@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

package/dist/chunk-AVS4IXEA.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/aggregateMatrix/model/AggMatrixModel.ts", "../plots/aggregateMatrix/settings/defaults.ts", "../plots/aggregateMatrix/viewModel/AggMatrixViewModel.ts", "../plots/aggregateMatrix/view/LegendRender.ts", "../plots/aggregateMatrix/view/AggMatrixView.ts", "../plots/aggregateMatrix/view/setControls.ts", "../plots/aggregateMatrix/AggregateMatrix.ts"],
+  "sourcesContent": ["import { type AggregateMatrix, validatePlotConfig } from '../AggregateMatrix.ts'\nimport type { AppApi } from '#rx'\n\nexport class AggMatrixModel {\n    ag: AggregateMatrix\n    app: AppApi\n\n    constructor(ag: AggregateMatrix) {\n        this.ag = ag\n        this.app = ag.app\n    }\n\n    async getData() {\n        const state = this.ag.state\n        const config = structuredClone(state.config)\n        \n        validatePlotConfig(config)\n\n        const settings = config.settings.aggregateMatrix || {}\n\n        const body = {\n            rows: config.rows,\n            columns: config.columns,\n            gradientMethod: settings.gradientMethod,\n            sizeMethod: settings.sizeMethod,\n            minDotSize: settings.minDotSize,\n            maxDotSize: settings.maxDotSize,\n            filter: state.termfilter.filter,\n            filter0: state.termfilter.filter0,\n            signal: this.ag.api?.getAbortSignal()\n        }\n\n        return await this.app.vocabApi.getAggregateMatrixData(body)\n    }\n}", "import type { AggregateMatrixSettings } from './Settings.ts'\n\nexport function getAggregateMatrixSettings(overrides = {}): AggregateMatrixSettings {\n    const defaults = {\n        startColor: '#ff9400',\n        stopColor: '#0080ff',\n        gradientMethod: 'mean',\n        sizeMethod: 'percent',\n        minDotSize: 5,\n        maxDotSize: 20,\n        dotInputMin: 2,\n        dotInputMax: 35\n    }\n\n    const mergedSettings = Object.assign({}, defaults, overrides)\n    const isValidMinMax = validateMinMax(mergedSettings, mergedSettings.minDotSize, mergedSettings.maxDotSize)\n    if (isValidMinMax !== null) {\n        throw new Error(`Invalid min/max dot size settings: ${isValidMinMax}`)\n    }\n\n    return mergedSettings\n}\n\nexport function validateMinMax(settings: AggregateMatrixSettings, min, max): string | null {\n    if (min < settings.dotInputMin) {\n        return `Minimum dot size must be greater than or equal to ${settings.dotInputMin}`\n    }\n    if (max > settings.dotInputMax) {\n        return `Maximum dot size must be less than or equal to ${settings.dotInputMax}`\n    }\n    if (min > max) {\n        return `Minimum dot size must be less than or equal to maximum dot size`\n    }\n    return null\n}", "import type { AggregateMatrix } from '../AggregateMatrix.ts'\nimport { getMaxLabelWidth, capitalizeFirstLetter } from '#dom'\nimport { scaleLinear } from 'd3-scale'\nimport type { AggMatrixDot, AxisLayoutColumns, AxisLayoutRows, ValidAggMatrixResponse } from '#types'\nimport type { AggregateMatrixSettings } from '../settings/Settings.ts'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport type { AggMatrixViewData, AggMatrixDotPosition } from './ViewModelDataTypes.ts'\n\nexport class AggMatrixViewModel {\n    ag: AggregateMatrix\n    viewData!: AggMatrixViewData\n    maxRowLabelLgth!: number\n    maxColLabelLgth!: number\n    rowTermLabelLgth!: number\n    colTermLabelLgth!: number\n    maxRowSectionLabelWdth!: number\n    maxColSectionLabelHght!: number\n    totalRowHght!: number\n    totalColWdth!: number\n    lastX!: number\n    lastY!: number\n    rowSectionRotateFlags: boolean[] = []\n    colSectionRotateFlags: boolean[] = []\n    sizeScale!: (value: number) => number\n\n    readonly topPad = 20\n    readonly hoziPad = 20\n    readonly bottomPad = 20\n    readonly sectionGap = 8\n    readonly colSectionGap = 4\n    readonly minColSectionLineInset = 2\n    readonly colSectionLabelLineGap = 3\n    readonly colSectionLabelGap = 8\n    readonly labelFontPx = 12\n\n    constructor(ag: AggregateMatrix) {\n        this.ag = ag\n        this.sizeScale = (value: number) => value\n    }\n\n    processData(data: ValidAggMatrixResponse) {\n        this.viewData = this.getDefaultViewData()\n\n        const settings = this.ag.state.config.settings.aggregateMatrix\n        // padding for either top/bottom or left/right of the dot\n        const dotPadding = settings.maxDotSize * 1.5 \n        const cellSize = settings.maxDotSize + dotPadding\n        const measureSvg = this.ag.dom.mainDiv.append('svg') as any\n\n        /** Must determine the maximum amount of space needed for the rows.