How \|weight\| maps onto webENA's colour ramps (saturation\n * 0.25–1, opacity 0.3–1):\n * \"model\" (default) — rescaled from the model's smallest to largest\n * non-zero weight (every unit), so plots of one\n * model share a colour scale;\n * \"plot\" — rescaled within this plot (webENA);\n * \"absolute\" — no ramps: saturation = opacity = \|weight\|.\n /\nexport class QEEdgesElement extends HTMLElement {\n static tagName = 'qe-edges' as const;\n}\n\n/\n <qe-trajectories> — renders epistemic cognitive trajectory curves and steps.\n * Presence = draw trajectories; absence = no trajectories.\n \n Attributes:\n * units Comma-separated unit IDs to show. Omit for all.\n * smooth \"none\" \| \"poly\" (default \"none\")\n * max-degree Upper bound on polynomial degree if smooth=\"poly\" (default 3)\n * degree-selection \"loocv_2d\" \| \"fixed\" (default \"loocv_2d\"). \"loocv_2d\"\n * picks the degree in 1..max-degree by joint 2D leave-one-out CV;\n * \"fixed\" always uses max-degree. Near-origin points are excluded\n * from the fit (still drawn).\n * points \"true\" \| \"false\" — show discrete point markers along trajectory\n * tips \"true\" \| \"false\" — show leading tip marker\n * playhead Number — current turn / time index for filtering/animation\n * line-style \"uniform\" \| \"tapered\" (default \"uniform\")\n * stroke-width Number (default 2)\n * stroke-width-range \"min,max\" for tapered lines (default \"1,6\")\n * opacity-range \"min,max\" for tapered lines (default \"0.3,1\")\n /\nexport class QETrajectoriesElement extends HTMLElement {\n static tagName = 'qe-trajectories' as const;\n}\n\n/\n <qe-axes> — renders the x/y axis lines and, per axis, an optional title.\n * Presence = draw axes; absence = no axes.\n \n Attributes:\n * x Show the x-axis label. A value sets custom text; an empty/boolean\n * attribute defaults to the x dimension name (e.g. \"SVD1\").\n * y Show the y-axis label. Same rule with the y dimension name.\n \n Examples:\n * <qe-axes></qe-axes> lines only, no labels\n * <qe-axes x y></qe-axes> \"SVD1\" / \"SVD2\"\n * <qe-axes x=\"Task focus\" y> \"Task focus\" / \"SVD2\"\n /\nexport class QEAxesElement extends HTMLElement {\n static tagName = 'qe-axes' as const;\n}\n\ncustomElements.define(QENodesElement.tagName, QENodesElement);\ncustomElements.define(QEMeansElement.tagName, QEMeansElement);\ncustomElements.define(QEPointsElement.tagName, QEPointsElement);\ncustomElements.define(QEEdgesElement.tagName, QEEdgesElement);\ncustomElements.define(QETrajectoriesElement.tagName, QETrajectoriesElement);\ncustomElements.define(QEAxesElement.tagName, QEAxesElement);\n","import { DefaultGraphOptions, Graph } from \"../objects/Graph\";\nimport { DrawableElement } from \"./DrawableElement\";\nimport { QEArray, QEElement, QELayer } from \"./QELayer\";\nimport QEVisualElement from \"./QEVisual\";\nimport { DataFrameRow } from \"../types/DataFrame\";\nimport { NodeEdge, TaperedWeightedMidpointEdge } from \"../objects/Edges\";\nimport { Label, Line, Point } from \"../objects/PlottedObject\";\nimport { Trajectory } from \"../objects/Trajectory\";\nimport { LayerLike } from \"../objects/Layers\";\nimport { Color } from \"../objects/Color\";\nimport { Extremes } from \"../objects/Extremes\";\nimport { QELabel } from \"./QELabel\";\nimport { DEFAULT_EDGE_WIDTH, OPACITY_RANGE, SATURATION_RANGE, UNCONNECTED_NODE_SIZE, nodeSizeForEdges, rampFor, widthPerWeight } from \"../objects/Sizing\";\nimport \"./QEChildElements.js\";\n\n// Accessible color palette for group assignment (Paul Tol's bright scheme)\nconst GROUP_PALETTE = [\n '#4477AA', '#EE6677', '#228833', '#CCBB44',\n '#66CCEE', '#AA3377', '#BBBBBB', '#000000',\n];\n\n/\n Parse an edge column name into the two code IDs it connects.\n * Edge columns use \".\" as separator between the two codes, but codes can\n * themselves contain \".\" (e.g. \"Technical.Constraints\"). We resolve the\n * ambiguity by trying every prefix that matches a known code.\n \n Self-connections (\"A.A\") are detected first — they return [A, A].\n * In directed (ONA) mode the full unfolded matrix is expected, so A→B and\n * B→A are distinct columns; both resolve correctly as ordered pairs.\n /\nfunction parseEdgePair(colName: string, codes: string[]): [string, string] \| null {\n // Self-connections first: exact match \"code.code\"\n for (const c of codes) {\n if (colName === `${c}.${c}`) return [c, c];\n }\n // Directed or undirected pairs: longest-prefix wins to handle dotted code names\n for (const c1 of codes) {\n if (colName.startsWith(c1 + '.')) {\n const c2 = colName.slice(c1.length + 1);\n if (codes.includes(c2)) return [c1, c2];\n }\n }\n return null;\n}\n\n/\n Compute half-width and half-height for a 95% CI rectangle on the group mean.\n \n Each axis is treated independently: half-extent = t(df,0.975) × SE,\n * where SE = sqrt(variance / n) and df = n − 1. This matches the standard\n * ENA rectangular CI displayed in the rENA / Web ENA tools.\n \n Inputs are the raw (un-scaled) variances; pointScale is applied here so\n * the returned values are in SVG coordinate space.\n /\nfunction computeCIRect(\n varX: number, varY: number, n: number, pointScale: number\n): { halfW: number; halfH: number } {\n // t(df, 0.975) — rough approximation good to ±0.02 for df ≥ 3\n const df = Math.max(1, n - 1);\n const t95 = df >= 120 ? 1.960\n : df >= 60 ? 2.000\n : df >= 30 ? 2.042\n : df >= 20 ? 2.086\n : df >= 10 ? 2.228\n : df >= 5 ? 2.571\n : 4.303; // df = 1\n const seX = Math.sqrt(Math.max(0, varX) / n) pointScale;\n const seY = Math.sqrt(Math.max(0, varY) / n) * pointScale;\n return { halfW: t95 * seX, halfH: t95 * seY };\n}\n\n/** Mean markers never exceed this fraction of their interval box's shorter\n * half-side. Marker size is otherwise arbitrary (extent- or pixel-based), so\n * without a cap a tight CI disappears underneath the mean square. /\nconst MEAN_MAX_FRACTION_OF_INTERVAL = 0.5;\n\nfunction capMeanToInterval(meanPt: Point \| undefined, halfW: number, halfH: number): void {\n if (!meanPt) return;\n const half = Math.min(Math.abs(halfW), Math.abs(halfH));\n if (!(half > 0)) return; // degenerate interval (n = 1, zero variance): keep default size\n (meanPt as any).meta = { ...((meanPt as any).meta ?? {}), maxRadius: half MEAN_MAX_FRACTION_OF_INTERVAL };\n}\n\nfunction readIntervalBounds(\n row: DataFrameRow, dim0: string, dim1: string, prefix = ''\n): { x_low: number; x_high: number; y_low: number; y_high: number } \| null {\n // prefix '' → CI ({dim}.low / .high); 'o' → outlier ({dim}.olow / .ohigh).\n const get = (col: string) => {\n const i = row.names.indexOf(col);\n const raw = i >= 0 ? row[i] : null;\n if (raw == null \|\| raw === '') return undefined; // Number(null) would be 0\n const v = Number(raw);\n return Number.isFinite(v) ? v : undefined;\n };\n const xLow = get(`${dim0}.${prefix}low`) ?? get(`${dim0}_${prefix}low`);\n const xHigh = get(`${dim0}.${prefix}high`) ?? get(`${dim0}_${prefix}high`);\n const yLow = get(`${dim1}.${prefix}low`) ?? get(`${dim1}_${prefix}low`);\n const yHigh = get(`${dim1}.${prefix}high`) ?? get(`${dim1}_${prefix}high`);\n if (xLow == null \|\| xHigh == null \|\| yLow == null \|\| yHigh == null) return null;\n return { x_low: xLow, x_high: xHigh, y_low: yLow, y_high: yHigh };\n}\n\n/*\n <qe-edges color-scale>: the range that edge weights are rescaled from onto\n * webENA's saturation (0.25–1) and opacity (0.3–1) ramps.\n * \"model\" (default) — min / max non-zero \|weight\| across the whole model\n * (every unit), so separate plots of one model share\n * one colour scale.\n * \"plot\" — this plot's own min / max (webENA's per-network\n * behaviour).\n * \"absolute\" — no rescaling: saturation = opacity = \|weight\|.\n /\ntype ColorScale = 'model' \| 'plot' \| 'absolute';\n\n/* One <qe-edges> element: a named network or an explicit `network` row. /\ntype EdgeLayerSpec = {\n group: string \| null; unit: string \| null;\n compare: string \| null; also: string \| null;\n network: string \| null;\n colors: [string, string \| null] \| null; // positive, negative (null → complement)\n threshold: [number, number] \| null; // min, max (max = Infinity when omitted)\n name: string \| null;\n};\n\nfunction parseEdgeLayer(el: Element): EdgeLayerSpec {\n const a = (k: string) => el.getAttribute(k);\n const cols = a('colors')?.split(',').map(c => c.trim()).filter(Boolean) ?? [];\n const thr = a('threshold')?.split(',').map(Number).filter(Number.isFinite) ?? [];\n return {\n group: a('group'), unit: a('unit'), compare: a('compare'), also: a('also'),\n network: a('network'),\n colors: cols.length ? [cols[0], cols[1] ?? null] : null,\n threshold: thr.length ? [thr[0], thr.length > 1 ? thr[1] : Infinity] : null,\n name: a('name'),\n };\n}\n\n/* Complementary hue (rENA: one colour → negatives use hue + 180°). /\nfunction complementColor(hex: string): string {\n const { r, g, b } = Color.parseColor(hex);\n const mx = Math.max(r, g, b), mn = Math.min(r, g, b);\n const f = (c: number) => (mx + mn - c).toString(16).padStart(2, '0');\n return `#${f(r)}${f(g)}${f(b)}`;\n}\n\nfunction parseColorScale(attr: string \| null): ColorScale {\n const a = attr?.trim().toLowerCase();\n return a === 'plot' \|\| a === 'absolute' ? a : 'model';\n}\n\n/\n Parse a label-mode attribute string into a Label.DISPLAY_TYPES integer.\n * \"on\" → 3 (ON)\n * \"off\" → 0 (OFF)\n * \"click\" → 2 (CLICK)\n * \"auto\" → 1 (AUTO)\n * Returns `defaultMode` for any unrecognized value or null.\n /\nfunction parseLabelMode(attr: string \| null, defaultMode: number): number {\n switch (attr?.toLowerCase()) {\n case 'on': return 3;\n case 'off': return 0;\n case 'click': return 2;\n case 'auto': return 1;\n default: return defaultMode;\n }\n}\n\nexport class QEGraphElement extends DrawableElement implements QEElement {\n static tagName: string = \"qe-graph\";\n\n static get observedAttributes(): string[] {\n // Only layout / shorthand attributes live on <qe-graph> itself.\n // Layer-specific config (group, unit, compare, also, points, edges,\n // confidence, groups) lives on child elements and is observed via\n // MutationObserver in connectedCallback().\n return [\n 'width', 'height', 'for',\n 'scale-points', 'point-scale', 'center',\n 'labels', 'label-nodes', 'label-means', 'label-points',\n ];\n }\n\n static style: string = `\n ${DrawableElement.style}\n\n :host {\n display: block;\n }\n\n .wrapper {\n width: 100%;\n height: 100%;\n }\n\n svg {\n width: 100%;\n height: 100%;\n aspect-ratio: 1 / 1;\n background-color: #FFF;\n }\n `;\n\n svg_element: SVGElement;\n graph: QEGraphElement;\n parent: SVGElement \| null;\n zoom_level: number = 1;\n\n __data__: Graph;\n __children__: QEArray = new QEArray();\n __name__: string;\n \n\n private _vizena!: QEVisualElement;\n get vizena() {\n return this._vizena;\n }\n\n private _hasModel = false;\n private _renderPending = false;\n private _childObserver: MutationObserver \| null = null;\n\n // SVG <rect> elements for per-group CI boxes, keyed by group name.\n // Managed directly (not via QELayer) so they render behind unit points.\n private _ciRects: Map<string, SVGRectElement> = new Map();\n private _outlierRects: Map<string, SVGRectElement> = new Map();\n private _ciCross: Map<string, SVGPathElement> = new Map();\n\n // Cached reference to the labels <g> layer — set once in connectedCallback()\n // after draw() so it is guaranteed to be in the SVG DOM.\n private _labelsGroup: SVGGElement \| null = null;\n\n // SVG <text> label elements for nodes, mean points, and unit points.\n private _nodeLabels: Map<string, QELabel> = new Map();\n private _meanLabels: Map<string, QELabel> = new Map();\n private _pointLabels: Map<string, QELabel> = new Map();\n\n // Axes (<qe-axes>): whether to show axis lines, and resolved label text\n // (null = no label for that axis). SVG <text> nodes are cached and positioned\n // in update_axis_labels() using the freshly-computed extremes.\n private _showAxes = false;\n private _axisXText: string \| null = null;\n private _axisYText: string \| null = null;\n private _axisLabelEls: Map<'x' \| 'y', SVGTextElement> = new Map();\n // \"(scaled 1.5x)\" label, drawn whenever <qe-edges magnify> is present.\n private _magnifyText: string \| null = null;\n private _magnifyEl: SVGTextElement \| null = null;\n // <qe-graph range> / plot-title / label-font- (qe_plot(range =, title =),\n // qe_labels(font_)); resolved each render.\n private _rangeExtent: number \| null = null;\n private _rangeMode: 'network' \| 'points' \| 'number' \| null = null;\n /* center=\"content\": centre the view on the drawn content, not the origin /\n private _centerContent = false;\n private _plotTitle: string \| null = null;\n private _titleEl: SVGTextElement \| null = null;\n private _resizeObs: ResizeObserver \| null = null;\n _labelFont: { size: number \| null; family: string \| null; color: string \| null } =\n { size: null, family: null, color: null };\n\n /* SVG user units per CSS pixel at the current size / zoom. /\n unitsPerPixel(): number {\n const extent = this.__data__.extremes.x_max \|\| 1;\n const rect = this.svg_element?.getBoundingClientRect?.