@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-BBNO6JLO.js

@@ -0,0 +1,200 @@
+import {
+  get$id,
+  renderTable,
+  sayerror
+} from "./chunk-2YC6ZVE4.js";
+
+// plots/shared/genePlotActions.ts
+function createLollipopFromGene(geneSymbol, app) {
+  const cfg = {
+    type: "plot_create",
+    config: {
+      chartType: "genomeBrowser",
+      snvindel: { shown: true },
+      // always set snvindel.shown=true so the mds3 tk is always shown; since grin2 works for this ds, it doesn't matter whether snvindel/cnv/svfusion any is present; all will be shown in mds3 tk
+      geneSearchResult: { geneSymbol }
+    }
+  };
+  if (app.vocabApi.termdbConfig.queries.trackLst?.activeTracks) {
+    cfg.config.trackLst = structuredClone(app.vocabApi.termdbConfig.queries.trackLst);
+    cfg.config.trackLst.activeTracks = [];
+  }
+  app.dispatch(cfg);
+}
+async function createMatrixFromGenes(geneSymbols, app) {
+  const MAX_GENES = 100;
+  const genesToUse = geneSymbols.slice(0, MAX_GENES);
+  try {
+    const termwrappers = await Promise.all(
+      genesToUse.map(async (gene) => {
+        const term = {
+          type: "geneVariant",
+          gene,
+          name: gene
+        };
+        const minTwCopy = app.vocabApi.getTwMinCopy({ term, q: {} });
+        return {
+          $id: await get$id(minTwCopy),
+          term,
+          q: {}
+        };
+      })
+    );
+    app.dispatch({
+      type: "plot_create",
+      config: {
+        chartType: "matrix",
+        dataType: "geneVariant",
+        termgroups: [
+          {
+            name: "Genomic Alterations",
+            lst: termwrappers
+          }
+        ]
+      }
+    });
+  } catch (error) {
+    sayerror(app.dom.div, `Error creating matrix: ${error instanceof Error ? error.message : error}`);
+  }
+}
+
+// plots/shared/resultsTable.ts
+function showResultsTable(opts) {
+  const {
+    tableDiv,
+    hits,
+    app,
+    clickMenu,
+    columns: prebuiltColumns,
+    rows: prebuiltRows,
+    dataItems: prebuiltDataItems,
+    getGene = (item) => item.gene,
+    matrixButtonFormat = "Matrix ({n})",
+    ...renderTableOpts
+  } = opts;
+  const dataItems = prebuiltDataItems || hits;
+  if (!dataItems || dataItems.length === 0) return;
+  const columns = prebuiltColumns || [
+    { label: "Gene" },
+    { label: `${hits[0].chrom.charAt(0).toUpperCase()}${hits[0].chrom.slice(1).toLowerCase()} pos` },
+    { label: "Type" },
+    { label: "Q-value", sortable: true },
+    { label: "Subject count", sortable: true }
+  ];
+  const rows = prebuiltRows || hits.map((d) => [
+    { value: d.gene },
+    { html: `<span style="font-size:.8em">${d.start}-${d.end}</span>` },
+    { html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}` },
+    { value: d.q_value.toPrecision(3) },
+    { value: d.nsubj }
+  ]);
+  const tableOptions = {
+    div: tableDiv,
+    columns,
+    rows,
+    showLines: false,
+    showHeader: true,
+    striped: true,
+    resize: "both",
+    header: { allowSort: true },
+    ...renderTableOpts
+  };
+  if (app) {
+    let lastTouchedGene = null;
+    let selectionOrder = [];
+    tableOptions.buttonsToLeft = true;
+    tableOptions.buttons = [
+      {
+        text: matrixButtonFormat.replace("{n}", "0"),
+        callback: (selectedIndices, buttonNode) => {
+          if (selectedIndices.length > 0) {
+            buttonNode.disabled = true;
+            const selectedGenes = selectedIndices.map((idx) => getGene(dataItems[idx]));
+            clickMenu?.hide();
+            createMatrixFromGenes(selectedGenes, app);
+          }
+        },
+        onChange: (selectedIndices, buttonNode) => {