\n         * If there isn't enough space to show the row section label above the \n         * relevant terms, the section label is shown horizontally. This extra\n         * space is taken into account here. */\n        const rowData = data.axesLayout.rows\n        this.rowTermLabelLgth = getMaxLabelWidth(measureSvg, [rowData.longestLabel])\n        const rowSectionLayout = this.getSectionLabelLayout(rowData.sections, cellSize, measureSvg, true)\n        this.rowSectionRotateFlags = rowSectionLayout.rotateFlags\n        this.maxRowSectionLabelWdth = rowSectionLayout.maxCrossAxisSpace\n        this.maxRowLabelLgth =\n            this.rowTermLabelLgth +\n            (this.maxRowSectionLabelWdth ? this.sectionGap + this.maxRowSectionLabelWdth : 0)\n        this.totalRowHght = cellSize * rowData.rowCount\n\n        /** Same as the rows above. Takes into account the extra space needed if >=1 col\n         * labels is rotated to be shown. */\n        const colData = data.axesLayout.columns\n        this.colTermLabelLgth = getMaxLabelWidth(measureSvg, [colData.longestLabel])\n        const colSectionLayout = this.getSectionLabelLayout(colData.sections, cellSize, measureSvg, false)\n        this.colSectionRotateFlags = colSectionLayout.rotateFlags\n        this.maxColSectionLabelHght = colSectionLayout.maxCrossAxisSpace\n        this.maxColLabelLgth =\n            this.colTermLabelLgth +\n            (this.maxColSectionLabelHght ? this.colSectionGap + this.maxColSectionLabelHght : 0)\n        this.totalColWdth = cellSize * colData.colCount\n        measureSvg.remove()\n\n        this.getPlotDimensions()\n        this.getAxisLabelPositions(rowData, colData, cellSize)\n        this.setColorScale(settings, data.colorScale)\n        this.sizeScale = scaleLinear()\n            .domain([data.sizeScale.min, data.sizeScale.max])\n            .range([settings.minDotSize, settings.maxDotSize]).clamp(true)\n        this.getDotPositions(data.data, cellSize, settings)\n    }\n\n    getSectionLabelLayout(sections: AxisLayoutRows['sections'], cellSize: number, measureSvg, isYaxis: boolean) {\n        const rotateFlags: boolean[] = []\n        const widthCache = new Map<string, number>()\n        let maxCrossAxisSpace = 0\n\n        for (const section of sections) {\n            const label = section.id || ''\n            let labelWidth = 0\n            if (label) {\n                if (!widthCache.has(label)) widthCache.set(label, getMaxLabelWidth(measureSvg, [label]))\n                labelWidth = widthCache.get(label) || 0\n            }\n            const sectionSpan = section.terms.length * cellSize\n\n            // If a section label cannot fit in the term span on its preferred orientation,\n            // flip orientation per axis: Y-axis becomes horizontal, X-axis becomes vertical.\n            const rotate = isYaxis ? labelWidth <= sectionSpan : labelWidth > sectionSpan\n            rotateFlags.push(rotate)\n\n            const crossAxisSpace = rotate\n                ? isYaxis\n                    ? this.labelFontPx\n                    : labelWidth\n                : isYaxis\n                    ? labelWidth\n                    : this.labelFontPx\n            maxCrossAxisSpace = Math.max(maxCrossAxisSpace, crossAxisSpace)\n        }\n\n        return { rotateFlags, maxCrossAxisSpace }\n    }\n\n    getPlotDimensions() {\n        const plotDim = {\n            svg: {\n                width: this.hoziPad + this.maxRowLabelLgth + this.totalColWdth + this.hoziPad,\n                height: this.topPad + this.totalRowHght + this.maxColLabelLgth + this.bottomPad\n            },\n            rowLabels: {\n                x: this.hoziPad + this.maxRowLabelLgth,\n                y: this.topPad\n            },\n            colLabels: {\n                x: 0,\n                y: this.topPad + this.totalRowHght\n            }\n        }\n        this.viewData.plotDim = plotDim\n    }\n\n    getDefaultViewData(): AggMatrixViewData {\n        return {\n            plotDim: {\n                svg: { width: 0, height: 0 },\n                rowLabels: { x: 0, y: 0 },\n                colLabels: { x: 0, y: 0 }\n            },\n            rowLabels: [],\n            colLabels: [],\n            rowSectionLabels: [],\n            colSectionLabels: [],\n            rowSectionLines: [],\n            colSectionLines: [],\n            dotPositions: [],\n            colorScale: {\n                //TODO: If the user cannot set the min and max for color values, \n                // revert to colorScale = scale\n                scale: () => '',\n                absMin: 0,\n                absMax: 0\n            }\n        }\n    }\n\n    getAxisLabelPositions(rowData: AxisLayoutRows, colData: AxisLayoutColumns, cellSize: number) {\n        const rowSectionLineX = -(this.rowTermLabelLgth + this.sectionGap / 2)\n        const rowSectionLabelGap = this.sectionGap / 2\n        const rowSectionRotateExtraGap = this.labelFontPx / 2 + 1\n        // Rotated term labels are end-anchored so their last letter sits on one reference line.