();\n const zoom = (this as any).zoom_level \|\| 1;\n return rect && rect.width > 0 ? (2 extent / rect.width) / zoom : extent * 0.004;\n }\n\n constructor() {\n super();\n\n this.graph = this;\n this.parent = null;\n\n this.__data__ = new Graph(DefaultGraphOptions);\n this.__name__ = this.__data__.name \|\| \"unnamed-graph\";\n this.svg_element = this.create();\n\n console.log(\"Created ena-graph svg element: \", this.svg_element);\n\n // Listen for the model-updated CustomEvent dispatched by VisualQEElement.\n // The Model object is carried in event.detail, so ena-graph works whether it\n // is a child, sibling, or anywhere else relative to ena-visual.\n document.addEventListener('model-updated', (e: Event) => {\n // When multiple qe-visual elements exist on the page, each qe-graph must\n // only react to events from its own associated visual. _vizena is resolved\n // in connectedCallback(); before that point we accept all events (initial\n // load), but once the association is known we filter strictly.\n // composedPath()[0]: inside a shadow root (e.g. a qe-visual in another\n // component), e.target is retargeted to the shadow host\n const origin = e.composedPath?.()[0] ?? e.target;\n if (this._vizena && origin !== this._vizena) return;\n\n const model = (e as CustomEvent).detail;\n if (!model) return;\n\n // Tweening (opt-in via `animate`): snapshot current mark/edge positions\n // BEFORE the rebuild so we can animate old→new after this.update().\n this._animateMs = this.hasAttribute('animate')\n ? (parseInt(this.getAttribute('animate') \|\| '', 10) \|\| 300)\n : 0;\n const tweenFrom = (this._animateMs > 0 && this._hasModel) ? this._captureTween() : null;\n\n this._hasModel = true;\n\n const dims = model.dimensions as string[];\n\n // Resolved column names from setModelData (auto-detected or caller-supplied)\n const unitIdCol = model.unit_id_col;\n const nodeIdCol = model.node_id_col;\n const groupColName = model.group_col;\n\n // ── Layer config (read once from child elements) ─────────────────────────\n const config = this._readLayerConfig();\n\n // ── Axes (<qe-axes>) ─────────────────────────────────────────────────────\n // Resolve label text now that dims are known: empty x/y attribute falls\n // back to the dimension name; a value is used verbatim; null = no label.\n this._showAxes = config.showAxes;\n this._axisXText = config.axisXLabel === null ? null : (config.axisXLabel \|\| String(dims?.[0] ?? 'x'));\n // Present on any <qe-edges magnify>, including \"1\" — as webENA labels\n // its side plots \"(scaled 1.0x)\" so an exported set says which plot was\n // magnified.\n this._magnifyText = config.edgeMagnify == null ? null\n : `(scaled ${config.edgeMagnify.toFixed(1)}x)`;\n this._axisYText = config.axisYLabel === null ? null : (config.axisYLabel \|\| String(dims?.[1] ?? 'y'));\n\n // ── Group color map ──────────────────────────────────────────────────────\n // Priority: (1) points groupCol, (2) groups frame row names, (3) empty.\n const groupColorMap: Record<string, string> = {};\n // Model palette (qe_plot(palette =)) or the default Tol \"bright\" scheme.\n const PALETTE: string[] = (model as any).palette?.length ? (model as any).palette : GROUP_PALETTE;\n if (groupColName && model.points?.names) {\n const groupCol = model.points.col(groupColName);\n if (groupCol) {\n const uniqueGroups: string[] = [...new Set([...groupCol].map(String))];\n uniqueGroups.forEach((g, i) => {\n groupColorMap[g] = PALETTE[i % PALETTE.length];\n });\n }\n }\n // Groups-frame rows: a `color` column overrides the palette, and rows that\n // are not groups of the points (e.g. the mean of an arbitrary subset,\n // qe_group(points =)) still get a colour so they count as known groups.\n if (model.groups?.rows && model.groups.rows().length > 0) {\n model.groups.rows().forEach((row: DataFrameRow) => {\n const g = row.rowName ?? String(row[0]);\n const ci = row.names.indexOf('color');\n const c = ci >= 0 ? row[ci] : null;\n if (c && String(c) !== 'NA') groupColorMap[g] = String(c);\n else if (!groupColorMap[g]) {\n groupColorMap[g] = PALETTE[Object.keys(groupColorMap).length % PALETTE.length];\n }\n });\n }\n\n // ── Active groups for MEANS display ─────────────────────────────────────\n // `groups` attribute: comma-separated list of group names whose means and\n // CI boxes should be rendered. Default (attribute absent or empty): show\n // means for ALL groups present in the model.\n //\n // Means display is intentionally independent of edge selection. The edge\n // section below reads `group` / `compare` / `also` to determine which\n // network(s) to draw; those attributes have no effect here.\n const _allGroupNames_ = Object.keys(groupColorMap);\n const activeMeanGroups: Set<string> = (config.activeMeanGroups && config.activeMeanGroups.trim())\n ? new Set(\n config.activeMeanGroups.split(',')\n .map(s => s.trim())\n .filter(g => groupColorMap[g]) // silently drop names not in model\n )\n : new Set(_allGroupNames_); // default: every group\n\n // ── Point-to-node coordinate scaling ────────────────────────────────────\n // Unit point coordinates are in a different (typically much smaller) range\n // Unit/mean point coordinates are rescaled by default so the outermost point\n // aligns with the outermost code node — matching the ENA Web Tool default.\n // Set scale-points=\"false\" on <qe-graph> to show raw SVD coordinates\n // (points cluster near origin relative to code nodes).\n const scalePointsEnabled = config.scalePoints;\n\n const getExtent = (rows: DataFrameRow[]): number => {\n let max = 0;\n rows.forEach(row => {\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n if (xIdx >= 0) max = Math.max(max, Math.abs(Number(row[xIdx])));\n if (yIdx >= 0) max = Math.max(max, Math.abs(Number(row[yIdx])));\n });\n return max;\n };\n\n const maxNodeExtent = model.nodes?.rows ? getExtent(model.nodes.rows()) : 0;\n const maxPointExtent = model.points?.rows ? getExtent(model.points.rows()) : 0;\n const maxTrajExtent = model.trajectories?.rows ? getExtent(model.trajectories.rows()) : 0;\n const effectivePointExtent = maxPointExtent > 0 ? maxPointExtent : maxTrajExtent;\n // point-scale=\"N\" (optional, unset by default): an explicit factor, e.g.\n // 1 for raw coordinates or another tool's rescaling, instead of fitting\n // the outermost point to the outermost node\n const pointScale = config.pointScale !== null ? config.pointScale\n : (scalePointsEnabled && effectivePointExtent > 0 && maxNodeExtent > 0)\n ? maxNodeExtent / effectivePointExtent\n : 1;\n\n // <qe-graph range>: a symmetric axis range, as rENA's scale.to —\n // \"network\" = ±max \|node\| × 1.2, \"points\" = ±max \|drawn point\| × 1.2, or\n // a number. Absent → qeviz's default (1.3 × the largest drawn mark).\n this._rangeExtent =\n config.range === 'network' ? maxNodeExtent * 1.2\n : config.range === 'points' ? effectivePointExtent * pointScale * 1.2\n : typeof config.range === 'number' ? config.range\n : null;\n this._rangeMode = config.range === 'network' \|\| config.range === 'points' ? config.range\n : typeof config.range === 'number' ? 'number' : null;\n this._centerContent = config.centerContent;\n this._plotTitle = config.plotTitle;\n this._labelFont = config.labelFont;\n\n // ── Label display modes — sourced from config (child elements or shorthand) ──\n const labelNodes = config.labelNodes;\n const labelMeans = config.labelMeans;\n const labelPoints = config.labelPoints;\n\n // Use the cached labels <g> reference (set once in connectedCallback).\n const labelSvg = this._labelsGroup;\n\n // ── Helper: build a Point from a DataFrame row ───────────────────────────\n // Looks up dimension values by column name so it works with any data format.\n // Y is negated because SVG y-axis points down while ENA convention is y-up.\n // `scale` multiplies x/y — use pointScale for unit/mean points, 1 for nodes.\n const rowToPoint = (row: DataFrameRow, idCol: string, colorStr?: string, scale = 1): Point => {\n const idIdx = row.names.indexOf(idCol);\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n const pt = new Point({\n ID: idIdx >= 0 ? String(row[idIdx]) : (row.rowName \|\| `pt-${Math.random().toString(36).slice(2)}`),\n dimensions: [\n xIdx >= 0 ? Number(row[xIdx]) * scale : 0,\n yIdx >= 0 ? -Number(row[yIdx]) * scale : 0, // negate Y: SVG y-down vs ENA y-up\n ],\n meta: {},\n });\n if (colorStr) pt.color = new Color(colorStr);\n return pt;\n };\n\n // ── Unit points + group means ────────────────────────────────────────────\n // groupSums is used later for mean edges and CI ellipses.\n // x2/y2/xy accumulate Σ(raw²) for variance computation.\n const groupSums: Record<string, {\n x: number; y: number; x2: number; y2: number; xy: number;\n n: number; color: string;\n }> = {};\n\n // <qe-points> presence controls unit-dot visibility.\n // <qe-means> presence controls mean markers and CI boxes.\n const showUnitPoints = config.showPoints;\n\n // ── Explicit point sets (qe_points(units =, points =)) ─────────────────\n // Each <qe-points set=\"…\"> draws that set's rows of model.pointsets, on\n // the same point scale as the unit points.\n const pointSetFrame = (model as any).pointsets;\n if (config.pointSets.length && pointSetFrame?.rows) {\n const psLayer = this.__children__.search('__children__', 'points') as QELayer;\n const col = (r: DataFrameRow, k: string) => { const i = r.names.indexOf(k); return i >= 0 ? r[i] : null; };\n config.pointSets.forEach((ps, si) => {\n pointSetFrame.rows().forEach((row: DataFrameRow) => {\n if (String(col(row, 'set')) !== ps.set) return;\n const id = String(col(row, 'id'));\n const group = col(row, 'group') != null && String(col(row, 'group')) !== 'NA' ? String(col(row, 'group')) : null;\n const color = col(row, 'color') && String(col(row, 'color')) !== 'NA' ? String(col(row, 'color'))\n : group && groupColorMap[group] ? groupColorMap[group]\n : PALETTE[si % PALETTE.length];\n const pt = rowToPoint(row, 'id', color, pointScale);\n pt.ID = `${ps.set}::${id}`;\n pt.size = ps.size ?? config.pointSize ?? 2.5;\n const shape = col(row, 'shape');\n if (shape && String(shape) !== 'NA') pt.shape = String(shape);\n const label = col(row, 'label');\n (pt as any).meta = {\n stroke: '#ffffff', kind: 'point',\n name: label != null && String(label) !== 'NA' ? String(label) : id,\n group: group ?? undefined, unit: id, set: ps.set,\n fixedSize: ps.fixedSize,\n };\n this.__data__.points.set(pt.ID, pt);\n psLayer?.__data__.objects.set(pt.ID, pt);\n });\n });\n }\n\n if (model.points?.rows) {\n const pointsLayer = this.__children__.search('__children__', 'points') as QELayer;\n if (pointsLayer) {\n model.points.rows().forEach((row: DataFrameRow) => {\n // Determine this point's group color\n const groupColIdx = groupColName ? row.names.indexOf(groupColName) : -1;\n const group = groupColIdx >= 0 ? String(row[groupColIdx]) : null;\n const colorStr = group ? (groupColorMap[group] ?? '#888888') : '#888888';\n\n // Only add unit dots to the layer when 'points' attribute is present.\n if (showUnitPoints) {\n const pt = rowToPoint(row, unitIdCol, colorStr, pointScale);\n // Unit-point size: <qe-points size=…> overrides the default 2.5.\n // (Point() defaults to 1, which renders smaller than code nodes.)\n pt.size = config.pointSize ?? 2.5;\n // White halo separates overlapping dots in dense clusters.\n // meta.kind/name/group feed the qe-node-* interaction events.\n (pt as any).meta = {\n ...((pt as any).meta ?? {}),\n stroke: '#ffffff', kind: 'point', name: pt.ID,\n group: group ?? undefined, unit: pt.ID,\n fixedSize: config.pointFixedSize,\n };\n this.__data__.points.set(pt.ID, pt);\n pointsLayer.__data__.objects.set(pt.ID, pt);\n }\n\n // Always accumulate for mean + variance (needed for Path B even without dots)\n if (group) {\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n if (!groupSums[group]) groupSums[group] = { x: 0, y: 0, x2: 0, y2: 0, xy: 0, n: 0, color: colorStr };\n const rx = xIdx >= 0 ? Number(row[xIdx]) : 0;\n const ry = yIdx >= 0 ? Number(row[yIdx]) : 0;\n groupSums[group].x += rx;\n groupSums[group].y += ry;\n groupSums[group].x2 += rx * rx;\n groupSums[group].y2 += ry * ry;\n groupSums[group].xy += rx * ry;\n groupSums[group].n += 1;\n }\n });\n\n // ── Group means + bounds ──────────────────────────────────────────────\n // Two paths:\n // A) model.groups frame present → use pre-computed means + bounds.\n // This is the Phase 3+ preferred path. qeviz renders; adapters compute.\n // B) No groups frame → compute means from unit-point accumulations\n // (legacy fallback; also used when only points are provided).\n //\n // Deprecated frames (model.confidence, model.outlier) are still respected\n // in path B for backward compatibility with rENA adapters not yet updated.\n //\n // Means rendering is guarded by config.showMeans (<qe-means> presence).\n // When absent, activeGroupRows is kept empty so the labels section below\n // also skips mean labels cleanly.\n\n const hasGroupsFrame = !!(model.groups?.rows && model.groups.rows().length > 0);\n\n // Rows from the groups frame that are active in the current view.