@sjcrh/proteinpaint-client 2.221.0 → 2.223.0

package/dist/chunk-WXSX5OQJ.js

@@ -1,296 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-5DI4UNH5.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-WD7FZ5EE.js";
-import {
-  isDictionaryType
-} from "./chunk-JHLF2ZC2.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-WJLRU5OF.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-
-// plots/matrix/matrix.config.js
-async function getPlotConfig(opts = {}, app) {
-  const controlLabels = structuredClone(defaultUiLabels);
-  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
-  const config = {
-    // data configuration
-    termgroups: [],
-    samplegroups: [],
-    divideBy: null,
-    legendValueFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    legendGrpFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    filter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    // cnvCutoffs: {},
-    // rendering options
-    settings: {
-      matrix: {
-        svgCanvasSwitch: 1e3,
-        // the number of samples to trigger switching between svg and canvas
-        useMinPixelWidth: true,
-        // canvas may be hazy if false, but more accurately reflects column density
-        cellEncoding: "",
-        // can be "oncoprint" | "stacked" | "single"
-        margin: {
-          top: 10,
-          right: 5,
-          bottom: 20,
-          left: 50
-        },
-        // set any dataset-defined sample limits and sort priority, otherwise undefined
-        // put in settings, so that later may be overridden by a user
-        maxGenes: opts.settings?.maxGenes || 50,
-        maxSample: opts.settings?.maxSample || 1e3,
-        sampleNameFilter: "",
-        sortSamplesBy: "a",
-        sortPriority: void 0,
-        // will be filled-in
-        sortBySampleAncestry: app.vocabApi.termdbConfig.hasSampleAncestry ? "last" : false,
-        // indicates sorting priority by sample ancestry
-        mapChildren2Root: false,
-        // for a dataset with sample ancestry, show one column per root sample (e.g. patient)
-        // sortByMutation: 'consequence', computed
-        // sortByCNV: true, computed
-        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
-        sortSampleGrpsBy: "name",
-        // 'hits' | 'name' | 'sampleCount'
-        sortSamplesTieBreakers: [{
-          $id: "sample",
-          sortSamples: {}
-          /*split: {char: '', index: 0}*/
-        }],
-        sortTermsBy: "sampleCount",
-        // or 'as listed'
-        // do not show number of samples at hiercluster gene row labels
-        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
-        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
-        geneVariantCountSamplesSkipMclass: [],
-        cellbg: "#ececec",
-        showGrid: "",
-        // false | 'pattern' | 'rect'
-        // whether to show these controls buttons
-        addMutationCNVButtons: false,
-        truncatingMutations,
-        proteinChangingMutations,
-        synonymousMutations,
-        mutationClasses,
-        CNVClasses,
-        gridStroke: "#fff",
-        outlineStroke: "#ccc",
-        beamStroke: "#f00",
-        colw: 0,
-        colwMin: 0.1 / devicePixelRatio,
-        colwMax: 16,
-        colspace: 1,
-        colgspace: 8,
-        colglabelpos: true,
-        collabelpos: "bottom",
-        collabelvisible: true,
-        collabelgap: 5,
-        collabelpad: 1,
-        collabelmaxchars: 32,
-        rowh: 18,
-        //use 0 to auto-compute row height, previous default=18,
-        rowhMin: 1,
-        rowhMax: 20,
-        rowspace: 1,
-        rowgspace: 8,
-        rowlabelpos: "left",
-        // | 'right'
-        rowlabelgap: 5,
-        rowlabelvisible: true,
-        rowlabelpad: 1,
-        rowlabelmaxchars: 32,
-        legendGrpLabelMaxChars: 26,
-        grpLabelFontSize: 12,
-        minLabelFontSize: 6,
-        maxLabelFontSize: 14,
-        transpose: false,
-        // 'auto' shows column labels only when columns are wide enough (colw >= minLabelFontSize);
-        sampleLabelsToggle: "auto",
-        // 'auto' | 'hide'
-        sampleLabelOffset: 120,
-        sampleGrpLabelOffset: 120,
-        sampleGrpLabelMaxChars: 32,
-        termLabelOffset: 80,
-        termGrpLabelOffset: 80,
-        termGrpLabelMaxChars: 32,
-        duration: 0,
-        zoomLevel: 1,
-        zoomCenterPct: 0,
-        zoomIndex: 0,
-        zoomGrpIndex: 0,
-        zoomMin: 0.5,