\n        const colTermY = this.labelFontPx\n        const colTermBandDepth = colTermY + this.colTermLabelLgth\n        const colSectionBandStart =\n            colTermBandDepth +\n            (this.maxColSectionLabelHght ? this.colSectionGap : 0)\n        const colSectionLineY = Math.max(0, colSectionBandStart - this.colSectionLabelLineGap)\n        const colSectionLineInset = Math.max(this.minColSectionLineInset, cellSize * 0.06)\n\n        this.lastY = 0\n        this.lastX = this.hoziPad + this.maxRowLabelLgth\n\n        this.viewData.rowLabels = []\n        this.viewData.colLabels = []\n        this.viewData.rowSectionLabels = []\n        this.viewData.colSectionLabels = []\n        this.viewData.rowSectionLines = []\n        this.viewData.colSectionLines = []\n\n        for (const [rowSectionIndex, section] of rowData.sections.entries()) {\n            const sectionStartY = this.lastY\n            for (const term of section.terms) {\n                const row = {\n                    x: 0,\n                    y: this.lastY + (cellSize / 2),\n                    label: term.label || term.id\n                }\n                this.viewData.rowLabels.push(row)\n                this.lastY += cellSize\n            }\n\n            const sectionCenterY = sectionStartY + (section.terms.length * cellSize) / 2\n            const sectionEndY = sectionStartY + section.terms.length * cellSize\n            const rotate = this.rowSectionRotateFlags[rowSectionIndex]\n            this.viewData.rowSectionLabels.push({\n                x: rowSectionLineX - rowSectionLabelGap - (rotate ? rowSectionRotateExtraGap : 0),\n                y: sectionCenterY,\n                label: section.id,\n                rotate\n            })\n            this.viewData.rowSectionLines.push({\n                x: rowSectionLineX,\n                y1: sectionStartY + cellSize / 2,\n                y2: sectionEndY - cellSize / 2\n            })\n        }\n\n        for (const [colSectionIndex, section] of colData.sections.entries()) {\n            const sectionStartX = this.lastX\n            for (const term of section.terms) {\n                const col = {\n                    x: this.lastX + (cellSize / 2),\n                    y: colTermY,\n                    label: term.label || term.id\n                }\n                this.viewData.colLabels.push(col)\n                this.lastX += cellSize\n            }\n\n            const sectionCenterX = sectionStartX + (section.terms.length * cellSize) / 2\n            const rotate = this.colSectionRotateFlags[colSectionIndex]\n            const colSectionLabelY = colSectionLineY + this.colSectionLabelGap + (rotate ? 0 : this.labelFontPx / 2)\n            this.viewData.colSectionLabels.push({\n                x: sectionCenterX,\n                y: colSectionLabelY,\n                label: section.id,\n                rotate\n            })\n            this.viewData.colSectionLines.push({\n                y: colSectionLineY,\n                x1: sectionStartX + colSectionLineInset,\n                x2: this.lastX - colSectionLineInset\n            })\n        }\n    }\n\n    setColorScale(settings: AggregateMatrixSettings, colorScaleData: ValidAggMatrixResponse['colorScale']) {\n        const domain = colorScaleData.min === colorScaleData.max\n            /** Instances, like count, may return identical min and max values. \n             * Slightly adjust the domain to avoid having identical min and max values.\n             * Circumvents ColorScale requirement for unique values. \n             * If reverted, reinstate check in agg matrix route. */\n            ? [\n                    colorScaleData.min - Math.max(Math.abs(colorScaleData.min) * 0.01, 1e-12),\n                    colorScaleData.max + Math.max(Math.abs(colorScaleData.max) * 0.01, 1e-12)\n              ]\n            : [colorScaleData.min, colorScaleData.max]\n        const scale = scaleLinear()\n            .domain(domain)\n            .range([(settings.startColor as any), (settings.stopColor as any)])\n        this.viewData.colorScale = {\n            scale, \n            absMin: colorScaleData.min,\n            absMax: colorScaleData.max\n        }\n    }\n\n    getDotPositions(data: AggMatrixDot[][], cellSize: number, settings: AggregateMatrixSettings) {\n        const startX = this.hoziPad + this.maxRowLabelLgth\n        const startY = this.topPad\n\n        this.lastY = startY\n        this.lastX = startX\n\n        for (const [i, row] of data.entries()) {\n            for (const dot of row) {\n                const hasData = dot.colorValue !