\n // Empty when <qe-means> is absent so downstream label logic is consistent.\n const activeGroupRows: DataFrameRow[] = (config.showMeans && hasGroupsFrame)\n ? model.groups.rows().filter((r: DataFrameRow) => {\n const g = r.rowName ?? String(r[0]);\n return activeMeanGroups.size === 0 \|\| activeMeanGroups.has(g);\n })\n : [];\n\n if (config.showMeans) {\n const pointsLayerSvg = pointsLayer.svg_element as SVGGElement \| null;\n // Interval stroke scales with the displayed range, so a plot zoomed to\n // its points (range=\"points\", or a number) keeps thin lines; with\n // range=\"network\" (= maxNodeExtent × 1.2) this is maxNodeExtent.\n const ciExtent = this._rangeExtent ? this._rangeExtent / 1.2 : maxNodeExtent;\n const sw = (ciExtent > 0 ? ciExtent : 1) * 0.008;\n\n if (hasGroupsFrame) {\n // ── Path A: groups frame ─────────────────────────────────────────\n // Remove CI/outlier rects for groups no longer active.\n const activeNames = new Set(activeGroupRows.map((r: DataFrameRow) => r.rowName ?? String(r[0])));\n this._ciRects.forEach((el, g) => { if (!activeNames.has(g)) { el.remove(); this._ciRects.delete(g); } });\n this._outlierRects.forEach((el, g) => { if (!activeNames.has(g)) { el.remove(); this._outlierRects.delete(g); } });\n this._ciCross.forEach((el, k) => { if (!activeNames.has(k.slice(2))) { el.remove(); this._ciCross.delete(k); } });\n\n activeGroupRows.forEach((row: DataFrameRow) => {\n const group = row.rowName ?? String(row[0]);\n const color = groupColorMap[group] ?? '#888888';\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n const mx = xIdx >= 0 ? Number(row[xIdx]) * pointScale : 0;\n const my = yIdx >= 0 ? -Number(row[yIdx]) * pointScale : 0;\n\n // Mean marker — square, larger than unit points\n const meanPt = new Point({\n ID: `mean-${group}`,\n dimensions: [mx, my],\n meta: { kind: 'mean', name: group, group, fixedSize: config.meanFixedSize },\n });\n meanPt.color = new Color(color);\n meanPt.size = 4; // radius = extent × 0.006 × 4 ≈ 0.024 for a unit extent\n const shapeIdx = row.names.indexOf('shape');\n const rowShape = shapeIdx >= 0 ? row[shapeIdx] : null;\n meanPt.shape = rowShape && String(rowShape) !== 'NA' ? String(rowShape) : 'rect';\n this.__data__.points.set(meanPt.ID, meanPt);\n pointsLayer.__data__.objects.set(meanPt.ID, meanPt);\n\n // Per-mean overrides (explicit means, as rENA's ena.plot.group\n // sets them per call): groups-frame `intervals` / `outlier`\n // columns win over the <qe-means> attributes when present.\n const cell = (name: string): any => {\n const i = row.names.indexOf(name);\n const v = i >= 0 ? row[i] : null;\n return v == null \|\| String(v) === 'NA' \|\| String(v) === '' ? null : v;\n };\n const rowIv = cell('intervals');\n const iv: 'box' \| 'crosshairs' \| 'none' =\n rowIv === 'box' \|\| rowIv === 'crosshairs' \|\| rowIv === 'none' ? rowIv : config.intervals;\n const rowOut = cell('outlier');\n const showOut = rowOut == null ? config.showOutlier : (rowOut === true \|\| String(rowOut) === 'true');\n\n // Outlier interval (qe_group(outlier = TRUE)): {dim}.olow / .ohigh.\n const ob = showOut\n ? readIntervalBounds(row, dims[0] as string, dims[1] as string, 'o')\n : null;\n if (!ob) {\n this._outlierRects.get(group)?.remove(); this._outlierRects.delete(group);\n } else {\n let oel = this._outlierRects.get(group);\n if (!oel) {\n oel = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n oel.setAttribute('data-outlier-group', group);\n this._outlierRects.set(group, oel);\n }\n oel.setAttribute('x', (ob.x_low * pointScale).toString());\n oel.setAttribute('y', (-ob.y_high * pointScale).toString());\n oel.setAttribute('width', ((ob.x_high - ob.x_low) * pointScale).toString());\n oel.setAttribute('height', ((ob.y_high - ob.y_low) * pointScale).toString());\n oel.setAttribute('fill', 'none');\n oel.setAttribute('stroke', color);\n oel.setAttribute('stroke-width', sw.toString());\n oel.setAttribute('stroke-opacity', '0.5');\n oel.setAttribute('stroke-dasharray', `${sw * 2} ${sw * 2}`);\n if (pointsLayerSvg && !oel.parentElement) pointsLayerSvg.insertBefore(oel, pointsLayerSvg.firstChild);\n }\n\n // CI (<qe-means intervals=\"box\|crosshairs\|none\">, or the legacy\n // `confidence` flag = box). Gated so qe_group(intervals = \"none\")\n // draws nothing.\n const bounds = iv !== 'none'\n ? readIntervalBounds(row, dims[0] as string, dims[1] as string)\n : null;\n const crossKey = `x:${group}`;\n if (!bounds \|\| iv !== 'crosshairs') {\n this._ciCross.get(crossKey)?.remove(); this._ciCross.delete(crossKey);\n }\n if (bounds && iv === 'crosshairs') {\n this._ciRects.get(group)?.remove(); this._ciRects.delete(group);\n // Two arms through the mean: x_lo..x_hi at the mean's y, and\n // y_lo..y_hi at the mean's x.\n const x0 = bounds.x_low * pointScale, x1 = bounds.x_high * pointScale;\n const y0 = -bounds.y_high * pointScale, y1 = -bounds.y_low * pointScale;\n capMeanToInterval(meanPt, (x1 - x0) / 2, (y1 - y0) / 2);\n let cel = this._ciCross.get(crossKey);\n if (!cel) {\n cel = document.createElementNS('http://www.w3.org/2000/svg', 'path') as SVGPathElement;\n cel.setAttribute('data-ci-group', group);\n cel.setAttribute('data-ci-kind', 'crosshairs');\n this._ciCross.set(crossKey, cel);\n }\n cel.setAttribute('d', `M${x0} ${my} L${x1} ${my} M${mx} ${y0} L${mx} ${y1}`);\n cel.setAttribute('fill', 'none');\n cel.setAttribute('stroke', color);\n cel.setAttribute('stroke-width', (sw * 1.25).toString());\n cel.setAttribute('stroke-opacity', '0.8');\n if (pointsLayerSvg && !cel.parentElement) pointsLayerSvg.insertBefore(cel, pointsLayerSvg.firstChild);\n } else if (!bounds) {\n const stale = this._ciRects.get(group);\n if (stale) { stale.remove(); this._ciRects.delete(group); }\n } else {\n const rect_x = bounds.x_low * pointScale;\n const rect_y = -bounds.y_high * pointScale;\n const rect_width = (bounds.x_high - bounds.x_low) * pointScale;\n const rect_height = (bounds.y_high - bounds.y_low) * pointScale;\n capMeanToInterval(meanPt, rect_width / 2, rect_height / 2);\n\n let el = this._ciRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-ci-group', group);\n this._ciRects.set(group, el);\n }\n el.setAttribute('x', rect_x.toString());\n el.setAttribute('y', rect_y.toString());\n el.setAttribute('width', rect_width.toString());\n el.setAttribute('height', rect_height.toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.8');\n el.setAttribute('stroke-dasharray', `${sw * 4} ${sw * 3}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n }\n });\n\n } else {\n // ── Path B: legacy — compute means from groupSums ────────────────\n // Add one mean point per group — larger (size=1.5) and same group color\n Object.entries(groupSums).forEach(([group, { x, y, n, color }]) => {\n const meanPt = new Point({\n ID: `mean-${group}`,\n dimensions: [x / n * pointScale, -(y / n) * pointScale],\n meta: { kind: 'mean', name: group, group, fixedSize: config.meanFixedSize },\n });\n meanPt.color = new Color(color);\n meanPt.size = 4; // radius = extent × 0.006 × 4 ≈ 0.024 for a unit extent\n meanPt.shape = 'rect';\n this.__data__.points.set(meanPt.ID, meanPt);\n pointsLayer.__data__.objects.set(meanPt.ID, meanPt);\n });\n\n // ── CI boxes (deprecated confidence frame or JS fallback) ────────\n const showCI = config.showCI;\n if (showCI) {\n this._ciRects.forEach((el, g) => {\n if (!groupSums[g]) { el.remove(); this._ciRects.delete(g); }\n });\n\n if (model.confidence?.rows) {\n // Pre-computed path: deprecated model.confidence frame\n model.confidence.rows().forEach((row: DataFrameRow) => {\n const groupIdx = row.names.indexOf(groupColName ?? 'group');\n const group = groupIdx >= 0 ? String(row[groupIdx]) : (row.rowName ?? null);\n if (!group) return;\n const color = groupColorMap[group] ?? '#888888';\n const bounds = readIntervalBounds(row, dims[0] as string, dims[1] as string);\n if (!bounds) return;\n const rect_x = bounds.x_low * pointScale;\n const rect_y = -bounds.y_high * pointScale;\n const rect_width = (bounds.x_high - bounds.x_low) * pointScale;\n const rect_height = (bounds.y_high - bounds.y_low) * pointScale;\n capMeanToInterval(this.__data__.points.get(`mean-${group}`) as Point \| undefined,\n rect_width / 2, rect_height / 2);\n let el = this._ciRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-ci-group', group);\n this._ciRects.set(group, el);\n }\n el.setAttribute('x', rect_x.toString());\n el.setAttribute('y', rect_y.toString());\n el.setAttribute('width', rect_width.toString());\n el.setAttribute('height', rect_height.toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.8');\n el.setAttribute('stroke-dasharray', `${sw * 4} ${sw * 3}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n });\n } else {\n // JS fallback: compute CI from accumulated variance\n Object.entries(groupSums).forEach(([group, { x, y, x2, y2, n, color }]) => {\n if (n < 2) return;\n const μx = x / n, μy = y / n;\n const rawVarX = x2 / n - μx * μx;\n const rawVarY = y2 / n - μy * μy;\n const { halfW, halfH } = computeCIRect(rawVarX, rawVarY, n, pointScale);\n const cx = μx * pointScale, cy = -(μy) * pointScale;\n capMeanToInterval(this.__data__.points.get(`mean-${group}`) as Point \| undefined,\n halfW, halfH);\n let el = this._ciRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-ci-group', group);\n this._ciRects.set(group, el);\n }\n el.setAttribute('x', (cx - halfW).toString());\n el.setAttribute('y', (cy - halfH).toString());\n el.setAttribute('width', (halfW * 2).toString());\n el.setAttribute('height', (halfH * 2).toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.8');\n el.setAttribute('stroke-dasharray', `${sw * 4} ${sw * 3}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n });\n }\n }\n\n // ── Outlier boxes (deprecated model.outlier frame) ───────────────\n const showOutlier = true; // legacy frame; presence of model.outlier guards rendering\n if (showOutlier && model.outlier?.rows) {\n this._outlierRects.forEach((el, g) => {\n if (!groupColorMap[g]) { el.remove(); this._outlierRects.delete(g); }\n });\n model.outlier.rows().forEach((row: DataFrameRow) => {\n const groupIdx = row.names.indexOf(groupColName ?? 'group');\n const group = groupIdx >= 0 ? String(row[groupIdx]) : (row.rowName ?? null);\n if (!group) return;\n const color = groupColorMap[group] ?? '#888888';\n const bounds = readIntervalBounds(row, dims[0] as string, dims[1] as string);\n if (!bounds) return;\n const rect_x = bounds.x_low * pointScale;\n const rect_y = -bounds.y_high * pointScale;\n const rect_width = (bounds.x_high - bounds.x_low) * pointScale;\n const rect_height = (bounds.y_high - bounds.y_low) * pointScale;\n let el = this._outlierRects.get(group);\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'rect') as SVGRectElement;\n el.setAttribute('data-outlier-group', group);\n this._outlierRects.set(group, el);\n }\n el.setAttribute('x', rect_x.toString());\n el.setAttribute('y', rect_y.toString());\n el.setAttribute('width', rect_width.toString());\n el.setAttribute('height', rect_height.toString());\n el.setAttribute('fill', 'none');\n el.setAttribute('stroke', color);\n el.setAttribute('stroke-width', sw.toString());\n el.setAttribute('stroke-opacity', '0.5');\n el.setAttribute('stroke-dasharray', `${sw * 2} ${sw * 2}`);\n if (pointsLayerSvg && !el.parentElement) {\n pointsLayerSvg.insertBefore(el, pointsLayerSvg.firstChild);\n }\n });\n }\n } // end Path B\n } // end config.showMeans\n\n // ── Labels ──────────────────────────────────────────────────────────\n if (labelSvg) {\n // Remove labels for objects that no longer exist\n this._pointLabels.forEach((lbl, id) => {\n if (!pointsLayer.__data__.objects.get(id)) { lbl.remove(); this._pointLabels.delete(id); }\n });\n this._meanLabels.forEach((lbl, id) => {\n if (!pointsLayer.__data__.objects.get(`mean-${id}`)) { lbl.remove(); this._meanLabels.delete(id); }\n });\n\n // Unit point labels\n if (labelPoints !== 0) {\n model.points.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n const unitId = qIdx >= 0 ? String(row[qIdx]) : null;\n if (!unitId) return;\n const pt = pointsLayer.__data__.objects.get(unitId) as Point \| undefined;\n if (!pt) return;\n // Use the raw unit ID as the label text.\n // TODO: support a label-format attribute or callback so callers\n // can supply a custom display string (e.g. strip a prefix,\n // extract a sub-field from a compound ID, etc.)\n const displayText = unitId;\n let lbl = this._pointLabels.get(unitId);\n if (!lbl) {\n lbl = new QELabel(displayText, pt, labelSvg, this, labelPoints);\n this._pointLabels.set(unitId, lbl);\n } else {\n labelPoints === Label.DISPLAY_TYPES.ON ? lbl.show() : lbl.hide();\n }\n });\n }\n\n // Mean labels — use active groups frame rows if available, else groupSums keys\n if (labelMeans !== 0) {\n const meanGroupNames: string[] = hasGroupsFrame\n ? activeGroupRows.map((r: DataFrameRow) => r.rowName ?? String(r[0]))\n : Object.keys(groupSums);\n\n meanGroupNames.forEach((group: string) => {\n const meanId = `mean-${group}`;\n const pt = pointsLayer.