+          buttonNode.textContent = matrixButtonFormat.replace("{n}", String(selectedIndices.length));
+          buttonNode.disabled = selectedIndices.length === 0;
+        }
+      },
+      {
+        text: "Lollipop",
+        callback: (_selectedIndices, buttonNode) => {
+          if (lastTouchedGene) {
+            buttonNode.disabled = true;
+            clickMenu?.hide();
+            createLollipopFromGene(lastTouchedGene, app);
+          }
+        },
+        onChange: (selectedIndices, buttonNode) => {
+          const result = updateSelectionTracking(selectionOrder, selectedIndices, dataItems);
+          selectionOrder = result.selectionOrder;
+          lastTouchedGene = result.lastTouchedGene;
+          buttonNode.textContent = result.buttonText;
+          buttonNode.disabled = result.buttonDisabled;
+        }
+      }
+    ];
+  }
+  renderTable(tableOptions);
+}
+function updateSelectionTracking(currentSelectionOrder, selectedIndices, dataSource) {
+  const newlySelected = selectedIndices.filter((idx) => !currentSelectionOrder.includes(idx));
+  const updatedSelectionOrder = currentSelectionOrder.filter((idx) => selectedIndices.includes(idx));
+  updatedSelectionOrder.push(...newlySelected);
+  let lastTouchedGene = null;
+  let buttonText = "Lollipop";
+  if (updatedSelectionOrder.length > 0) {
+    const lastSelectedIdx = updatedSelectionOrder[updatedSelectionOrder.length - 1];
+    const dataItem = dataSource[lastSelectedIdx];
+    if (Array.isArray(dataItem)) {
+      const v = dataItem[0]?.value;
+      lastTouchedGene = v != null ? String(v) : null;
+    } else {
+      lastTouchedGene = dataItem.gene;
+    }
+    buttonText = `Lollipop (${lastTouchedGene})`;
+  }
+  return {
+    selectionOrder: updatedSelectionOrder,
+    lastTouchedGene,
+    buttonText,
+    buttonDisabled: lastTouchedGene === null
+  };
+}
+
+// plots/shared/quadtreeHitTest.ts
+function findPointsInRadius(qt, mx, my, hitRadius, getX = (d) => d.pixel_x, getY = (d) => d.pixel_y) {
+  const candidates = [];
+  qt.visit((node, x1, y1, x2, y2) => {
+    if (x1 > mx + hitRadius || x2 < mx - hitRadius || y1 > my + hitRadius || y2 < my - hitRadius) {
+      return true;
+    }
+    if (!node.length) {
+      let current = node;
+      while (current) {
+        const point = current.data;
+        if (point) {
+          const px = getX(point);
+          const py = getY(point);
+          const distance = Math.sqrt((mx - px) ** 2 + (my - py) ** 2);
+          if (distance <= hitRadius) {
+            candidates.push({ point, distance });
+          }
+        }
+        current = current.next;
+      }
+    }
+    return false;
+  });
+  return candidates;
+}
+
+export {
+  createLollipopFromGene,
+  showResultsTable,
+  findPointsInRadius
+};
+//# sourceMappingURL=chunk-BBNO6JLO.js.map

package/dist/chunk-BBNO6JLO.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/shared/genePlotActions.ts", "../plots/shared/resultsTable.ts", "../plots/shared/quadtreeHitTest.ts"],
+  "sourcesContent": ["import { sayerror } from '#dom'\nimport { get$id } from '#termsetting'\n\n/**\n * Dispatches a plot_create action that opens a Lollipop / genome-browser view\n * for a single gene. Used from gene-results tables (manhattan, grin2, volcano)\n * when the user picks one gene to drill into.