== null && dot.sizeValue !== null\n                const dotPos = {\n                    x: this.lastX + (cellSize / 2),\n                    y: this.lastY + (cellSize / 2),\n                    /** Regardless if the size and color value are available, the dot will render.\n                     * This will allow the tooltip to appear, displaying the data or lack thereof\n                     * to the user. */\n                    size: hasData ? this.sizeScale(dot.sizeValue!) : settings.maxDotSize,\n                    color: hasData ? this.viewData.colorScale.scale(dot.colorValue!) : 'transparent',\n                    hasData,\n                    row: dot.row,\n                    rowSection: dot.rowSection,\n                    column: dot.column,\n                    colSection: dot.colSection,\n                    tipData: [\n                        {\n                            label: dot.rowSection,\n                            value: dot.row\n                        },\n                        {\n                            label: dot.colSection,\n                            value: dot.column\n                        },\n                        {\n                            // Show the color value\n                            label: capitalizeFirstLetter(settings.gradientMethod),\n                            value: roundValueAuto(dot.colorValue) ?? 'No available data'\n                        },\n                        {\n                            // Show the size value\n                            label: capitalizeFirstLetter(settings.sizeMethod),\n                            value: roundValueAuto(dot.sizeValue) ?? 'No available data'\n                        }\n                    ]\n                } satisfies AggMatrixDotPosition\n                this.viewData.dotPositions.push(dotPos)\n                this.lastX += cellSize\n            }\n            this.lastX = startX\n            this.lastY = startY + (i + 1) * cellSize\n        }\n    }\n}", "import type { AggregateMatrix } from '../AggregateMatrix.ts'\nimport type { AggMatrixViewData } from '../viewModel/ViewModelDataTypes.ts'\nimport { ColorScale, LegendCircleReference, capitalizeFirstLetter} from '#dom'\nimport { rgb } from 'd3-color'\nimport { validateMinMax } from '../settings/defaults.ts'\n\nexport class LegendRender {\n    ag: AggregateMatrix\n    readonly xStart = 15\n\n    constructor(ag: AggregateMatrix) {\n        this.ag = ag\n    }\n\n    render(viewData: AggMatrixViewData, div: any) {\n        const settings = this.ag.state.config.settings.aggregateMatrix\n        const colorScaleSvg = div.append('svg').style('display', 'block').attr('height', 100)\n        const dotScaleSvg = div.append('svg').style('display', 'block').attr('height', settings.maxDotSize + 20 + 50) //20px for the title position, 50px for the title and padding around the rendering. \n        this.renderColorScale(viewData.colorScale, settings, colorScaleSvg)\n        this.renderDotScaleRef(dotScaleSvg, settings)\n    }\n\n    renderColorScale(colorScale, settings, svg) {\n        svg.append('text')\n            .attr('x', this.xStart)\n            .attr('y', 20)\n            .style('font-weight', 'bold')\n            .style('font-size', '0.8em')\n            .text(capitalizeFirstLetter(settings.gradientMethod))\n\n        new ColorScale({\n            holder: svg,\n            domain: colorScale.scale.domain(),\n            colors: [settings.startColor, settings.stopColor],\n            barheight: 20,\n            barwidth: 200,\n            position: `${this.xStart + 10}, 35`,\n            setColorsCallback: (val, idx) => {\n                const hexColor = rgb(val).formatHex()\n                const colorKey = idx == 0 ? 'startColor' : 'stopColor'\n                this.ag.app.dispatch({\n                    type: 'plot_edit',\n                    id: this.ag.id,\n                    config: {\n                        settings: {\n                            aggregateMatrix: {\n                                [colorKey]: hexColor\n                            }\n                        }\n                    }\n                })\n            }\n        })\n    }\n\n    renderDotScaleRef(svg, settings) {\n        new LegendCircleReference({\n            g: svg.append('g').attr('transform', `translate(${this.xStart}, 15)`),\n            inputMax: settings.dotInputMax,\n            inputMin: settings.dotInputMin,\n            maxRadius: settings.maxDotSize,\n            minRadius: settings.minDotSize,\n            isAscending: true,\n            title: capitalizeFirstLetter(settings.sizeMethod),\n            menu: {\n                minMaxLabel: 'pixels',\n\t\t\t\tcallback: async (obj: { min: number; max: number }) => {\n                    const { min, max } = obj\n                    const isValid = validateMinMax(settings, min, max)\n                    if (isValid !