__data__.objects.get(meanId) as Point \| undefined;\n if (!pt) return;\n let lbl = this._meanLabels.get(group);\n if (!lbl) {\n lbl = new QELabel(group, pt, labelSvg, this, labelMeans);\n this._meanLabels.set(group, lbl);\n } else {\n labelMeans === Label.DISPLAY_TYPES.ON ? lbl.show() : lbl.hide();\n }\n });\n }\n }\n\n pointsLayer.__data__.__state__.setVariable('layer_updated', pointsLayer.__data__);\n }\n }\n\n // ── Cognitive Trajectories Layer ──────────────────────────────────────────\n const trajectoriesLayer = this.__children__.search('__children__', 'trajectories') as QELayer;\n const trajectoriesEnabled = config.showTrajectories;\n if (trajectoriesEnabled && trajectoriesLayer) {\n trajectoriesLayer.__data__.objects.clear();\n this.__data__.trajectories.clear();\n\n const trajSource = model.trajectories?.rows ? model.trajectories : model.points;\n if (trajSource?.rows) {\n const unitRows: Record<string, Array<{ x: number; y: number; time: number }>> = {};\n const selectedUnits = config.trajectoryUnits ? config.trajectoryUnits.split(',').map(s => s.trim()) : null;\n\n trajSource.rows().forEach((row: DataFrameRow) => {\n const uIdx = row.names.indexOf(unitIdCol) >= 0 ? row.names.indexOf(unitIdCol) : (row.names.indexOf('unit') >= 0 ? row.names.indexOf('unit') : (row.names.indexOf('ENA_UNIT') >= 0 ? row.names.indexOf('ENA_UNIT') : -1));\n const unit = uIdx >= 0 ? String(row[uIdx]) : (row.rowName \|\| 'unit-1');\n\n if (selectedUnits && !selectedUnits.includes(unit)) return;\n\n const xIdx = row.names.indexOf(dims[0]);\n const yIdx = dims.length > 1 ? row.names.indexOf(dims[1]) : -1;\n const tIdx = row.names.indexOf('time') >= 0 ? row.names.indexOf('time') : (row.names.indexOf('ActivityNumber') >= 0 ? row.names.indexOf('ActivityNumber') : (row.names.indexOf('RowID') >= 0 ? row.names.indexOf('RowID') : -1));\n\n const time = tIdx >= 0 ? Number(row[tIdx]) : (unitRows[unit] ? unitRows[unit].length + 1 : 1);\n // Keep every row: the playhead is applied inside Trajectory via\n // currentTime so degree selection can run on the full trajectory\n // while only the visible prefix is fit and drawn.\n\n if (xIdx >= 0 && yIdx >= 0) {\n if (!unitRows[unit]) unitRows[unit] = [];\n unitRows[unit].push({\n x: Number(row[xIdx]) * pointScale,\n y: -Number(row[yIdx]) * pointScale,\n time\n });\n }\n });\n\n const unitKeys = Object.keys(unitRows);\n unitKeys.forEach((unitKey, uIdx) => {\n const rawPts = unitRows[unitKey];\n if (rawPts.length === 0) return;\n\n const colorStr = PALETTE[uIdx % PALETTE.length];\n\n const trajObj = new Trajectory({\n ID: `traj-${unitKey}`,\n unitId: unitKey,\n color: new Color(colorStr),\n lineStyle: config.trajectoryLineStyle,\n strokeWidth: config.trajectoryStrokeWidth,\n strokeWidthRange: config.trajectoryStrokeWidthRange,\n opacityRange: config.trajectoryOpacityRange,\n smooth: config.trajectorySmooth,\n maxDegree: config.trajectoryMaxDegree,\n degreeSelection: config.trajectoryDegreeSelection,\n currentTime: config.trajectoryPlayhead ?? Infinity,\n showPoints: config.trajectoryShowPoints,\n showTips: config.trajectoryShowTips,\n points: rawPts.map(p => ({ x: p.x, y: p.y, time: p.time }))\n });\n\n this.__data__.trajectories.set(unitKey, trajObj);\n trajectoriesLayer.__data__.objects.set(trajObj.ID, trajObj);\n });\n }\n trajectoriesLayer.__data__.__state__.setVariable('layer_updated', trajectoriesLayer.__data__);\n }\n\n // ── Mean network edges ───────────────────────────────────────────────────\n // For each group, compute the mean weight of every edge column across its\n // unit rows, then draw a Line for pairs whose mean weight is non-zero.\n const networkLayer = this.__children__.search('__children__', 'network') as QELayer;\n const edgeLayer = networkLayer?.__children__.search('__children__', 'edges') as QELayer;\n const nodeLayer = networkLayer?.__children__.search('__children__', 'nodes') as QELayer;\n // edgenodes sits above `nodes` in the layer tree — self-connections (NodeEdge)\n // must be drawn here so the dot is visible on top of the code node.\n const edgenodeLayer = networkLayer?.__children__.search('__children__', 'edgenodes') as QELayer;\n\n const edgesEnabled = config.showEdges;\n if (model.nodes?.rows && nodeLayer) {\n // ── Step 1: Populate node positions first ─────────────────────────────\n // Nodes are always placed so they anchor the coordinate space (extremes).\n // Sizes will be overwritten after edge weights are computed; when edges\n // are hidden the default size is used instead.\n model.nodes.rows().forEach((row: DataFrameRow) => {\n const pt = rowToPoint(row, nodeIdCol, '#444444');\n pt.size = 2; // default when no edge weights available\n // Display text: the nodes frame's optional `label` column\n // (qe_nodes(labels =)); the code id stays the node's identity.\n const li = row.names.indexOf('label');\n const lv = li >= 0 ? row[li] : null;\n (pt as any).meta = { ...((pt as any).meta ?? {}), kind: 'node',\n name: lv != null && String(lv) !== 'NA' && String(lv) !== '' ? String(lv) : pt.ID };\n nodeLayer.__data__.objects.set(pt.ID, pt);\n });\n\n if (edgesEnabled && edgeLayer && model.edges?.rows) {\n // ── Step 2: Build unit→group lookup from points data ─────────────────\n const unitGroupMap: Record<string, string> = {};\n if (groupColName && model.points?.rows) {\n model.points.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n const gIdx = row.names.indexOf(groupColName!);\n if (qIdx >= 0 && gIdx >= 0) unitGroupMap[String(row[qIdx])] = String(row[gIdx]);\n });\n }\n\n // ── Step 3: Collect valid edge-column → code-pair mappings ───────────\n const codeNames: string[] = model.nodes.rows().map((r: DataFrameRow) => {\n const idx = r.names.indexOf(nodeIdCol);\n return idx >= 0 ? String(r[idx]) : '';\n }).filter(Boolean);\n\n const edgePairs: Array<{ col: string; pair: [string, string] }> = [];\n (model.edges.names ?? []).forEach((col: string) => {\n const pair = parseEdgePair(col, codeNames);\n if (pair) edgePairs.push({ col, pair });\n });\n\n // ── Step 4: Edge-weight helpers ───────────────────────────────────────\n type EdgeWeights = Record<string, number>;\n\n /** Raw weights for a single unit row. /\n const getUnitEdges = (unitId: string): EdgeWeights => {\n const result: EdgeWeights = {};\n model.edges.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n if (qIdx < 0 \|\| String(row[qIdx]) !== unitId) return;\n edgePairs.forEach(({ col }) => {\n const colIdx = row.names.indexOf(col);\n if (colIdx >= 0) result[col] = Number(row[colIdx]) \|\| 0;\n });\n });\n return result;\n };\n\n /* Mean weights across all units in a group. /\n const getGroupEdges = (groupName: string): EdgeWeights => {\n const sums: EdgeWeights = {};\n let count = 0;\n model.edges.rows().forEach((row: DataFrameRow) => {\n const qIdx = row.names.indexOf(unitIdCol);\n const unitId = qIdx >= 0 ? String(row[qIdx]) : null;\n const gColIdx = groupColName ? row.names.indexOf(groupColName) : -1;\n const group = gColIdx >= 0 ? String(row[gColIdx]) : (unitId ? unitGroupMap[unitId] : null);\n if (group !== groupName) return;\n count++;\n edgePairs.forEach(({ col }) => {\n const colIdx = row.names.indexOf(col);\n if (colIdx >= 0) { const v = Number(row[colIdx]); if (!isNaN(v)) sums[col] = (sums[col] ?? 0) + v; }\n });\n });\n if (count === 0) return {};\n const result: EdgeWeights = {};\n edgePairs.forEach(({ col }) => { result[col] = (sums[col] ?? 0) / count; });\n return result;\n };\n\n /* Resolve an identifier to edge weights + color.\n * Checks group names first, then treats the value as a unit ID. /\n const resolve = (id: string): { weights: EdgeWeights; color: string; label: string } => {\n if (groupColorMap[id]) {\n return { weights: getGroupEdges(id), color: groupColorMap[id], label: id };\n }\n // Unit: color from its group, or neutral grey\n const groupOfUnit = unitGroupMap[id] ?? null;\n const color = groupOfUnit ? (groupColorMap[groupOfUnit] ?? '#888888') : '#888888';\n return { weights: getUnitEdges(id), color, label: id };\n };\n\n // ── Steps 5–6: Build the edges to draw, one <qe-edges> layer at a time ─\n //\n // Named layers (as before):\n // group=\"A\" — group mean\n // unit=\"u\" — one unit's network\n // group=\"A\" compare=\"B\" — subtraction A − B (sign → colour)\n // group=\"A\" also=\"B\" — two groups overlaid\n // Explicit layers (0.5):\n // network=\"n1\" — a row of model.networks (signed)\n // Per layer: colors=\"pos,neg\" overrides the palette; threshold=\"min,max\"\n // drops \|w\| < min and caps \|w\| > max (rENA semantics).\n // Each entry's weight is ≥ 0; the sign is carried by its colour.\n type DrawEdge = { col: string; pair: [string, string]; weight: number; color: string;\n layer: number; name?: string; group?: string; unit?: string };\n const drawEdges: DrawEdge[] = [];\n\n const networkRow = (name: string): EdgeWeights \| null => {\n const frame = (model as any).networks;\n const row = frame?.rows?.().find((r: DataFrameRow) => r.rowName === name);\n if (!row) return null;\n const w: EdgeWeights = {};\n edgePairs.forEach(({ col }) => {\n const i = row.names.indexOf(col);\n if (i >= 0) { const v = Number(row[i]); if (Number.isFinite(v)) w[col] = v; }\n });\n return w;\n };\n const thresholded = (w: number, thr: [number, number] \| null): number => {\n if (!thr) return w;\n const a = Math.abs(w);\n if (a < thr[0]) return 0;\n return a > thr[1] ? Math.sign(w) thr[1] : w;\n };\n\n config.edgeLayers.forEach((L, li) => {\n const push = (col: string, pair: [string, string], w: number, color: string,\n meta: { name?: string; group?: string; unit?: string }) => {\n w = thresholded(w, L.threshold);\n if (Math.abs(w) < 1e-6) return;\n drawEdges.push({ col: `${li}:${col}`, pair, weight: Math.abs(w), color, layer: li, ...meta });\n };\n const signColors = (pos: string, neg: string): [string, string] => {\n if (!L.colors) return [pos, neg];\n return [L.colors[0], L.colors[1] ?? complementColor(L.colors[0])];\n };\n\n if (L.network) {\n // Explicit network: signed weights from model.networks.\n const w = networkRow(L.network);\n if (!w) return;\n const [pos, neg] = signColors(PALETTE[0], PALETTE[1]);\n const meta = { name: L.name ?? L.network };\n edgePairs.forEach(({ col, pair }) => {\n const v = w[col] ?? 0;\n push(col, pair, v, v >= 0 ? pos : neg, meta);\n });\n return;\n }\n\n // Named layer — unit overrides group; no default to the first group.\n const primaryId = L.unit ?? L.group ?? null;\n if (!primaryId) return;\n const primary = resolve(primaryId);\n const secondaryId = L.compare ?? L.also ?? null;\n const secondary = secondaryId ? resolve(secondaryId) : null;\n const meta = { name: L.name ?? primaryId, group: L.group ?? undefined, unit: L.unit ?? undefined };\n const [pos, neg] = signColors(primary.color, secondary?.color ?? primary.color);\n\n if (secondary && L.compare) {\n // A − B: positive → primary colour, negative → secondary colour\n edgePairs.forEach(({ col, pair }) => {\n const d = (primary.weights[col] ?? 0) - (secondary.weights[col] ?? 0);\n push(col, pair, d, d > 0 ? pos : neg, meta);\n });\n } else if (secondary && L.also) {\n // Overlay: both networks, each in its own colour\n edgePairs.forEach(({ col, pair }) => {\n const wA = primary.weights[col] ?? 0, wB = secondary.weights[col] ?? 0;\n if (wA > 0) push(col + '-a', pair, wA, pos, meta);\n if (wB > 0) push(col + '-b', pair, wB, neg, { ...meta, name: L.also ?? undefined, group: L.also ?? undefined });\n });\n } else {\n edgePairs.forEach(({ col, pair }) => {\n const w = primary.weights[col] ?? 0;\n if (w > 0) push(col, pair, w, pos, meta);\n });\n }\n });\n\n // Thin edges on top (rENA's thin.lines.in.front): later objects draw\n // over earlier ones, so add the heaviest first.\n drawEdges.sort((a, b) => b.weight - a.weight);\n\n // ── Step 7: Mark sizes and colour ────────────────────────────────────\n // Width is absolute (webENA): raw weight × one width-per-weight set by\n // <qe-graph edge-width>, shared by edges, directed wide ends,\n // self-connection dots and nodes (diameter = Σ edge widths).\n const isDirected = !!(model as any).directed;\n // <qe-edges magnify> scales this plot's widths and node sizes (not\n // colour) — e.g. to read a faint subtraction — and is always\n // labelled \"(scaled Nx)\" so it is never mistaken for the shared scale.\n const widthFrac = widthPerWeight(config.edgeWidth) * (config.edgeMagnify ?? 1);\n\n // Colour (webENA ramps): each class (lines vs self-loops) rescales\n // \|weight\| from [min, max] onto saturation 0.25–1 / opacity 0.3–1.\n // The range comes from the whole model — every non-zero weight in\n // the edges frame — so plots of one model share a colour scale;\n // webENA takes it from each plotted network (\"plot\").\n const rangeOf = (ws: number[]): [number, number] => {\n const nz = ws.map(Math.abs).filter(v => v > 0);\n return nz.length ? [Math.min(...nz), Math.max(...nz)] : [0, 0];\n };\n const modelRange = (self: boolean): [number, number] => {\n const vals: number[] = [];\n edgePairs.forEach(({ col, pair }) => {\n if ((pair[0] === pair[1]) !