-        zoomIncrement: 0.1,
-        zoomStep: 1,
-        // renderedWMax should not be exposed as a user-input
-        // 60000 pixels is based on laptop and external monitor tests,
-        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
-        imgWMax: 6e4 / devicePixelRatio,
-        scrollHeight: 12,
-        controlLabels,
-        cnvUnit: "log2ratio",
-        ignoreCnvValues: false,
-        //will ignore numeric CNV values if true
-        barh: 32,
-        // default bar height for continuous terms,
-        // possible string entries:
-        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
-        // - may add other optional hints later
-        showHints: [],
-        genesetEditUiVersion: "",
-        // '' | 'withTabs'
-        // settings for a specific tw
-        twSpecificSettings: {},
-        oncoPrintSNVindelCellBorder: false,
-        // whether to show white cell border for SNVindel in oncoPrint mode
-        cnvValues: {
-          //Properties match the args for the ColorScales
-          //numericInput arg
-          cutoffMode: "percentile",
-          defaultPercentile: 99,
-          min: null,
-          max: null,
-          percentile: 99
-        }
-      }
-    }
-  };
-  const s = config.settings;
-  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
-  s.legend = {
-    ontop: false,
-    lineh: 25,
-    padx: 5,
-    padleft: 0,
-    //150,
-    padright: 20,
-    padbtm: 30,
-    fontsize,
-    iconh: fontsize - 2,
-    iconw: fontsize - 2,
-    hangleft: 1,
-    linesep: false
-  };
-  const overrides = app.vocabApi.termdbConfig.matrix || {};
-  copyMerge(config.settings.matrix, overrides.settings);
-  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
-  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
-  if (overrides.filter) config.filter = overrides.filter;
-  if (opts.name) {
-    const data = await app.vocabApi.getMatrixByName(opts.name);
-    if (!data) throw "error from getMatrixByName()";
-    if (data.error) throw data.error;
-    copyMerge(config, data);
-  }
-  const os = opts?.settings?.matrix;
-  if (os) {
-    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
-      os.sortSamplesBy = "a";
-    }
-    if (os.sortOptions) {
-      delete os.sortOptions.custom;
-      delete os.sortOptions.asListed;
-    }
-  }
-  copyMerge(config, opts);
-  const m = config.settings.matrix;
-  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
-  m.duration = 0;
-  m.colw = 0;
-  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
-  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
-  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
-  if (window.location.hostname == "localhost") {
-    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
-  }
-  for (const grp of config.termgroups) {
-    const promises = [];
-    for (const tw of grp.lst) {
-      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
-        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
-          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
-          tw.id = tw.term.id;
-        }
-        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    grp.lst = await Promise.all(promises);
-  }
-  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
-  return config;
-}
-function setComputedConfig(config) {
-  const s = config.settings.matrix;
-  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
-  s.filterByClass = { isAtomic: true };
-  for (const f of config.legendGrpFilter.lst) {
-    if (!f.dt) continue;
-    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
-      s.filterByClass[key2] = "value";
-    });
-  }
-  for (const f of config.legendValueFilter.lst) {
-    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
-    if (f.tvs.values?.[0].mclasslst)
-      f.tvs.values[0].mclasslst.forEach((key2) => {
-        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
-      });
-    else if (f.tvs.values)
-      f.tvs.values.forEach((v) => {
-        s.filterByClass[key] = "value";
-      });
-    else throw `unhandled tvs from legendValueFilter`;
-  }
-  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
-  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
-  s.hiddenCNVs = [...hiddenCNVs];
-  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
-  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
-  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
-  s.hiddenMutations = [...hiddenMutations];