== null) {\n                        alert(isValid)\n                        return\n                    }\n\t\t\t\t\tthis.ag.app.dispatch({\n                        type: 'plot_edit',\n                        id: this.ag.id,\n                        config: {\n                            settings: {\n                                aggregateMatrix: {\n                                    minDotSize: min,\n                                    maxDotSize: max\n                                }\n                            }\n                        }\n                    })\n\t\t\t\t}\n\t\t\t}\n        })\n    }\n}", "import { table2col } from '#dom'\nimport type { AggregateMatrix } from '../AggregateMatrix.ts'\nimport type { AggMatrixDotPosition, AggMatrixViewData } from '../viewModel/ViewModelDataTypes.ts'\nimport { LegendRender } from './LegendRender.ts'\nimport { PSEUDOBULK } from '#types'\n\nexport class AggMatrixView {\n    ag: AggregateMatrix\n    legendRender: LegendRender\n    dom!: any\n\n    constructor(ag: AggregateMatrix) {\n        this.ag = ag\n        this.legendRender = new LegendRender(ag)\n    }\n\n    render(viewData: AggMatrixViewData) {\n        this.initDom(viewData.plotDim)\n        this.renderAxesLabels(\n            viewData.colLabels,\n            viewData.rowLabels,\n            viewData.colSectionLabels,\n            viewData.rowSectionLabels,\n            viewData.colSectionLines,\n            viewData.rowSectionLines\n        )\n        this.renderDots(viewData.dotPositions)\n        this.legendRender.render(viewData, this.dom.legendDiv)\n    }\n\n    initDom(plotDim: AggMatrixViewData['plotDim']) {\n        const mainDiv = this.ag.dom.mainDiv as any\n        mainDiv.selectAll('*').remove()\n\n        const svg = mainDiv.append('svg')\n            .attr('width', plotDim.svg.width)\n            .attr('height', plotDim.svg.height)\n            .attr('data-testid', 'sjpp-ag-matrix-svg')\n\n        const rowLabels = svg.append('g')\n            .attr('class', 'sjpp-ag-matrix-row-labels')\n            .attr('transform', `translate(${plotDim.rowLabels.x}, ${plotDim.rowLabels.y}) `)\n\n        const colLabels = svg.append('g')\n            .attr('class', 'sjpp-ag-matrix-col-labels')\n            .attr('transform', `translate(${plotDim.colLabels.x}, ${plotDim.colLabels.y})`)\n\n        const legendDiv = mainDiv.append('div')\n            .attr('class', 'sjpp-ag-matrix-legend')\n            .attr('data-testid', 'sjpp-ag-matrix-legend')\n            .style('vertical-align', 'top')\n            .style('display', 'inline-block')\n            .style('padding', `${this.ag.viewModel.topPad}px ${this.ag.viewModel.hoziPad}px`)\n\n        this.dom = {\n            svg,\n            rowLabels,\n            colLabels,\n            legendDiv\n        }\n    }\n\n    renderAxesLabels(\n        colLabels: AggMatrixViewData['colLabels'],\n        rowLabels: AggMatrixViewData['rowLabels'],\n        colSectionLabels: AggMatrixViewData['colSectionLabels'],\n        rowSectionLabels: AggMatrixViewData['rowSectionLabels'],\n        colSectionLines: AggMatrixViewData['colSectionLines'],\n        rowSectionLines: AggMatrixViewData['rowSectionLines']\n    ) {\n        const { rowLabels: rowLabelsGroup, colLabels: colLabelsGroup } = this.dom\n\n        rowLabelsGroup.selectAll('text')\n            .data(rowLabels)\n            .enter()\n            .append('text')\n            .attr('class', 'sjpp-ag-matrix-row-label')\n            .attr('text-anchor', 'end')\n            .attr('dominant-baseline', 'middle')\n            .attr('fill', '#3f3f46')\n            .attr('font-size', 12)\n            .attr('font-weight', 400)\n            .attr('transform', (d) => `translate(${d.x}, ${d.y})`)\n            .text(d => d.label)\n\n        rowLabelsGroup.selectAll('.sjpp-ag-matrix-row-section-label')\n            .data(rowSectionLabels)\n            .enter()\n            .append('text')\n            .attr('class', 'sjpp-ag-matrix-row-section-label')\n            .attr('text-anchor', d => d.rotate ? 