== self) return;\n const column = model.edges.col(col);\n if (column) for (const v of column) vals.push(Number(v));\n });\n return rangeOf(vals);\n };\n const plotRange = (self: boolean): [number, number] =>\n rangeOf(drawEdges.filter(e => (e.pair[0] === e.pair[1]) === self).map(e => e.weight));\n const cscale = config.edgeColorScale;\n const colourRange = (self: boolean): [number, number] =>\n cscale === 'plot' ? plotRange(self) : modelRange(self);\n const lineRange = colourRange(false), selfRange = colourRange(true);\n const colourOf = (w: number, self: boolean) => {\n if (cscale === 'absolute') { const a = Math.min(1, Math.abs(w)); return { saturation: a, opacity: a }; }\n const [lo, hi] = self ? selfRange : lineRange;\n return { saturation: rampFor(w, lo, hi, SATURATION_RANGE), opacity: rampFor(w, lo, hi, OPACITY_RANGE) };\n };\n\n // Weight accumulated at each node:\n // Undirected: every edge touching the node (both endpoints).\n // Directed: only edges directed at the node (pair[1] is the\n // target; its wide end is drawn there), including the\n // node's self-connection.\n const nodeWeightSum: Record<string, number> = {};\n drawEdges.forEach(({ pair, weight }) => {\n const isSelf = pair[0] === pair[1];\n if (isSelf && !isDirected) return; // skip illegal undirected diagonals\n const add = (id: string) => { nodeWeightSum[id] = (nodeWeightSum[id] ?? 0) + Math.abs(weight); };\n if (isDirected) { add(pair[1]); return; }\n add(pair[0]); add(pair[1]);\n });\n\n // Node sizes: diameter = Σ widths of the edges counted above. Nodes\n // with nothing counted get a tiny dot, or are hidden with\n // <qe-nodes unconnected=\"hide\">.\n model.nodes.rows().forEach((row: DataFrameRow) => {\n const codeIdx = row.names.indexOf(nodeIdCol);\n const id = codeIdx >= 0 ? String(row[codeIdx]) : '';\n if (!id) return;\n const pt = nodeLayer.__data__.objects.get(id) as Point \| undefined;\n if (!pt) return;\n const w = nodeWeightSum[id] ?? 0;\n const unconnected = !(w > 0);\n pt.size = unconnected ? (config.hideUnconnectedNodes ? 0 : UNCONNECTED_NODE_SIZE)\n : nodeSizeForEdges(w, widthFrac);\n (pt as any).meta = { ...((pt as any).meta ?? {}),\n hidden: unconnected && config.hideUnconnectedNodes };\n });\n\n // ── Step 8: Create edge objects ───────────────────────────────────────\n // For directed models, TaperedWeightedMidpointEdge needs the combined\n // weight of both directions (A→B + B→A) so the apex can be positioned\n // proportionally along the edge. Build a lookup keyed by \"A.B\" per\n // drawn network: an `also` overlay draws two networks in one layer,\n // and pooling them left every triangle short of its counterpart.\n const totalWeightByPair: Record<string, number> = {};\n const pairKey = (layer: number, net: string \| undefined, a: string, b: string) =>\n `${layer}:${net ?? ''}:${a}.${b}`;\n if (isDirected) {\n drawEdges.forEach(({ pair, weight, layer, name }) => {\n const key = pairKey(layer, name, pair[0], pair[1]);\n totalWeightByPair[key] = (totalWeightByPair[key] ?? 0) + weight;\n });\n }\n\n drawEdges.forEach(({ col, pair, weight, color, layer, name, group, unit }) => {\n const fromNode = nodeLayer.__data__.objects.get(pair[0]);\n const toNode = nodeLayer.__data__.objects.get(pair[1]);\n if (!fromNode \|\| !toNode) return;\n\n const isSelf = pair[0] === pair[1];\n if (isSelf && !isDirected) return; // undirected ENA has zero diagonal\n\n // Colour ramps rescale within each visual class (lines vs\n // self-loops), since self-weights are typically smaller.\n const { saturation, opacity } = colourOf(weight, isSelf);\n const fromPt = new Point({ ID: `${pair[0]}-src`, dimensions: [fromNode.x, fromNode.y], meta: {} });\n const toPt = new Point({ ID: `${pair[1]}-dst`, dimensions: [toNode.x, toNode.y], meta: {} });\n // Pick the edge class by topology:\n // • self-connection (A→A) → NodeEdge (filled circle at the node)\n // • directed (A→B) → TaperedWeightedMidpointEdge (triangle\n // whose apex is placed proportionally\n // to weight(A→B) / (weight(A→B) + weight(B→A)))\n // • undirected → Line (straight stroke)\n let edgeLine: Line;\n if (isSelf) {\n edgeLine = new NodeEdge({}, fromPt as any, toPt as any);\n // Actual display size is deferred to QELine.update() so it uses\n // the live extremes.x_max (which is not yet computed here).\n // Set a placeholder weight; update() will overwrite it.\n (edgeLine as any).weight = 0;\n } else if (isDirected) {\n const fwd = totalWeightByPair[pairKey(layer, name, pair[0], pair[1])] ?? weight;\n const bwd = totalWeightByPair[pairKey(layer, name, pair[1], pair[0])] ?? 0;\n const totalweight = fwd + bwd;\n edgeLine = new TaperedWeightedMidpointEdge(\n { weight, totalweight },\n fromPt as any,\n toPt as any\n );\n } else {\n edgeLine = new Line({}, fromPt, toPt);\n }\n edgeLine.ID = `edge-${col}`;\n edgeLine.color = new Color(color);\n (edgeLine as any).meta = {\n isMeanEdge: true,\n weight,\n // Width per unit weight (extent units), shared by all marks.\n widthFrac,\n saturation,\n opacity,\n isDirected,\n isSelf,\n // Identity for the qe-edge-* interaction events.\n source: pair[0],\n target: pair[1],\n group,\n unit,\n layer: name,\n };\n // Self-connections go in the `edgenodes` layer (above `nodes` in\n // draw order) so the dot is visible on top of the code node.\n const targetLayer = isSelf ? (edgenodeLayer ?? edgeLayer) : edgeLayer;\n targetLayer.__data__.objects.set(edgeLine.ID, edgeLine);\n });\n\n edgeLayer.__data__.__state__.setVariable('layer_updated', edgeLayer.__data__);\n if (edgenodeLayer) edgenodeLayer.__data__.__state__.setVariable('layer_updated', edgenodeLayer.__data__);\n }\n\n // ── Node visibility ──────────────────────────────────────────────────\n // Node positions come from the model and stay in the layer either way,\n // so they keep anchoring the extent (the plot does not rescale when\n // nodes are toggled); <qe-nodes> presence only controls the drawing,\n // as <qe-axes> does for the axis sub-tree.\n const nodesVisible = config.showNodes;\n if (nodeLayer.svg_element) {\n (nodeLayer.svg_element as SVGElement).style.display = nodesVisible ? '' : 'none';\n }\n if (!nodesVisible) {\n this._nodeLabels.forEach(lbl => lbl.remove());\n this._nodeLabels.clear();\n }\n\n // ── Node labels ──────────────────────────────────────────────────────\n if (labelSvg && labelNodes !== 0 && nodesVisible) {\n // Clean up stale node labels\n this._nodeLabels.forEach((lbl, id) => {\n if (!nodeLayer.__data__.objects.get(id)) { lbl.remove(); this._nodeLabels.delete(id); }\n });\n model.nodes.rows().forEach((row: DataFrameRow) => {\n const codeIdx = row.names.indexOf(nodeIdCol);\n const id = codeIdx >= 0 ? String(row[codeIdx]) : '';\n if (!id) return;\n const pt = nodeLayer.__data__.objects.get(id) as Point \| undefined;\n if (!pt) return;\n if ((pt as any).meta?.hidden) {\n this._nodeLabels.get(id)?.remove();\n this._nodeLabels.delete(id);\n return;\n }\n const text = String((pt as any).meta?.name ?? id);\n let lbl = this._nodeLabels.get(id);\n if (lbl && lbl.text !== text) { lbl.remove(); this._nodeLabels.delete(id); lbl = undefined; }\n if (!lbl) {\n lbl = new QELabel(text, pt, labelSvg, this, labelNodes);\n this._nodeLabels.set(id, lbl);\n } else {\n labelNodes === Label.DISPLAY_TYPES.ON ? lbl.show() : lbl.hide();\n }\n });\n }\n\n // Fire after both positions and sizes are set\n nodeLayer.__data__.__state__.setVariable('layer_updated', nodeLayer.__data__);\n }\n\n // ── Axis lines / points ──────────────────────────────────────────────────\n const axisPointsLayer = this.__children__.search('__children__', 'axis_points');\n const axisLinesLayer = this.__children__.search('__children__', 'axis_lines');\n if (axisPointsLayer) this.__data__.__state__.setVariable('graph_updated_axis_points', axisPointsLayer.__data__.objects);\n if (axisLinesLayer) this.__data__.__state__.setVariable('graph_updated_axis_lines', axisLinesLayer.__data__.objects);\n\n this.update();\n\n // Animate marks/edges from their pre-rebuild positions to the new ones.\n if (tweenFrom) this._runTween(tweenFrom);\n });\n }\n\n // ── Shared re-render scheduler ───────────────────────────────────────────────\n // Batches synchronous attribute / child-list changes into a single microtask\n // so that e.g. adding <qe-edges> and setting its attributes in the same tick\n // only triggers one render cycle.\n private _scheduleRerender(): void {\n if (!this._vizena \|\| !this._hasModel) return;\n if (this._renderPending) return;\n this._renderPending = true;\n queueMicrotask(() => {\n this._renderPending = false;\n this._vizena?.dispatchEvent(new CustomEvent('model-updated', {\n detail: this._vizena.model,\n bubbles: true,\n composed: true,\n }));\n });\n }\n\n // ── Layer configuration reader ────────────────────────────────────────────────\n // Reads child element presence / attributes to determine what each layer\n // should render. Called once at the top of every model-updated handler so\n // all rendering decisions are derived from a single snapshot.\n private _readLayerConfig(): {\n // Nodes\n labelNodes: number;\n showNodes: boolean;\n edgeWidth: number;\n range: 'network' \| 'points' \| number \| null;\n centerContent: boolean;\n plotTitle: string \| null;\n labelFont: { size: number \| null; family: string \| null; color: string \| null };\n hideUnconnectedNodes: boolean;\n scalePoints: boolean;\n pointScale: number \| null;\n // Means\n showMeans: boolean;\n activeMeanGroups: string \| null;\n showCI: boolean;\n intervals: 'box' \| 'crosshairs' \| 'none';\n showOutlier: boolean;\n labelMeans: number;\n meanFixedSize: boolean;\n // Points\n showPoints: boolean;\n pointSets: Array<{ set: string; size: number \| null; fixedSize: boolean }>;\n labelPoints: number;\n pointSize: number \| null;\n pointFixedSize: boolean;\n // Edges\n showEdges: boolean;\n edgeLayers: EdgeLayerSpec[];\n edgeColorScale: ColorScale;\n edgeMagnify: number \| null;\n\n showTrajectories: boolean;\n trajectoryUnits: string \| null;\n trajectorySmooth: 'none' \| 'poly';\n trajectoryMaxDegree: number;\n trajectoryDegreeSelection: 'loocv_2d' \| 'fixed';\n trajectoryShowPoints: boolean;\n trajectoryShowTips: boolean;\n trajectoryPlayhead: number \| null;\n trajectoryLineStyle: 'uniform' \| 'tapered';\n trajectoryStrokeWidth: number;\n trajectoryStrokeWidthRange: [number, number];\n trajectoryOpacityRange: [number, number];\n // Axes\n showAxes: boolean;\n axisXLabel: string \| null;\n axisYLabel: string \| null;\n } {\n const nodesEl = this.querySelector('qe-nodes');\n const meansEl = this.querySelector('qe-means');\n // <qe-points> without `set` = all unit points; with `set` = an explicit set.\n const allPointsEls = [...this.querySelectorAll('qe-points')];\n const pointsEl = allPointsEls.find(e => !e.hasAttribute('set')) ?? null;\n const setEls = allPointsEls.filter(e => e.hasAttribute('set'));\n // Every <qe-edges> child is one layer (0.5): a named network (group / unit\n // / compare / also) or an explicit one (network=\"name\" → model.networks).\n const edgeEls = [...this.querySelectorAll('qe-edges')];\n const firstAttr = (a: string) => edgeEls.find(e => e.hasAttribute(a))?.getAttribute(a) ?? null;\n const magnifyEl = edgeEls.find(e => e.hasAttribute('magnify'));\n const trajectoriesEl = this.querySelector('qe-trajectories');\n const axesEl = this.querySelector('qe-axes');\n const labelsShorthand = this.getAttribute('labels');\n\n return {\n // Nodes — always placed from the model (they anchor the coordinate\n // space); <qe-nodes> presence draws them, like every other layer.\n labelNodes: parseLabelMode(\n nodesEl?.getAttribute('label') ?? this.getAttribute('label-nodes') ?? labelsShorthand,\n Label.DISPLAY_TYPES.ON\n ),\n showNodes: !!nodesEl,\n range: (() => {\n const v = this.getAttribute('range');\n if (v === 'network' \|\| v === 'points') return v;\n const n = Number(v);\n return v != null && Number.isFinite(n) && n > 0 ? n : null;\n })(),\n plotTitle: this.getAttribute('plot-title') \|\| null,\n labelFont: {\n size: (() => { const n = Number(this.getAttribute('label-font-size'));\n return Number.isFinite(n) && n > 0 ? n : null; })(),\n family: this.getAttribute('label-font-family') \|\| null,\n color: this.getAttribute('label-font-color') \|\| null,\n },\n edgeWidth: (() => {\n const v = Number(this.getAttribute('edge-width'));\n return Number.isFinite(v) && v > 0 && v <= 1 ? v : DEFAULT_EDGE_WIDTH;\n })(),\n hideUnconnectedNodes: nodesEl?.getAttribute('unconnected')?.toLowerCase() === 'hide',\n scalePoints: this.getAttribute('scale-points') !== 'false',\n pointScale: (() => {\n const v = Number(this.getAttribute('point-scale'));\n return this.hasAttribute('point-scale') && Number.isFinite(v) && v > 0 ? v : null;\n })(),\n centerContent: this.getAttribute('center') === 'content',\n\n // Means — presence of <qe-means> = show; absence = hide.\n showMeans: !!meansEl,\n activeMeanGroups: meansEl?.getAttribute('groups') ?? null,\n showCI: !!meansEl && meansEl.hasAttribute('confidence'),\n // intervals=\"box\|crosshairs\|none\"; absent → the legacy `confidence` flag.\n intervals: (() => {\n const v = meansEl?.getAttribute('intervals');\n if (v === 'box' \|\| v === 'crosshairs' \|\| v === 'none') return v;\n return meansEl?.hasAttribute('confidence') ? 