\n */\nexport function createLollipopFromGene(geneSymbol: string, app: any) {\n\tconst cfg: any = {\n\t\ttype: 'plot_create',\n\t\tconfig: {\n\t\t\tchartType: 'genomeBrowser',\n\t\t\tsnvindel: { shown: true }, // always set snvindel.shown=true so the mds3 tk is always shown; since grin2 works for this ds, it doesn't matter whether snvindel/cnv/svfusion any is present; all will be shown in mds3 tk\n\t\t\tgeneSearchResult: { geneSymbol }\n\t\t}\n\t}\n\tif (app.vocabApi.termdbConfig.queries.trackLst?.activeTracks) {\n\t\tcfg.config.trackLst = structuredClone(app.vocabApi.termdbConfig.queries.trackLst)\n\t\tcfg.config.trackLst.activeTracks = [] // clear all active tracks as they are not related to grin2 analysis\n\t\t// cannot do cfg.config.trackLst={activeTracks:[]}; breaks\n\t}\n\tapp.dispatch(cfg)\n}\n\n/**\n * Dispatches a plot_create action that opens a Matrix view for a set of genes.\n * Capped at 100 genes \u2014 the table caller is expected to have already filtered\n * to the user's selection.\n */\nexport async function createMatrixFromGenes(geneSymbols: string[], app: any): Promise<void> {\n\t// TODO: Improve this by maybe adding sayInfo that has a little div that shows a message letting the user know the matrix is being created with only the first N genes if they selected too many\n\tconst MAX_GENES = 100\n\tconst genesToUse = geneSymbols.slice(0, MAX_GENES)\n\n\ttry {\n\t\tconst termwrappers = await Promise.all(\n\t\t\tgenesToUse.map(async (gene: string) => {\n\t\t\t\tconst term = {\n\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\tgene: gene,\n\t\t\t\t\tname: gene\n\t\t\t\t}\n\t\t\t\tconst minTwCopy = app.vocabApi.getTwMinCopy({ term, q: {} })\n\t\t\t\treturn {\n\t\t\t\t\t$id: await get$id(minTwCopy),\n\t\t\t\t\tterm,\n\t\t\t\t\tq: {}\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\n\t\tapp.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tdataType: 'geneVariant',\n\t\t\t\ttermgroups: [\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Genomic Alterations',\n\t\t\t\t\t\tlst: termwrappers\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t})\n\t} catch (error) {\n\t\tsayerror(app.dom.div, `Error creating matrix: ${error instanceof Error ? error.message : error}`)\n\t}\n}\n", "import { renderTable } from '#dom'\nimport { createLollipopFromGene, createMatrixFromGenes } from './genePlotActions'\nimport type { ShowResultsTableOpts, ResultsDataItem } from './resultsTableTypes'\n\n/**\n * Renders a results table for biological items (genes, promoters, etc.).\n * Used by manhattan/volcano hover tooltips, click menus, and the grin2\n * top-genes table. Data-agnostic \u2014 pass `columns`/`rows` for custom shapes.\n *\n * When `app` is provided, the gene-specific Matrix/Lollipop buttons are\n * auto-injected; omit `app` for read-only or non-gene contexts.\n */\nexport function showResultsTable(opts: ShowResultsTableOpts): void {\n\tconst {\n\t\ttableDiv,\n\t\thits,\n\t\tapp,\n\t\tclickMenu,\n\t\tcolumns: prebuiltColumns,\n\t\trows: prebuiltRows,\n\t\tdataItems: prebuiltDataItems,\n\t\tgetGene = (item: any) => item.gene,\n\t\tmatrixButtonFormat = 'Matrix ({n})',\n\t\t...renderTableOpts\n\t} = opts\n\n\tconst dataItems = prebuiltDataItems || hits\n\n\tif (!dataItems || dataItems.length === 0) return\n\n\tconst columns = prebuiltColumns || [\n\t\t{ label: 'Gene' },\n\t\t{ label: `${hits![0].chrom.charAt(0).toUpperCase()}${hits![0].chrom.slice(1).toLowerCase()} pos` },\n\t\t{ label: 'Type' },\n\t\t{ label: 'Q-value', sortable: true },\n\t\t{ label: 'Subject count', sortable: true }\n\t]\n\n\tconst rows =\n\t\tprebuiltRows ||\n\t\thits!.map(d => [\n\t\t\t{ value: d.gene },\n\t\t\t{ html: `<span style=\"font-size:.8em\">${d.start}-${d.end}</span>` },\n\t\t\t{ html: `<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}` },\n\t\t\t{ value: d.q_value.toPrecision(3) },\n\t\t\t{ value: d.nsubj }\n\t\t])\n\n\tconst tableOptions: any = {\n\t\tdiv: tableDiv,\n\t\tcolumns,\n\t\trows,\n\t\tshowLines: false,\n\t\tshowHeader: true,\n\t\tstriped: true,\n\t\tresize: 'both',\n\t\theader: { allowSort: true },\n\t\t...renderTableOpts\n\t}\n\n\tif (app) {\n\t\tlet lastTouchedGene: string | null = null\n\t\tlet selectionOrder: number[] = []\n\n\t\ttableOptions.buttonsToLeft = true\n\t\ttableOptions.buttons = [\n\t\t\t{\n\t\t\t\ttext: matrixButtonFormat.replace('{n}', '0'),\n\t\t\t\tcallback: (selectedIndices: number[], buttonNode: HTMLButtonElement) => {\n\t\t\t\t\tif (selectedIndices.length > 0) {\n\t\t\t\t\t\tbuttonNode.disabled = true\n\t\t\t\t\t\tconst selectedGenes = selectedIndices.map(idx => getGene(dataItems[idx]))\n\t\t\t\t\t\tclickMenu?.hide()\n\t\t\t\t\t\tcreateMatrixFromGenes(selectedGenes, app)\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tonChange: (selectedIndices: number[], buttonNode: HTMLButtonElement) => {\n\t\t\t\t\tbuttonNode.textContent = matrixButtonFormat.replace('{n}', String(selectedIndices.length))\n\t\t\t\t\tbuttonNode.disabled = selectedIndices.length === 0\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: 'Lollipop',\n\t\t\t\tcallback: (_selectedIndices: number[], buttonNode: HTMLButtonElement) => {\n\t\t\t\t\tif (lastTouchedGene) {\n\t\t\t\t\t\tbuttonNode.disabled = true\n\t\t\t\t\t\tclickMenu?.hide()\n\t\t\t\t\t\tcreateLollipopFromGene(lastTouchedGene, app)\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tonChange: (selectedIndices: number[], buttonNode: HTMLButtonElement) => {\n\t\t\t\t\tconst result = updateSelectionTracking(selectionOrder, selectedIndices, dataItems)\n\t\t\t\t\tselectionOrder = result.selectionOrder\n\t\t\t\t\tlastTouchedGene = result.lastTouchedGene\n\t\t\t\t\tbuttonNode.textContent = result.buttonText\n\t\t\t\t\tbuttonNode.disabled = result.buttonDisabled\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t}\n\n\trenderTable(tableOptions)\n}\n\n/**\n * Updates selection-order tracking and determines the last-touched gene.\n * Used by the Lollipop button to remember which gene the user touched most\n * recently across multi-select changes. Lives next to showResultsTable since\n * the button-state logic is its only caller.\n */\nexport function updateSelectionTracking(\n\tcurrentSelectionOrder: number[],\n\tselectedIndices: number[],\n\tdataSource: ResultsDataItem[]\n): { selectionOrder: number[]; lastTouchedGene: string | null; buttonText: string; buttonDisabled: boolean } {\n\tconst newlySelected = selectedIndices.filter(idx => !currentSelectionOrder.includes(idx))\n\n\tconst updatedSelectionOrder = currentSelectionOrder.filter(idx => selectedIndices.includes(idx))\n\tupdatedSelectionOrder.push(...newlySelected)\n\n\tlet lastTouchedGene: string | null = null\n\tlet buttonText = 'Lollipop'\n\n\tif (updatedSelectionOrder.length > 0) {\n\t\tconst lastSelectedIdx = updatedSelectionOrder[updatedSelectionOrder.length - 1]\n\t\tconst dataItem = dataSource[lastSelectedIdx]\n\n\t\tif (Array.isArray(dataItem)) {\n\t\t\t// First cell is by convention the gene/feature name; coerce to string\n\t\t\t// since `value` is widened to string | number across the table API.\n\t\t\tconst v = dataItem[0]?.value\n\t\t\tlastTouchedGene = v != null ? String(v) : null\n\t\t} else {\n\t\t\tlastTouchedGene = (dataItem as { gene: string }).gene\n\t\t}\n\n\t\tbuttonText = `Lollipop (${lastTouchedGene})`\n\t}\n\n\treturn {\n\t\tselectionOrder: updatedSelectionOrder,\n\t\tlastTouchedGene,\n\t\tbuttonText,\n\t\tbuttonDisabled: lastTouchedGene === null\n\t}\n}\n", "import type { Quadtree } from 'd3-quadtree'\n\n/**\n * Searches a quadtree for all points within a specified radius of target coordinates.