'middle' : 'end')\n            .attr('dominant-baseline', 'middle')\n            .attr('fill', '#111827')\n            .attr('font-size', 12)\n            .attr('letter-spacing', '0.02em')\n            .attr('transform', (d) =>\n                d.rotate\n                    ? `translate(${d.x}, ${d.y}) rotate(-90)`\n                    : `translate(${d.x}, ${d.y})`\n            )\n            .text(d => d.label)\n\n        rowLabelsGroup.selectAll('.sjpp-ag-matrix-row-section-line')\n            .data(rowSectionLines)\n            .enter()\n            .append('line')\n            .attr('class', 'sjpp-ag-matrix-row-section-line')\n            .attr('stroke', '#6b7280')\n            .attr('stroke-width', 1)\n            .attr('opacity', 0.9)\n            .attr('x1', d => d.x)\n            .attr('x2', d => d.x)\n            .attr('y1', d => d.y1)\n            .attr('y2', d => d.y2)\n\n        colLabelsGroup.selectAll('text')\n            .data(colLabels)\n            .enter()\n            .append('text')\n            .attr('class', 'sjpp-ag-matrix-col-label')\n            .attr('text-anchor', 'end')\n            .attr('dominant-baseline', 'middle')\n            .attr('fill', '#3f3f46')\n            .attr('font-size', 12)\n            .attr('font-weight', 400)\n            .attr('transform', (d) => `translate(${d.x}, ${d.y}) rotate(-90)`)\n            .text(d => d.label)\n\n        colLabelsGroup.selectAll('.sjpp-ag-matrix-col-section-label')\n            .data(colSectionLabels)\n            .enter()\n            .append('text')\n            .attr('class', 'sjpp-ag-matrix-col-section-label')\n            .attr('text-anchor', d => d.rotate ? 'end' : 'middle')\n            .attr('dominant-baseline', 'middle')\n            .attr('fill', '#111827')\n            .attr('font-size', 12)\n            .attr('letter-spacing', '0.02em')\n            .attr('transform', (d) =>\n                d.rotate\n                    ? `translate(${d.x}, ${d.y}) rotate(-90)`\n                    : `translate(${d.x}, ${d.y})`\n            )\n            .text(d => d.label)\n\n        colLabelsGroup.selectAll('.sjpp-ag-matrix-col-section-line')\n            .data(colSectionLines)\n            .enter()\n            .append('line')\n            .attr('class', 'sjpp-ag-matrix-col-section-line')\n            .attr('stroke', '#6b7280')\n            .attr('stroke-width', 1)\n            .attr('opacity', 0.9)\n            .attr('x1', d => d.x1)\n            .attr('x2', d => d.x2)\n            .attr('y1', d => d.y)\n            .attr('y2', d => d.y)\n    }\n\n    renderDots(dotPositions: AggMatrixDotPosition[]) {\n        for (const dot of dotPositions) {\n            const circle = this.dom.svg.append('circle')\n                .attr('class', 'sjpp-ag-matrix-dot')\n                .attr('data-testid', `sjpp-ag-matrix-dot-${dot.row}-${dot.column}`)\n                .attr('cx', dot.x)\n                .attr('cy', dot.y)\n                .attr('r', dot.size)\n                .attr('fill', dot.color)\n                .on('mouseover', (event: MouseEvent) => {\n                    this.ag.dom.tip.clear().show(event.clientX, event.clientY)\n                    const table = table2col({ holder: this.ag.dom.tip.d })\n                    for (const v of dot.tipData) {\n                        addTableRow(table, v.label, v.value)\n                    }\n                })\n                .on('mouseout', () => {\n                    this.ag.dom.tip.clear().hide()\n                })\n            if (dot.hasData) {\n                circle.on('click', () => {\n                    const config = this.ag.state.config\n                    const colTerms = config.columns?.[dot.colSection] || []\n                    const colTerm = colTerms.find(term => term.id === dot.column)\n                    if (!colTerm) return\n                    if (colTerm.type !== PSEUDOBULK) return\n                    const tmp = structuredClone(colTerm)\n\n                    //TODO: Move this to interactions\n                    const idName = `geneExpression ${dot.row} ${dot.column}`\n                    tmp.gene = dot.row\n                    tmp.category = dot.column\n                    tmp.id = idName\n                    tmp.name = idName\n                    this.ag.app.dispatch({\n                        type: 'plot_create',\n                        config: {\n                            chartType: 'summary',\n                            term: {\n                                term: tmp,\n                                q: { mode: 'continuous' }\n                            }\n                        }\n                    })\n                })\n            }\n        }\n    }\n}\n\nfunction addTableRow(table: any, label: string, value: any) {\n    const [td1, td2] = table.addRow()\n    td1.text(label)\n    td2.text(value)\n}", "import type { AggregateMatrix } from \"../AggregateMatrix\"\nimport { controlsInit } from '#plots/controls.js'\nimport { validateMinMax } from '../settings/defaults.ts'\nimport { capitalizeFirstLetter, DownloadMenu } from '#dom'\n\n\nexport async function setControls(controlsDiv, ag: AggregateMatrix, initConfig: any) {\n\tconst settings = initConfig.settings.aggregateMatrix\n\tconst chartType = initConfig.chartType\n\tconst gradientLabel = capitalizeFirstLetter(settings.gradientMethod)\n\n\tconst inputs: any = [\n\t\t{\n\t\t\t\tlabel: `${gradientLabel} start color`,\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType,\n\t\t\t\tsettingsKey: 'startColor'\n\t\t},\n\t\t{\n\t\t\t\tlabel: `${gradientLabel} stop color`,\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType,\n\t\t\t\tsettingsKey: 'stopColor'\n\t\t},\n\t\t{\n\t\t\tlabel: 'Min dot size',\n\t\t\ttitle: 'Set the minimum dot size. Number must be between 2 and 35',\n\t\t\ttype: 'number',\n\t\t\tchartType,\n\t\t\tsettingsKey: 'minDotSize',\n\t\t\tstep: 1,\n\t\t\tmax: settings.dotInputMax,\n\t\t\tmin: settings.dotInputMin,\n\t\t\twidth: 55,\n\t\t\tdebounceInterval: 300,\n\t\t\tprocessInput: (val: number) => {\n\t\t\t\tconst currentSettings = ag.state.config.settings.aggregateMatrix\n\t\t\t\tconst isValid = validateMinMax(currentSettings, val, currentSettings.maxDotSize)\n\t\t\t\tif (isValid !== null) {\n\t\t\t\t\talert(isValid)\n\t\t\t\t\treturn currentSettings.minDotSize\n\t\t\t\t}\n\t\t\t\treturn val\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Max dot size',\n\t\t\ttitle: 'Set the maximum dot size. Number must be between 2 and 35',\n\t\t\ttype: 'number',\n\t\t\tchartType,\n\t\t\tsettingsKey: 'maxDotSize',\n\t\t\tstep: 1,\n\t\t\tmax: settings.dotInputMax,\n\t\t\tmin: settings.dotInputMin,\n\t\t\twidth: 55,\n\t\t\tdebounceInterval: 300,\n\t\t\tprocessInput: (val: number) => {\n\t\t\t\tconst currentSettings = ag.state.config.settings.aggregateMatrix\n\t\t\t\tconst isValid = validateMinMax(currentSettings, currentSettings.minDotSize, val)\n\t\t\t\tif (isValid !== null) {\n\t\t\t\t\talert(isValid)\n\t\t\t\t\treturn currentSettings.maxDotSize\n\t\t\t\t}\n\t\t\t\treturn val\n\t\t\t}\n\t\t}\n\t]\n\n\tag.components.controls = await controlsInit({\n\t\tapp: ag.app,\n\t\tid: ag.id,\n\t\tholder: controlsDiv,\n\t\tinputs: inputs\n\t})\n\n\tag.components.controls.on('downloadClick.aggregateMatrix', async event => {\n\t\tconst name = ag.state.config.name || 'Aggregate matrix'\n\t\tconst svg = ag.dom.mainDiv.select('svg')\n\t\tconst chartImages = [{ name, svg }]\n\t\tnew DownloadMenu(chartImages, name).show(event.clientX, event.clientY)\n\t})\n}", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { getCombinedTermFilter } from '#filter'\nimport { AggMatrixModel } from './model/AggMatrixModel'\nimport { getAggregateMatrixSettings } from './settings/defaults.ts'\nimport { AggMatrixViewModel } from './viewModel/AggMatrixViewModel.ts'\nimport { AggMatrixView } from './view/AggMatrixView.ts'\nimport { setControls } from './view/setControls.ts'\nimport { Menu, formatHeaderText } from '#dom'\nimport { isNonDictionaryType } from '#shared/terms.js'\n\n/**** Plot in development ***\n * The aggregate matrix displays two aggregate values for two terms in a matrix format\n * by size and color gradient.*/\nexport class AggregateMatrix extends PlotBase implements RxComponent {\n    static type = 'aggregateMatrix'\n\n    type: string\n    components: { controls: ComponentApi }\n    dom: { [index: string]: any }\n    model!: AggMatrixModel\n    viewModel!: AggMatrixViewModel\n    view!: AggMatrixView\n\n\n    constructor(opts: any, api: ComponentApi) {\n        super(opts, api)\n        this.type = AggregateMatrix.type\n        this.components = { controls: {} as ComponentApi }\n\n        const dom = super.getStandardDomLayout(opts.holder)\n        this.dom = {\n            holder: opts.holder,\n            controls: dom.controls.attr('data-testid', 'sjpp-ag-matrix-controls'),\n            errorDiv: dom.errdiv.attr('data-testid', 'sjpp-ag-matrix-error'),\n            loadingDiv: dom.loadingDiv.attr('data-testid', 'sjpp-ag-matrix-loading'),\n            mainDiv: dom.charts.attr('data-testid', 'sjpp-ag-matrix-main').style('padding', '10px'),\n            tip: new Menu({ padding: '3px' })\n        }\n\n        if (opts.header) formatHeaderText({\n            header: opts.header,\n            chartType: 'AGGREGATE MATRIX'\n        })\n    }\n\n    getState(appState: any) {\n        const config = appState.plots.find((p: any) => p.id === this.id)\n        if (!config) {\n            throw new Error(\n                `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n            )\n        }\n        const parentConfig = appState.plots.find(p => p.id === this.parentId)\n        const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n        return {\n            termfilter,\n            config\n        }\n    }\n\n    async init(appState) {\n        this.model = new AggMatrixModel(this)\n        this.viewModel = new AggMatrixViewModel(this)\n        this.view = new AggMatrixView(this)\n\n        const config = this.getState(appState).config\n        await setControls(this.dom.controls, this, config)\n    }\n\n    async main() {\n        if (!this.model) throw new Error(`Model not initialized`)\n        if (!this.viewModel) throw new Error(`ViewModel not initialized`)\n        if (!this.view) throw new Error(`View not initialized`)\n\n        super.toggleLoadingDiv()\n\n        try {\n            const data = await this.model.getData()\n            if (!data || data.error) {\n                super.toggleLoadingDiv('none')\n                super.printError(data?.error || 'No data returned from server')\n                return\n            }\n            this.viewModel.processData(data)\n        } catch (e: any) {\n            if (e instanceof Error) console.error(`${e.message || e} [AggregateMatrix main()]`)\n            else if (e.stack) console.log(e.stack)\n            super.toggleLoadingDiv('none')\n            super.printError(e.message || e)\n            return\n        }\n        this.view.render(this.viewModel.viewData)\n        super.toggleLoadingDiv('none')\n    }\n}\n\nexport const aggMatrixInit = getCompInit(AggregateMatrix)\nexport const componentInit = aggMatrixInit\n\nexport function getPlotConfig(opts: any) {\n    const config = {\n        hidePlotFilter: true,\n        settings: {\n            aggregateMatrix: getAggregateMatrixSettings(opts?.settings?.aggregateMatrix)\n        }\n    }\n\n    const returnConfig = copyMerge(config, opts)\n    validatePlotConfig(returnConfig)\n\n    return returnConfig\n}\n\nexport function validatePlotConfig(config: any) {\n    if (!config || typeof config !== 'object') throw new Error(`Invalid config provided for aggregate matrix plot`)\n    validateAxis(config.rows, 'rows')\n    validateAxis(config.columns, 'columns')\n\n    const settings = config.settings?.aggregateMatrix || {}\n    if (typeof settings.sizeMethod != 'string' || !settings.sizeMethod) {\n        throw new Error(`Invalid aggregate method for dot size`)\n    }\n    if (typeof settings.gradientMethod != 'string' || !settings.gradientMethod) {\n        throw new Error(`Invalid aggregate method for color gradient`)\n    }\n    if (settings.gradientMethod == settings.sizeMethod) throw new Error('Aggregate method for the color gradient cannot be the same as the aggregate method for the dot size.')\n}\n\nfunction validateAxis(axis: any, name: 'rows' | 'columns') {\n    if (!axis || typeof axis != 'object' || Array.isArray(axis) || !Object.keys(axis).length) {\n        throw new Error(`No ${name} provided for aggregate matrix plot`)\n    }\n    for (const [section, terms] of Object.entries<any>(axis)) {\n        if (!section.trim()) throw new Error(`Every ${name} section requires a name`)\n        if (!Array.isArray(terms) || !terms.length) throw new Error(`${name} section '${section}' has no terms`)\n        const types = new Set(terms.map(item => (item.term || item)?.type))\n        if (types.size != 1 || types.has(undefined)) {\n            throw new Error(`${name} section '${section}' must contain exactly one term type`)\n        }\n        const termType = (terms[0].term || terms[0]).type\n        if (!isNonDictionaryType(termType) && terms.length != 1) {\n            throw new Error(`${name} dictionary section '${section}' can contain only one term`)\n        }\n    }\n}\n"],
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+  "names": []
+}

package/dist/chunk-BFXZBZEV.js

@@ -0,0 +1,176 @@
+import {
+  appInit
+} from "./chunk-CPIPN5F6.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-QJ3HYZH3.js";
+import {
+  mclass
+} from "./chunk-4EZLVENZ.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (![5, 7, 9].includes(l.length)) {
+      errors.push("snv input not equal to 5, 7, or 9 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+      const vafs = parseOptionalVafs(l, errors);
+      if (vafs.length) m.vafs = vafs;
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseOptionalVafs(line, errors) {
+  const vafs = [];
+  const addVaf = (id, totalIndex, altIndex) => {
+    if (line.length <= altIndex) return;
+    const totalCount = Number(line[totalIndex]);
+    const altCount = Number(line[altIndex]);
+    if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
+      errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
+      return;
+    }
+    vafs.push({ id, totalCount, altCount });
+  };
+  addVaf("DNA", 5, 6);
+  addVaf("RNA", 7, 8);
+  return vafs;
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-BFXZBZEV.js.map