'box' : 'none';\n })() as 'box' \| 'crosshairs' \| 'none',\n showOutlier: !!meansEl && meansEl.hasAttribute('outlier'),\n labelMeans: parseLabelMode(\n meansEl?.getAttribute('label') ?? this.getAttribute('label-means') ?? labelsShorthand,\n Label.DISPLAY_TYPES.ON\n ),\n // fixed-size keeps mean markers a constant on-screen px size (webENA parity).\n meanFixedSize: !!meansEl && meansEl.hasAttribute('fixed-size'),\n\n // Points — presence of <qe-points> = show unit dots.\n showPoints: !!pointsEl,\n pointSets: setEls.map(e => ({\n set: e.getAttribute('set')!,\n size: e.getAttribute('size') ? parseFloat(e.getAttribute('size')!) : null,\n fixedSize: e.hasAttribute('fixed-size'),\n })),\n labelPoints: parseLabelMode(\n pointsEl?.getAttribute('label') ?? this.getAttribute('label-points') ?? labelsShorthand,\n Label.DISPLAY_TYPES.OFF\n ),\n pointSize: pointsEl?.getAttribute('size') ? parseFloat(pointsEl.getAttribute('size')!) : null,\n // fixed-size keeps unit dots a constant on-screen px size (webENA parity).\n pointFixedSize: !!pointsEl && pointsEl.hasAttribute('fixed-size'),\n\n // Edges — presence of <qe-edges> = draw a network.\n showEdges: edgeEls.length > 0,\n edgeLayers: edgeEls.map(parseEdgeLayer),\n // Plot-wide edge settings: the first <qe-edges> that sets them.\n edgeColorScale: parseColorScale(firstAttr('color-scale')),\n edgeMagnify: magnifyEl ? (() => {\n const v = Number(magnifyEl.getAttribute('magnify'));\n return Number.isFinite(v) && v > 0 ? v : 1;\n })() : null,\n\n // Trajectories — presence of <qe-trajectories> = draw cognitive trajectories\n showTrajectories: !!trajectoriesEl,\n trajectoryUnits: trajectoriesEl?.getAttribute('units') ?? null,\n trajectorySmooth: (trajectoriesEl?.getAttribute('smooth') as 'none' \| 'poly') ?? 'none',\n trajectoryMaxDegree: trajectoriesEl?.getAttribute('max-degree') ? parseInt(trajectoriesEl.getAttribute('max-degree')!, 10) : 3,\n trajectoryDegreeSelection: (trajectoriesEl?.getAttribute('degree-selection') as 'loocv_2d' \| 'fixed') ?? 'loocv_2d',\n trajectoryShowPoints: trajectoriesEl?.getAttribute('points') !== 'false',\n trajectoryShowTips: trajectoriesEl?.getAttribute('tips') !== 'false',\n trajectoryPlayhead: trajectoriesEl?.getAttribute('playhead') ? parseFloat(trajectoriesEl.getAttribute('playhead')!) : null,\n trajectoryLineStyle: (trajectoriesEl?.getAttribute('line-style') as 'uniform' \| 'tapered') ?? 'uniform',\n trajectoryStrokeWidth: trajectoriesEl?.getAttribute('stroke-width') ? parseFloat(trajectoriesEl.getAttribute('stroke-width')!) : 2,\n trajectoryStrokeWidthRange: this._parseNumberPair(trajectoriesEl?.getAttribute('stroke-width-range'), [1, 6]),\n trajectoryOpacityRange: this._parseNumberPair(trajectoriesEl?.getAttribute('opacity-range'), [0.3, 1]),\n\n // Axes — presence of <qe-axes> = draw axis lines. The x / y attributes add\n // a per-axis label: a value is used verbatim, an empty attribute falls back\n // to the dimension name (resolved later, where dims are known). null = no\n // label for that axis.\n showAxes: !!axesEl,\n axisXLabel: axesEl?.hasAttribute('x') ? (axesEl.getAttribute('x') ?? '') : null,\n axisYLabel: axesEl?.hasAttribute('y') ? (axesEl.getAttribute('y') ?? '') : null,\n };\n }\n\n private _parseNumberPair(value: string \| null \| undefined, fallback: [number, number]): [number, number] {\n if (!value) return fallback;\n const parts = value.split(',').map(part => Number(part.trim()));\n if (parts.length < 2 \|\| !parts.every(Number.isFinite)) return fallback;\n return [parts[0], parts[1]];\n }\n\n attributeChangedCallback(_name: string, oldValue: string \| null, newValue: string \| null): void {\n if (oldValue === newValue) return;\n this._scheduleRerender();\n }\n\n connectedCallback(): void {\n // Apply width/height HTML attributes as CSS dimensions on the host element\n // so the shadow-DOM wrapper's height:100% resolves to a real pixel value.\n const w = this.getAttribute('width');\n const h = this.getAttribute('height');\n this.style.display = 'block'; // custom elements are inline by default\n if (w) this.style.width = isNaN(Number(w)) ? w : `${w}px`;\n if (h) this.style.height = isNaN(Number(h)) ? h : `${h}px`;\n\n this.appendChild(this.svg_element);\n QEGraphElement._instances.add(this); // registry for getGraph()/instances()\n\n // Watch for child layer element additions/removals and attribute changes.\n // Any mutation schedules a re-render via the same microtask batch used by\n // attributeChangedCallback, so synchronous DOM mutations collapse to one pass.\n this._childObserver = new MutationObserver(() => this._scheduleRerender());\n this._childObserver.observe(this, {\n childList: true,\n attributes: true,\n subtree: true,\n attributeFilter: [\n 'group', 'unit', 'compare', 'also', 'color-scale', 'magnify',\n 'network', 'colors', 'threshold', 'name',\n 'groups', 'confidence', 'label', 'intervals', 'outlier', 'set', 'unconnected',\n 'scale-points', 'point-scale', 'edge-width', 'labels', 'range', 'center', 'plot-title',\n 'label-font-size', 'label-font-family', 'label-font-color', 'label-nodes', 'label-means', 'label-points',\n 'units', 'smooth', 'degree', 'points', 'tips', 'playhead',\n 'line-style', 'stroke-width', 'stroke-width-range', 'opacity-range',\n 'x', 'y', 'size', 'fixed-size',\n ],\n });\n // Find the associated ena-visual: check 'for' attribute first, then nearest\n // ancestor, then first one on the page. This lets ena-graph work as a child,\n // a sibling, or anywhere else in the document.\n const forId = this.getAttribute('for');\n this._vizena = (\n (forId ? document.getElementById(forId) : null) ??\n this.closest('qe-visual') ??\n this.parentElement?.closest('qe-visual') ??\n document.querySelector('qe-visual')\n ) as QEVisualElement;\n this.draw();\n\n // Cache the labels <g> after draw() has connected all layer elements to\n // the SVG DOM. We do this once here rather than searching on every\n // model-updated event to guarantee we always have a valid reference.\n const labelsLayer = this.__children__.search('__children__', 'labels') as QELayer;\n if (labelsLayer?.svg_element) {\n this._labelsGroup = labelsLayer.svg_element as SVGGElement;\n } else {\n // Fallback: create a new <g> directly inside the outermost graph layer.\n console.warn('[ena-graph] labels layer not found in layer tree; creating fallback <g>');\n const graphLayer = this.__children__[0] as QELayer;\n if (graphLayer?.svg_element) {\n this._labelsGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g') as SVGGElement;\n this._labelsGroup.setAttribute('data-layer-name', 'labels-fallback');\n graphLayer.svg_element.appendChild(this._labelsGroup);\n }\n }\n }\n\n disconnectedCallback(): void {\n this._childObserver?.disconnect();\n this._childObserver = null;\n this._resizeObs?.disconnect();\n this._resizeObs = null;\n QEGraphElement._instances.delete(this);\n // Remove the body-level tooltip node so it doesn't outlive the graph.\n this._tooltipEl?.remove();\n this._tooltipEl = null;\n }\n\n // ── Instance registry + read APIs (webENA integration) ──────────────────────\n private static _instances: Set<QEGraphElement> = new Set();\n\n /** All connected <qe-graph> instances (newest membership order). /\n static instances(): QEGraphElement[] { return [...QEGraphElement._instances]; }\n\n /* Look up a graph by its `id` or `plot-group` attribute. /\n static getGraph(key: string): QEGraphElement \| null {\n for (const g of QEGraphElement._instances) {\n if (g.id === key \|\| g.getAttribute('plot-group') === key) return g;\n }\n return null;\n }\n\n /* Resolved code nodes with their current graph-space coordinates. /\n getNodes(): Array<{ id: string; name: string; x: number; y: number }> {\n const layer = this.__children__.search('__children__', 'nodes') as QELayer \| undefined;\n if (!layer) return [];\n return [...layer.__data__.objects.values()].map((o: any) => ({\n id: o.ID, name: o.meta?.name ?? o.ID, x: o.x, y: o.y,\n }));\n }\n\n /* Resolved edges of the current network with weights and direction. /\n getEdges(): Array<{ source: string; target: string; weight: number; directed: boolean; self: boolean }> {\n const collect = (name: string) => {\n const l = this.__children__.search('__children__', name) as QELayer \| undefined;\n return l ? [...l.__data__.objects.values()] : [];\n };\n return [...collect('edges'), ...collect('edgenodes')]\n .map((o: any) => {\n const m = o.meta ?? {};\n return { source: m.source, target: m.target, weight: m.weight ?? 0,\n directed: !!m.isDirected, self: !!m.isSelf };\n })\n .filter(e => e.source != null && e.target != null);\n }\n\n // ── Transition tweening (opt-in via the `animate` attribute; webENA P2.1) ───\n private _animateMs = 0;\n private _tweenRaf: number \| null = null;\n\n /* Matches every numeric token in an SVG path `d` string (ints, decimals,\n * scientific notation, leading sign) while leaving command letters intact. /\n private static _PATH_NUM_RE = /-?\\d\\.?\\d+(?:e[-+]?\\d+)?/gi;\n\n /** Marks (circles/rects), undirected edge lines, and directed / self-edge\n * triangle paths all participate in tweening. /\n private _tweenTargets(): SVGElement[] {\n return [...this.svg_element.querySelectorAll(\n 'circle[data-point-id], rect[data-point-id], line[data-edge-source], path[data-edge-source]'\n )] as SVGElement[];\n }\n\n private _readCoords(el: SVGElement): any {\n const tag = el.tagName.toLowerCase();\n const n = (a: string) => parseFloat(el.getAttribute(a) \|\| '0');\n if (tag === 'circle') return { t: 'c', cx: n('cx'), cy: n('cy') };\n if (tag === 'rect') return { t: 'r', x: n('x'), y: n('y') };\n if (tag === 'line') return { t: 'l', x1: n('x1'), y1: n('y1'), x2: n('x2'), y2: n('y2') };\n if (tag === 'path') {\n const d = el.getAttribute('d') \|\| '';\n return { t: 'p', d, nums: (d.match(QEGraphElement._PATH_NUM_RE) \|\| []).map(Number) };\n }\n return null;\n }\n\n /* Snapshot current tween-target positions keyed by element. /\n private _captureTween(): Map<SVGElement, any> {\n const m = new Map<SVGElement, any>();\n this._tweenTargets().forEach(el => { const c = this._readCoords(el); if (c) m.set(el, c); });\n return m;\n }\n\n /* Animate each still-present element from its snapshot to its new position. /\n private _runTween(from: Map<SVGElement, any>): void {\n if (this._tweenRaf !== null) { cancelAnimationFrame(this._tweenRaf); this._tweenRaf = null; }\n const to = new Map<SVGElement, any>();\n this._tweenTargets().forEach(el => { if (from.has(el)) { const c = this._readCoords(el); if (c) to.set(el, c); } });\n if (!to.size) return;\n\n const dur = this._animateMs;\n const t0 = performance.now();\n const ease = (t: number) => (t < 0.5 ? 2 t * t : 1 - Math.pow(-2 * t + 2, 2) / 2);\n const lerp = (a: number, b: number, k: number) => a + (b - a) * k;\n\n const step = (now: number) => {\n const t = Math.min(1, (now - t0) / dur);\n const k = ease(t);\n to.forEach((nc, el) => {\n const oc = from.get(el);\n if (!oc \|\| oc.t !== nc.t) return;\n if (nc.t === 'c') {\n el.setAttribute('cx', String(lerp(oc.cx, nc.cx, k)));\n el.setAttribute('cy', String(lerp(oc.cy, nc.cy, k)));\n } else if (nc.t === 'r') {\n el.setAttribute('x', String(lerp(oc.x, nc.x, k)));\n el.setAttribute('y', String(lerp(oc.y, nc.y, k)));\n } else if (nc.t === 'l') {\n el.setAttribute('x1', String(lerp(oc.x1, nc.x1, k)));\n el.setAttribute('y1', String(lerp(oc.y1, nc.y1, k)));\n el.setAttribute('x2', String(lerp(oc.x2, nc.x2, k)));\n el.setAttribute('y2', String(lerp(oc.y2, nc.y2, k)));\n } else {\n // Directed / self-edge triangle path: interpolate the numeric tokens\n // in `d` when the command structure is stable (equal token count).\n // Otherwise leave the freshly-built `d` in place (graceful snap).\n if (!oc.nums \|\| oc.nums.length !== nc.nums.length) return;\n let i = 0;\n const d = nc.d.replace(QEGraphElement._PATH_NUM_RE,\n () => String(lerp(oc.nums[i], nc.nums[i++], k)));\n el.setAttribute('d', d);\n }\n });\n this._tweenRaf = t < 1 ? requestAnimationFrame(step) : null;\n };\n this._tweenRaf = requestAnimationFrame(step);\n }\n\n /** Serialize the current plot as a standalone SVG string (webENA P2.3). /\n toSVG(): string {\n const svg = this.svg_element.cloneNode(true) as SVGSVGElement;\n svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg');\n svg.setAttribute('xmlns:xlink', 'http://www.w3.org/1999/xlink');\n const rect = this.svg_element.getBoundingClientRect();\n if (rect.width) svg.setAttribute('width', String(Math.round(rect.width)));\n if (rect.height) svg.setAttribute('height', String(Math.round(rect.height)));\n return new XMLSerializer().serializeToString(svg);\n }\n\n /* Rasterize the current plot to a PNG data URL (webENA P2.3). `scale`\n * multiplies the pixel dimensions for a higher-resolution image. /\n toPNG(scale = 2): Promise<string> {\n const svgStr = this.toSVG();\n const rect = this.svg_element.getBoundingClientRect();\n const w = Math.max(1, Math.round(rect.width));\n const h = Math.max(1, Math.round(rect.height));\n return new Promise((resolve, reject) => {\n const blob = new Blob([svgStr], { type: 'image/svg+xml;charset=utf-8' });\n const url = URL.createObjectURL(blob);\n const img = new Image();\n img.onload = () => {\n try {\n const canvas = document.createElement('canvas');\n canvas.width = w scale;\n canvas.height = h * scale;\n const ctx = canvas.getContext('2d');\n if (!ctx) { URL.revokeObjectURL(url); reject(new Error('no 2d context')); return; }\n ctx.scale(scale, scale);\n ctx.drawImage(img, 0, 0, w, h);\n URL.revokeObjectURL(url);\n resolve(canvas.toDataURL('image/png'));\n } catch (err) { URL.revokeObjectURL(url); reject(err); }\n };\n img.onerror = (e) => { URL.revokeObjectURL(url); reject(e); };\n img.src = url;\n });\n }\n\n /** Unit points with their current graph-space coordinates. /\n getPoints(): Array<{ id: string; group?: string; set?: string; x: number; y: number }> {\n const layer = this.