\n *\n * Generic over the point type T. By default reads `pixel_x`/`pixel_y` from each\n * datum (matching ManhattanPoint); pass `getX`/`getY` to use other coordinate\n * fields (e.g. `x`/`y` for the volcano plot).\n *\n * @param qt - D3 quadtree containing T-typed point data\n * @param mx - Target x coordinate (in pixels, in quadtree-local space)\n * @param my - Target y coordinate (in pixels, in quadtree-local space)\n * @param hitRadius - Search radius (in pixels)\n * @param getX - Optional accessor for the point's x coord (default: d.pixel_x)\n * @param getY - Optional accessor for the point's y coord (default: d.pixel_y)\n * @returns Array of points within radius with their distances\n */\nexport function findPointsInRadius<T>(\n\tqt: Quadtree<T>,\n\tmx: number,\n\tmy: number,\n\thitRadius: number,\n\tgetX: (d: T) => number = (d: any) => d.pixel_x,\n\tgetY: (d: T) => number = (d: any) => d.pixel_y\n): Array<{ point: T; distance: number }> {\n\tconst candidates: Array<{ point: T; distance: number }> = []\n\n\tqt.visit((node, x1, y1, x2, y2) => {\n\t\t// Skip this node if it's outside the search radius\n\t\tif (x1 > mx + hitRadius || x2 < mx - hitRadius || y1 > my + hitRadius || y2 < my - hitRadius) {\n\t\t\treturn true // Skip this branch\n\t\t}\n\n\t\t// If this is a leaf node, check ALL points (including coincident ones)\n\t\tif (!node.length) {\n\t\t\t// Traverse the linked list of coincident points\n\t\t\tlet current: any = node\n\t\t\twhile (current) {\n\t\t\t\tconst point = current.data as T | undefined\n\t\t\t\tif (point) {\n\t\t\t\t\tconst px = getX(point)\n\t\t\t\t\tconst py = getY(point)\n\t\t\t\t\tconst distance = Math.sqrt((mx - px) ** 2 + (my - py) ** 2)\n\n\t\t\t\t\tif (distance <= hitRadius) {\n\t\t\t\t\t\tcandidates.push({ point, distance })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcurrent = current.next // Move to next coincident point\n\t\t\t}\n\t\t}\n\n\t\treturn false // Don't stop early - check all nodes in radius\n\t})\n\n\treturn candidates\n}\n"],
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+  "names": []
+}

package/dist/chunk-CVRYZMDE.js

@@ -0,0 +1,148 @@
+import {
+  storeInit
+} from "./chunk-OEUI4CYZ.js";
+import {
+  recoverInit
+} from "./chunk-HZETQJGD.js";
+import {
+  AppBase,
+  sayerror,
+  vocabInit
+} from "./chunk-2YC6ZVE4.js";
+import {
+  importPlot
+} from "./chunk-RYCOJY7M.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  AppApi
+} from "./chunk-MVTCBVSX.js";
+
+// plots/plot.app.ts
+var PlotApp = class _PlotApp extends AppBase {
+  constructor(opts, api) {
+    super(opts);
+    this.components = {};
+    this.wasDestroyed = false;
+    this.api = api;
+    this.type = _PlotApp.type;
+    this.dom = this.getDom(opts);
+  }
+  static {
+    this.type = "app";
+  }
+  getDom(opts) {
+    const dom = {
+      holder: opts.holder,
+      errdiv: opts.holder.append("div"),
+      plotDiv: opts.holder.append("div")
+    };
+    const controls = opts.violin?.mode == "minimal" ? null : opts.holder.append("div").style("white-space", "nowrap");
+    if (controls) {
+      dom.plotControls = controls.append("div").style("display", "inline-block");
+      dom.recoverControls = controls.append("div").style("display", "inline-block");
+    }
+    return dom;
+  }
+  async preApiFreeze(api) {
+    try {
+      api.tip = new Menu({ padding: "5px" });
+      api.printError = (e) => this.printError(e);
+      const vocab = this.opts.state.vocab;
+      api.vocabApi = this.opts.vocabApi ? this.opts.vocabApi : await vocabInit({
+        app: api,
+        state: {
+          vocab: {
+            // either (genome + dslabel) XOR (terms) can be undefined
+            genome: vocab?.genome || this.opts.state.genome,
+            dslabel: vocab?.dslabel || this.opts.state.dslabel,
+            terms: vocab?.terms
+          }
+        },
+        fetchOpts: this.opts.fetchOpts
+      });
+      this.opts.state.vocab = api.vocabApi.vocab;
+    } catch (e) {
+      console.log(`preApiFreeze error`, e);
+      throw e;
+    }
+  }
+  async init() {
+    try {
+      this.opts.state.nav = { header_mode: "hidden" };
+      this.store = await storeInit({ app: this.api, state: this.opts.state });
+      this.state = await this.store.copyState();
+      this.components = {
+        plots: {}
+      };
+      if (this.opts.app?.features?.includes("recover"))
+        this.components.recover = await recoverInit({
+          app: this.api,
+          holder: this.dom.recoverControls,
+          // TODO: ???? may limit the tracked state to only the filter, activeCohort ???
+          getState: (appState) => appState,
+          //reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',
+          maxHistoryLen: 10
+        });
+      if (this.opts.app?.doNotAwaitInitRender) {
+        this.api.dispatch();
+      } else {
+        await this.api.dispatch();
+      }
+    } catch (e) {
+      this.printError(e);
+      throw e;
+    }
+  }
+  async main() {
+    this.api.vocabApi.main();
+    for (const id in this.components.plots) {
+      const plot = this.components.plots[id];
+      if (!this.state.plots.find((p) => p.id === plot.id)) {
+        plot.destroy();
+        delete this.components.plots[id];
+      }
+    }
+    for (const plot of this.state.plots.values()) {
+      if (plot.parentId) continue;
+      if (!this.components.plots[plot.id]) {
+        const holder = this.opts?.app?.getPlotHolder ? this.opts.app.getPlotHolder(plot, this.dom.holder) : this.dom.holder.append("div");
+        if (!this.dom.plotDiv) this.dom.plotDiv = holder;
+        const { componentInit } = await importPlot(plot.chartType);
+        const plotApi = await componentInit({
+          id: plot.id,
+          app: this.api,
+          holder,
+          controls: this.dom.plotControls
+        });
+        this.components.plots[plot.id] = plotApi;
+      }
+    }
+  }
+  printError(e) {
+    sayerror(this.dom.errdiv, "Error: " + (e.message || e));
+    if (e.stack) console.log(e.stack);
+    this.bus.emit("error");
+  }
+  skipPrevActionAbort(action) {
+    if (!action) return false;
+    if (action.type.startsWith("filter")) return false;
+    if (action.type.startsWith("cohort")) return false;
+    if (action.type == "app_refresh") {
+      if (action.subactions) {
+        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
+      }
+    }
+    return true;
+  }
+  destroy() {
+    if (this.dom?.holder) this.dom.holder.selectAll("*").remove();
+  }
+};
+var appInit = AppApi.getInitFxn(PlotApp);
+
+export {
+  appInit
+};
+//# sourceMappingURL=chunk-CVRYZMDE.js.map

package/dist/chunk-DGUTCYH2.js

@@ -0,0 +1,276 @@
+import {
+  parsesample
+} from "./chunk-I55NLUCQ.js";
+import {
+  dtfusionrna,
+  dtsv,
+  mclassfusionrna,
+  mclasssv
+} from "./chunk-AMYSEKPF.js";
+
+// ../shared/utils/src/bulk.sv.js
+function parseheader(line, flag, issv) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene_a", "gene1", "genea");
+  if (i == -1) return "gene_a missing from header";
+  header[i] = "gene1";
+  i = htry("gene_b", "gene2", "geneb");
+  if (i == -1) return "gene_b missing from header";
+  header[i] = "gene2";
+  i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_a missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_b missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