__children__.search('__children__', 'points') as QELayer \| undefined;\n if (!layer) return [];\n return [...layer.__data__.objects.values()]\n .filter((o: any) => o.meta?.kind === 'point')\n .map((o: any) => ({ id: o.meta?.unit ?? o.ID, group: o.meta?.group, set: o.meta?.set,\n x: o.x, y: o.y }));\n }\n\n /* Ids of unit points inside a graph-space rectangle (for drag/lasso select). /\n pointsInRect(rect: { x: number; y: number; w: number; h: number }): string[] {\n return this.getPoints()\n .filter(p => p.x >= rect.x && p.x <= rect.x + rect.w &&\n p.y >= rect.y && p.y <= rect.y + rect.h)\n .map(p => p.id);\n }\n\n // ── Host-driven highlight / selection (webENA P1.1) ─────────────────────────\n // Rendered as an overlay group so it never mutates the marks themselves, and\n // is re-applied after every render so selection survives model updates.\n private _highlight: { edges: Set<string>; nodes: Set<string> } = { edges: new Set(), nodes: new Set() };\n private _highlightGroup: SVGGElement \| null = null;\n\n /* Order-independent key so an undirected pair matches either direction. /\n private _edgeKey(a: string, b: string): string {\n return a <= b ? `${a}\u0000${b}` : `${b}\u0000${a}`;\n }\n\n /* Mark edges/nodes as highlighted. Replaces the previous selection. /\n setHighlight(sel: { edges?: Array<{ source: string; target: string }>; nodes?: Array<string> }): void {\n this._highlight.edges = new Set((sel.edges ?? []).map(e => this._edgeKey(e.source, e.target)));\n this._highlight.nodes = new Set((sel.nodes ?? []).map(String));\n this._applyHighlights();\n }\n\n /* Clear all highlighting. /\n clearHighlight(): void {\n this._highlight.edges.clear();\n this._highlight.nodes.clear();\n this._applyHighlights();\n }\n\n private _applyHighlights(): void {\n if (!this.svg_element) return;\n if (!this._highlightGroup) {\n this._highlightGroup = document.createElementNS('http://www.w3.org/2000/svg', 'g') as SVGGElement;\n this._highlightGroup.setAttribute('data-layer-name', 'highlight');\n this._highlightGroup.setAttribute('pointer-events', 'none');\n }\n // Keep the overlay on top.\n this.svg_element.appendChild(this._highlightGroup);\n const g = this._highlightGroup;\n g.textContent = '';\n\n const extent = (this.__data__ as Graph).extremes.x_max \|\| 1;\n const HL = '#f5a623';\n const mk = (tag: string, attrs: Record<string, string \| number>) => {\n const el = document.createElementNS('http://www.w3.org/2000/svg', tag);\n for (const k in attrs) el.setAttribute(k, String(attrs[k]));\n return el;\n };\n\n // Edges — a translucent glow line between the two code-node centres.\n if (this._highlight.edges.size) {\n const xy: Record<string, { x: number; y: number }> = {};\n this.getNodes().forEach(n => { xy[n.id] = { x: n.x, y: n.y }; });\n this._highlight.edges.forEach(key => {\n const [a, b] = key.split('\u0000');\n const A = xy[a], B = xy[b];\n if (!A \|\| !B) return;\n g.appendChild(mk('line', {\n x1: A.x, y1: A.y, x2: B.x, y2: B.y,\n stroke: HL, 'stroke-width': extent 0.02, 'stroke-opacity': 0.6, 'stroke-linecap': 'round',\n }));\n });\n }\n\n // Nodes / means / points — a ring around the mark.\n this._highlight.nodes.forEach(id => {\n const el = this.svg_element.querySelector(`[data-point-id=\"${(window as any).CSS?.escape ? CSS.escape(id) : id}\"]`) as SVGElement \| null;\n if (!el) return;\n const tag = el.tagName.toLowerCase();\n let cx: number, cy: number, r: number;\n if (tag === 'rect') {\n const w = parseFloat(el.getAttribute('width') \|\| '0');\n cx = parseFloat(el.getAttribute('x') \|\| '0') + w / 2;\n cy = parseFloat(el.getAttribute('y') \|\| '0') + parseFloat(el.getAttribute('height') \|\| '0') / 2;\n r = w / 2;\n } else {\n cx = parseFloat(el.getAttribute('cx') \|\| '0');\n cy = parseFloat(el.getAttribute('cy') \|\| '0');\n r = parseFloat(el.getAttribute('r') \|\| '0');\n }\n g.appendChild(mk('circle', {\n cx, cy, r: r * 1.7 + extent * 0.004, fill: 'none', stroke: HL, 'stroke-width': extent * 0.006,\n }));\n });\n }\n\n create(): SVGElement {\n const\n svg = document.createElementNS(\"http://www.w3.org/2000/svg\", \"svg\")\n ;\n svg.classList.add(\"graph\");\n // Fill the host and keep the square ENA drawing centered (equal x/y scaling\n // preserves distances). Without this the SVG collapses to an intrinsic size\n // and pins to the left, leaving dead space in the container.\n svg.style.display = 'block';\n svg.style.width = '100%';\n svg.style.height = '100%';\n svg.setAttribute(\"preserveAspectRatio\", \"xMidYMid meet\");\n svg.setAttribute(\"viewBox\", (this.__data__ as Graph).extremes.as_viewBox());\n svg.setAttribute(\"transform\", (this.__data__ as Graph).transform.toString());\n svg.setAttribute(\"role\", \"figure\");\n svg.setAttribute(\"data-graph-size\", `${Math.min((this.__data__ as Graph).extremes.width, (this.__data__ as Graph).extremes.height)}`);\n this.svg_element = svg;\n\n // Pre-generate one arrowhead marker per palette color. Per-color markers are\n // the most reliable approach: `context-stroke` and `currentColor` inheritance\n // through SVG markers is inconsistent across browsers and shadow-DOM contexts.\n // Reference as url(#qe-arrow-RRGGBB) where RRGGBB is the hex without '#'.\n const defs = document.createElementNS('http://www.w3.org/2000/svg', 'defs');\n // Arrow dimensions in SVG user-space units (viewBox is ~4.8×4.8).\n // AW must be large enough so the body of the arrowhead is visible before it\n // disappears behind the target node circle. ~5% of the viewport (0.24 units)\n // works well. markerUnits=\"userSpaceOnUse\" keeps the size fixed regardless\n // of stroke-width, so even thin edges get a readable direction indicator.\n const AW = 0.22, AH = 0.15; // arrow length (along edge) and base width (perp)\n const makeArrow = (id: string, fill: string) => {\n const m = document.createElementNS('http://www.w3.org/2000/svg', 'marker');\n m.setAttribute('id', id);\n m.setAttribute('markerWidth', String(AW));\n m.setAttribute('markerHeight',String(AH));\n m.setAttribute('refX', String(AW)); // tip at reference point\n m.setAttribute('refY', String(AH / 2));\n m.setAttribute('orient', 'auto');\n m.setAttribute('markerUnits', 'userSpaceOnUse');\n const p = document.createElementNS('http://www.w3.org/2000/svg', 'path');\n p.setAttribute('d', `M0,0 L0,${AH} L${AW},${AH/2} z`);\n p.setAttribute('fill', fill);\n m.appendChild(p);\n defs.appendChild(m);\n };\n // One marker per GROUP_PALETTE entry (covers all possible edge colors)\n GROUP_PALETTE.forEach(color => makeArrow(`qe-arrow-${color.slice(1)}`, color));\n svg.appendChild(defs);\n\n this.__data__.layers.forEach((layer: LayerLike) => {\n const layer_g: QELayer = new QELayer(layer as any, this.svg_element, this);\n this.__children__.push(layer_g);\n });\n\n this.__data__.__state__.setVariable(\"graph_updated\", this.__data__ );\n\n this.attach_events();\n\n return svg;\n }\n\n attach_events() {\n // Attach event for zooming\n this.svg_element.addEventListener(\"wheel\", (ev: WheelEvent) => {\n console.log(\"Wheel event: \", ev);\n ev.preventDefault();\n const delta = Math.sign(ev.deltaY);\n if (delta < 0) {\n this.zoom_level = 1.1;\n } else {\n this.zoom_level /= 1.1;\n }\n this.__data__.transform.zoom(this.zoom_level);\n this.update();\n });\n\n // Attach event for panning\n let isPanning = false;\n let startX: number, startY: number;\n\n this.svg_element.addEventListener(\"mousedown\", (ev: MouseEvent) => {\n isPanning = true;\n startX = ev.clientX;\n startY = ev.clientY;\n });\n let panAnimationFrame: number \| null = null;\n let pendingPan: { dx: number, dy: number } \| null = null;\n\n const panUpdate = () => {\n if (pendingPan) {\n this.__data__.transform.pan(pendingPan.dx, pendingPan.dy);\n this.__children__[0].svg_element.setAttribute(\"transform\", this.__data__.transform.toString());\n pendingPan = null;\n }\n panAnimationFrame = null;\n };\n\n this.svg_element.addEventListener(\"mousemove\", (ev: MouseEvent) => {\n if (!isPanning) return;\n const \n dx = ev.clientX - startX,\n dy = ev.clientY - startY\n ;\n pendingPan = { dx: dx / 100, dy: dy / 100 };\n startX = ev.clientX;\n startY = ev.clientY;\n \n if (panAnimationFrame === null) {\n panAnimationFrame = requestAnimationFrame(panUpdate);\n }\n });\n\n this.svg_element.addEventListener(\"mouseup\", (ev: MouseEvent) => {\n isPanning = false;\n });\n\n // ── Label interactions ───────────────────────────────────────────────────\n // CLICK mode: toggle label on point-clicked event\n this.svg_element.addEventListener('point-clicked', ((ev: CustomEvent) => {\n const id = ev.detail?.pointData?.ID;\n if (!id) return;\n const lbl = this._pointLabels.get(id)\n ?? this._meanLabels.get(id.replace('mean-', ''))\n ?? this._nodeLabels.get(id);\n if (lbl && lbl.displayMode === Label.DISPLAY_TYPES.CLICK) lbl.toggle();\n }) as EventListener);\n\n // AUTO mode: show/hide labels via event delegation on the SVG.\n // We look for the nearest ancestor (or the target itself) that has\n // data-point-id so the hit-area works even on complex shapes.\n const findPointId = (el: SVGElement \| null): string \| null => {\n while (el && el !== this.svg_element) {\n const id = el.getAttribute?.('data-point-id');\n if (id) return id;\n el = el.parentElement as SVGElement \| null;\n }\n return null;\n };\n\n const getAutoLabel = (id: string): QELabel \| undefined => {\n return this._pointLabels.get(id)\n ?? this._meanLabels.get(id.replace(/^mean-/, ''))\n ?? this._nodeLabels.get(id);\n };\n\n this.svg_element.addEventListener('mouseover', (ev: MouseEvent) => {\n const id = findPointId(ev.target as SVGElement);\n if (!id) return;\n const lbl = getAutoLabel(id);\n if (lbl?.displayMode === Label.DISPLAY_TYPES.AUTO) lbl.show();\n });\n\n this.svg_element.addEventListener('mouseout', (ev: MouseEvent) => {\n // Only hide when the mouse leaves the point element entirely,\n // not when it enters a child (e.g., a nested SVG element).\n const id = findPointId(ev.target as SVGElement);\n if (!id) return;\n // relatedTarget is where the mouse went — if it's still inside\n // the same point element, don't hide.\n const related = ev.relatedTarget as SVGElement \| null;\n const relatedId = findPointId(related);\n if (relatedId === id) return; // still inside the same point\n const lbl = getAutoLabel(id);\n if (lbl?.displayMode === Label.DISPLAY_TYPES.AUTO) lbl.hide();\n });\n\n // ── Public interaction events (webENA integration surface) ────────────────\n // Dispatched on the public <qe-graph> element with bubbles+composed so a\n // host app can subscribe regardless of shadow DOM. See README \"Events\".\n this._attachInteractionEvents();\n }\n\n /* Emit a namespaced CustomEvent on the public element (bubbles + composed). /\n private _emit(name: string, detail: Record<string, any>): void {\n this.dispatchEvent(new CustomEvent(name, { detail, bubbles: true, composed: true }));\n }\n\n /* Walk up from a hit element to the nearest ancestor carrying `attr`. /\n private _closestWith(el: SVGElement \| null, attr: string): SVGElement \| null {\n while (el && el !== this.svg_element) {\n if (el.getAttribute?.(attr) != null && el.hasAttribute?.(attr)) return el;\n el = el.parentElement as SVGElement \| null;\n }\n return null;\n }\n\n /* Resolve an edge hit element to a qe-edge-* detail, or null. /\n private _edgeDetail(el: SVGElement \| null): Record<string, any> \| null {\n const e = this._closestWith(el, 'data-edge-source');\n if (!e) return null;\n const d: Record<string, any> = {\n source: e.getAttribute('data-edge-source'),\n target: e.getAttribute('data-edge-target'),\n weight: parseFloat(e.getAttribute('data-edge-weight') \|\| '0'),\n directed: e.getAttribute('data-edge-directed') === 'true',\n self: e.getAttribute('data-edge-self') === 'true',\n };\n if (e.hasAttribute('data-edge-group')) d.group = e.getAttribute('data-edge-group');\n if (e.hasAttribute('data-edge-unit')) d.unit = e.getAttribute('data-edge-unit');\n return d;\n }\n\n /* Resolve a node/mean/point hit element to a qe-node-* detail, or null. /\n private _nodeDetail(el: SVGElement \| null): Record<string, any> \| null {\n const n = this._closestWith(el, 'data-point-id');\n if (!n) return null;\n const tag = n.tagName.toLowerCase();\n let x: number, y: number;\n if (tag === 'rect') {\n x = parseFloat(n.getAttribute('x') \|\| '0') + parseFloat(n.getAttribute('width') \|\| '0') / 2;\n y = parseFloat(n.getAttribute('y') \|\| '0') + parseFloat(n.getAttribute('height') \|\| '0') / 2;\n } else {\n x = parseFloat(n.getAttribute('cx') \|\| '0');\n y = parseFloat(n.getAttribute('cy') \|\| '0');\n }\n const id = n.getAttribute('data-point-id')!;\n const d: Record<string, any> = {\n id,\n kind: n.getAttribute('data-kind') \|\| 'point',\n name: n.getAttribute('data-name') \|\| id,\n x, y,\n };\n if (n.hasAttribute('data-group')) d.group = n.getAttribute('data-group');\n if (n.hasAttribute('data-unit')) d.unit = n.getAttribute('data-unit');\n return d;\n }\n\n private _attachInteractionEvents(): void {\n const svg = this.svg_element;\n\n svg.addEventListener('click', (ev: MouseEvent) => {\n const target = ev.target as SVGElement;\n const edge = this._edgeDetail(target);\n if (edge) { this._emit('qe-edge-click', { ...edge, originalEvent: ev }); return; }\n const node = this._nodeDetail(target);\n if (node) this._emit('qe-node-click', { ...node, originalEvent: ev });\n });\n\n // Hover enter/leave, tracked so we emit one unhover→hover pair per change.