+  if (i == -1) return "isoform_a missing from header";
+  header[i] = "isoform1";
+  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
+  if (i == -1) return "isoform_b missing from header";
+  header[i] = "isoform2";
+  i = htry("strand_a", "orta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  if (issv) {
+    flag.sv.loaded = true;
+    flag.sv.header = header;
+  } else {
+    flag.fusion.loaded = true;
+    flag.fusion.header = header;
+  }
+  return false;
+}
+function parseline(i, line, flag, issv) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  const header = issv ? flag.sv.header : flag.fusion.header;
+  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) {
+    badlines.push([i, "missing chr1", lst]);
+    return;
+  }
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) {
+    badlines.push([i, "missing chr2", lst]);
+    return;
+  }
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  let v = m.position1;
+  if (!v) {
+    badlines.push([i, "missing position1", lst]);
+    return;
+  }
+  let v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position1", lst]);
+    return;
+  }
+  m.position1 = v2;
+  v = m.position2;
+  if (!v) {
+    badlines.push([i, "missing position2", lst]);
+    return;
+  }
+  v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position2", lst]);
+    return;
+  }
+  m.position2 = v2;
+  if (parsesample(m, flag, i, lst, badlines)) {
+    return;
+  }
+  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
+    const lst2 = m.isoform1.split(",");
+    m.isoform1 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform1 = t;
+    }
+  }
+  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
+    const lst2 = m.isoform2.split(",");
+    m.isoform2 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform2 = t;
+    }
+  }
+  if (!m.gene1) {
+    m.isoform1 = void 0;
+  }
+  if (!m.gene2) {
+    m.isoform2 = void 0;
+  }
+  if (m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : mclassfusionrna,
+      isoform: m.isoform1,
+      mname: m.gene2 || m.chr2,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+  if (m.gene2 && m.gene2 != m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : mclassfusionrna,
+      isoform: m.isoform2,
+      mname: m.gene1 || m.chr1,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+}
+function duplicate(m) {
+  const n = {};
+  for (const k in m) {
+    if (k == "pairlst") continue;
+    const v = m[k];
+    const type = typeof v;
+    if (type == "object") {
+      continue;
+    }
+    n[k] = v;
+  }
+  if (m.pairlst) {
+    n.pairlst = [];
+    for (const pair of m.pairlst) {
+      const p = {};
+      for (const k in pair) {
+        if (k == "a" || k == "b" || k == "interstitial") {
+          continue;
+        }
+        p[k] = pair[k];
+      }
+      if (pair.a) {
+        p.a = {};
+        for (const k in pair.a) {
+          const v = pair.a[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.a[k] = v;
+        }
+      }
+      if (pair.b) {
+        p.b = {};
+        for (const k in pair.b) {
+          const v = pair.b[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.b[k] = v;
+        }
+      }
+      if (pair.interstitial) {
+        p.interstitial = {};
+        for (const k in pair.interstitial) {
+          const v = pair.interstitial[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.interstitial[k] = v;
+        }
+      }
+      n.pairlst.push(p);
+    }
+  }
+  return n;
+}
+
+export {
+  parseheader,
+  parseline,
+  duplicate
+};
+//# sourceMappingURL=chunk-DGUTCYH2.js.map