\n let hovered: { type: 'edge' \| 'node'; key: string } \| null = null;\n const keyOf = (t: 'edge' \| 'node', d: Record<string, any>) =>\n t === 'edge' ? `${d.source}\u0000${d.target}` : String(d.id);\n\n svg.addEventListener('mousemove', (ev: MouseEvent) => {\n const target = ev.target as SVGElement;\n const edge = this._edgeDetail(target);\n const node = edge ? null : this._nodeDetail(target);\n const next = edge ? { type: 'edge' as const, detail: edge }\n : node ? { type: 'node' as const, detail: node }\n : null;\n const nextKey = next ? keyOf(next.type, next.detail) : null;\n if (hovered && (!next \|\| hovered.key !== nextKey)) {\n this._emit(hovered.type === 'edge' ? 'qe-edge-unhover' : 'qe-node-unhover', { key: hovered.key });\n hovered = null;\n }\n if (next && (!hovered \|\| hovered.key !== nextKey)) {\n this._emit(next.type === 'edge' ? 'qe-edge-hover' : 'qe-node-hover', { ...next.detail, originalEvent: ev });\n hovered = { type: next.type, key: nextKey! };\n }\n // Opt-in built-in tooltip (P1.3 bonus): shown only when <qe-graph tooltip>.\n // The host is free to build its own from the hover events instead.\n if (this.hasAttribute('tooltip') && next) {\n this._showTooltip(this._tooltipText(next.type, next.detail), ev.clientX, ev.clientY);\n } else {\n this._hideTooltip();\n }\n });\n\n svg.addEventListener('mouseleave', () => {\n if (hovered) {\n this._emit(hovered.type === 'edge' ? 'qe-edge-unhover' : 'qe-node-unhover', { key: hovered.key });\n hovered = null;\n }\n this._hideTooltip();\n });\n }\n\n // ── Opt-in built-in tooltip ─────────────────────────────────────────────────\n private _tooltipEl: HTMLDivElement \| null = null;\n\n /* \"source – target (weight)\" for edges; the mark name for nodes/means/points. /\n private _tooltipText(type: 'edge' \| 'node', d: Record<string, any>): string {\n if (type === 'edge') {\n const w = Number(d.weight);\n const wStr = Number.isFinite(w) ? ` (${(+w.toFixed(3))})` : '';\n return `${d.source} – ${d.target}${wStr}`;\n }\n return String(d.name ?? d.id);\n }\n\n private _showTooltip(text: string, clientX: number, clientY: number): void {\n if (!this._tooltipEl) {\n const el = document.createElement('div');\n el.setAttribute('data-qe-tooltip', '');\n Object.assign(el.style, {\n position: 'fixed', zIndex: '2147483647', pointerEvents: 'none',\n background: 'rgba(20,20,20,0.92)', color: '#fff',\n font: '12px/1.4 system-ui, sans-serif', padding: '3px 7px',\n borderRadius: '4px', whiteSpace: 'nowrap',\n transform: 'translate(-50%, calc(-100% - 8px))',\n } as CSSStyleDeclaration);\n document.body.appendChild(el);\n this._tooltipEl = el;\n }\n this._tooltipEl.textContent = text;\n this._tooltipEl.style.left = `${clientX}px`;\n this._tooltipEl.style.top = `${clientY}px`;\n this._tooltipEl.style.display = 'block';\n }\n\n private _hideTooltip(): void {\n if (this._tooltipEl) this._tooltipEl.style.display = 'none';\n }\n\n draw() {\n if(!this.svg_element) {\n console.error(\"No element to draw to: \", this);\n return;\n }\n \n this.wrapper?.appendChild(this.svg_element);\n\n (this.__children__ as QELayer[]).forEach((enaLayer: QELayer) => {\n enaLayer.draw();\n });\n\n // Pixel-sized text (label-font-size, the plot title) is converted to model\n // units at the current width, so re-lay it out when the plot is resized.\n if (!this._resizeObs && typeof ResizeObserver !== 'undefined' && this.svg_element) {\n let lastW = 0;\n this._resizeObs = new ResizeObserver(entries => {\n const w = entries[0]?.contentRect.width ?? 0;\n if (w > 0 && Math.abs(w - lastW) > 0.5) {\n lastW = w;\n this.update_labels();\n this.update_axes();\n }\n });\n this._resizeObs.observe(this.svg_element);\n }\n }\n\n update() {\n // Two-pass update: first pass lays out elements and computes extremes;\n // second pass re-syncs the viewBox now that all element positions are final.\n this.update_extremes();\n this.update_layers();\n this.update_labels(); // positions labels using the freshly-computed extent\n this.update_extremes(); // re-apply viewBox after label/layer repositioning\n this.update_axes(); // axis line visibility + labels (uses final extent)\n this._applyHighlights(); // re-apply host highlight over the fresh render\n }\n\n /\n Axes (<qe-axes>): toggle the axis-line cross by presence, and draw/position\n * per-axis labels at the positive ends using the current extent. Labels are\n * cached SVG <text> nodes in the labels group; null text removes them.\n /\n update_axes(): void {\n // Show or hide the whole axis sub-tree (lines + origin) by <qe-axes> presence.\n const axesLayer = this.__children__.search('__children__', 'axes') as QELayer \| undefined;\n if (axesLayer?.svg_element) {\n (axesLayer.svg_element as SVGElement).style.display = this._showAxes ? '' : 'none';\n }\n\n const parent = this._labelsGroup;\n const extent = this.__data__.extremes.x_max;\n const { cx, cy } = this.__data__.extremes;\n if (!parent \|\| extent <= 0) return;\n\n const fontSize = extent 0.06;\n const gap = fontSize * 0.6;\n\n const place = (axis: 'x' \| 'y', text: string \| null) => {\n let el = this._axisLabelEls.get(axis);\n if (!this._showAxes \|\| text == null) { // remove when hidden / no label\n if (el) { el.remove(); this._axisLabelEls.delete(axis); }\n return;\n }\n if (!el) {\n el = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n el.setAttribute('data-axis-label', axis);\n el.setAttribute('pointer-events', 'none');\n parent.appendChild(el);\n this._axisLabelEls.set(axis, el);\n }\n el.textContent = text;\n el.setAttribute('font-size', fontSize.toString());\n el.setAttribute('font-family', 'system-ui, sans-serif');\n el.setAttribute('font-weight', '600');\n el.setAttribute('fill', '#556');\n if (axis === 'x') {\n // At the right (+x) tip, anchored end so any-length text grows inward\n // and never clips past the viewBox edge; nudged just above the axis.\n el.setAttribute('x', (cx + extent - gap).toString());\n el.setAttribute('y', (-gap).toString());\n el.setAttribute('text-anchor', 'end');\n } else {\n // Just below the top (−y) tip, centered on the y-axis, inside the box.\n el.setAttribute('x', (gap).toString());\n el.setAttribute('y', (cy - extent + fontSize + gap).toString());\n el.setAttribute('text-anchor', 'start');\n }\n };\n\n place('x', this._axisXText);\n place('y', this._axisYText);\n\n // Magnification label, top-left inside the plot; independent of axes.\n if (this._magnifyText == null) {\n this._magnifyEl?.remove();\n this._magnifyEl = null;\n } else {\n if (!this._magnifyEl) {\n this._magnifyEl = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n this._magnifyEl.setAttribute('data-magnify-label', '');\n this._magnifyEl.setAttribute('pointer-events', 'none');\n }\n if (!this._magnifyEl.parentElement) parent.appendChild(this._magnifyEl);\n const el = this._magnifyEl;\n el.textContent = this._magnifyText;\n el.setAttribute('font-size', (fontSize * 0.85).toString());\n el.setAttribute('font-family', 'system-ui, sans-serif');\n el.setAttribute('font-style', 'italic');\n el.setAttribute('fill', '#556');\n el.setAttribute('x', (cx - extent + gap).toString());\n el.setAttribute('y', (cy - extent + fontSize + gap).toString());\n el.setAttribute('text-anchor', 'start');\n }\n\n // Plot title (qe_plot(title =)), top centre, drawn into the SVG so it is\n // part of toSVG() / toPNG() exports.\n if (!this._plotTitle) {\n this._titleEl?.remove(); this._titleEl = null;\n } else {\n if (!this._titleEl) {\n this._titleEl = document.createElementNS('http://www.w3.org/2000/svg', 'text') as SVGTextElement;\n this._titleEl.setAttribute('data-plot-title', '');\n this._titleEl.setAttribute('pointer-events', 'none');\n }\n if (!this._titleEl.parentElement) parent.appendChild(this._titleEl);\n const px = (this._labelFont.size ?? 12) * 1.35;\n const ts = px * this.unitsPerPixel();\n const t = this._titleEl;\n t.textContent = this._plotTitle;\n t.setAttribute('font-size', ts.toString());\n t.setAttribute('font-family', this._labelFont.family ?? 'system-ui, sans-serif');\n t.setAttribute('font-weight', '600');\n t.setAttribute('fill', this._labelFont.color ?? '#223');\n t.setAttribute('x', cx.toString());\n t.setAttribute('y', (cy - extent + ts * 1.1).toString());\n t.setAttribute('text-anchor', 'middle');\n }\n }\n\n update_labels(): void {\n this._nodeLabels.forEach(lbl => lbl.update());\n this._meanLabels.forEach(lbl => lbl.update());\n this._pointLabels.forEach(lbl => lbl.update());\n }\n\n update_extremes() {\n const graph = this.__data__ as Graph;\n graph.update_extremes(this._centerContent);\n if (this._rangeExtent && this._rangeExtent > 0) {\n // A centred view measures range=\"network\" from its centre, not the origin\n const { cx, cy } = graph.extremes;\n const r = this._centerContent && this._rangeMode === 'network'\n ? graph.nodeExtentFrom(cx, cy) * 1.2\n : this._rangeExtent;\n graph.extremes = new Extremes(r, r, cx, cy);\n }\n\n const svgRect = this.svg_element?.getBoundingClientRect();\n if(this.svg_element && svgRect) {\n console.log(\"SVG rect: \", svgRect);\n let w, h;\n if(svgRect.width === 0 \|\| svgRect.height === 0) {\n w = 1;\n h = 1;\n }\n else {\n w = svgRect.width;\n h = svgRect.height;\n }\n this.__data__.scale_x = 1 / (w / (4 * this.__data__.extremes.x_max));\n this.__data__.scale_y = 1 / (h / (4 * this.__data__.extremes.y_max));\n\n // this.svg_element.setAttribute(\"transform\", this.__data__.transform.toString());\n this.__children__[0].svg_element.setAttribute(\"transform\", this.__data__.transform.toString());\n\n this.svg_element.setAttribute(\"viewBox\", (this.__data__ as Graph).extremes.as_viewBox());\n\n let axisLineLayer: LayerLike \| undefined = this.__data__.layers.search(\"layers\", \"axis_lines\");\n if (axisLineLayer) {\n let \n axis_x = axisLineLayer.objects.get(\"axis-x\") as Line,\n axis_y = axisLineLayer.objects.get(\"axis-y\") as Line\n ;\n if (axis_x && axis_y) {\n const ex = this.__data__.extremes;\n axis_x.from = new Point({ ID: \"axis-x-start\", dimensions: [ex.cx - ex.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] });\n axis_x.to = new Point({ ID: \"axis-x-end\", dimensions: [ex.cx + ex.x_max, 0], classes: [\"ena.dimension\", \"ena.dimension\"] });\n axis_y.from = new Point({ ID: \"axis-y-start\", dimensions: [0, ex.cy - ex.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] });\n axis_y.to = new Point({ ID: \"axis-y-end\", dimensions: [0, ex.cy + ex.y_max], classes: [\"ena.dimension\", \"ena.dimension\"] });\n }\n }\n }\n }\n\n update_layers() {\n (this.__children__ as QELayer[]).forEach((enaLayer: QELayer) => {\n enaLayer.update();\n });\n }\n}\ncustomElements.define(QEGraphElement.tagName, QEGraphElement);\n","// QEViz standalone entry point — no arbor/webr dependency.\n// Import this bundle directly from rENA or any non-arbor context.\n\nexport { QEVisualElement, vizENA } from './elements/QEVisual.js';\nexport { QEGraphElement } from './elements/QEGraph.js';\nimport { QEGraphElement as _QEGraph } from './elements/QEGraph.js';\n/** Look up a connected <qe-graph> by its `id` or `plot-group` attribute. /\nexport const getGraph = (key: string) => _QEGraph.getGraph(key);\n/* All connected <qe-graph> instances. */\nexport const getGraphs = () => _QEGraph.instances();\nexport { QENodesElement, QEMeansElement, QEPointsElement, QEEdgesElement, QETrajectoriesElement, QEAxesElement } from './elements/QEChildElements.js';\nexport { QELayer } from './elements/QELayer.js';\nexport { QEPoint } from './elements/QEPoint.js';\nexport { QELine } from './elements/QELine.js';\nexport { QETrajectory } from './elements/QETrajectory.js';\n\nexport type { ModelData, QEFrame, ONAModelData, ENAModelData, ENADataFrame } from './types/ModelData.js';\n\nexport { Graph } from './objects/Graph.js';\nexport { Edge } from './objects/Edges.js';\nexport { Trajectory } from './objects/Trajectory.js';\nexport { fitTrajectory, selectDegree, sampleCurve, nearOriginFilter, TRAJECTORY_ZERO_EPS } from './objects/polyfit.js';\nexport type { XY, DegreeSelection, TrajectoryFit } from './objects/polyfit.js';\nexport { Color, WeightedColor } from './objects/Color.js';\n\nexport { DataFrame, DataFrameRow, DataFrameColumn, DataFrameColumnType } from 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