-  const PCset = new Set(s.proteinChangingMutations);
-  const TMset = new Set(s.truncatingMutations);
-  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
-  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
-  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
-  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
-  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
-}
-
-export {
-  getPlotConfig,
-  setComputedConfig
-};
-//# sourceMappingURL=chunk-WXSX5OQJ.js.map

package/dist/chunk-WY3IORKG.js

@@ -1,194 +0,0 @@
-import {
-  violinRenderer
-} from "./chunk-WD7FZ5EE.js";
-import {
-  getValueConversionFactor
-} from "./chunk-W5J3LTYS.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import {
-  drag_default
-} from "./chunk-5R63Q5KH.js";
-import {
-  pointer_default,
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// termsetting/handlers/NumericDensity.ts
-var NumericDensity = class {
-  constructor(opts) {
-    this.dom = {};
-    // WeakMap allows deletion of value when the object/DOM key is deleted,
-    // so better for avoiding memory leak
-    this.vrByDiv = /* @__PURE__ */ new WeakMap();
-    this.ranges = [];
-    this.no_density_data = false;
-    this.brushes = [];
-    this.plot_size = {
-      width: 500,
-      height: 100,
-      xpad: 10,
-      ypad: 20,
-      radius: 8
-    };
-    this.opts = opts;
-    this.termsetting = opts.termsetting;
-    this.tw = opts.termsetting.tw;
-  }
-  /* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in
-  	the term's user-facing unit; density_data is in the unit the values are stored in. only the two
-  	getters below cross that line, to put the plot's endpoints in the same unit as those values.
-  
-  	they multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown
-  	in an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown
-  	digit, and collapses the domain outright when the converted range is smaller than that (a stored
-  	range of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose
-  	axis this plot's lines overlay and which scales its own domain unrounded */
-  get scaleFactor() {
-    return getValueConversionFactor(this.tw.term);
-  }
-  get displayMin() {
-    return this.density_data.min * this.scaleFactor;
-  }
-  get displayMax() {
-    return this.density_data.max * this.scaleFactor;
-  }
-  async setData() {
-    const self = this.termsetting;
-    const d = await self.vocabApi.getViolinBox(
-      {
-        plotType: "violin",
-        tw: { type: self.tw.type, term: self.term, q: self.q },
-        svgw: this.plot_size.width,
-        radius: this.plot_size.radius,
-        filter: self.filter
-      },
-      self.opts.getBodyParams?.()
-    );
-    if (d.error) throw d;
-    this.density_data = d;
-    return this.density_data;
-  }
-  async showViolin(div, boundaryOpts) {
-    await this.setData();
-    if (!this.vrByDiv.has(div)) {
-      div.style("padding", "5px").selectAll("*").remove();
-      const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
-      const densityDiv = div.append("div");
-      loadingDiv.remove();
-      const vr = new violinRenderer({
-        holder: densityDiv,
-        rd: this.density_data,
-        width: this.plot_size.width,
-        height: this.plot_size.height,
-        radius: this.plot_size.radius,
-        // axis ticks are labeled in the term's user-facing unit, e.g. years and not days
-        scaleFactor: this.scaleFactor
-      });
-      this.vrByDiv.set(div, vr);
-    }
-    this.vr = this.vrByDiv.get(div);
-    this.dom.svg = this.vr.svg;
-    this.vr.render();
-    if (boundaryOpts) await this.setBinLines(boundaryOpts);
-    return this.density_data;
-  }
-  async setBinLines(boundaryOpts) {
-    if (this.density_data.max == this.density_data.min) {
-      this.handleNoDensity();
-    } else {
-      if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
-      this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
-      const maxvalue = this.displayMax;
-      const minvalue = this.displayMin;
-      this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
-      this.ranges = [];
-      this.brushes = [];
-      this.renderBinLines(boundaryOpts);
-    }
-  }
-  handleNoDensity() {
-    this.no_density_data = true;
-    this.ranges = [];
-    this.brushes = [];
-  }
-  renderBinLines(boundaryOpts) {
-    const { plot_size, tw, xscale, scaleFactor } = this;
-    if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
-    const scaledMinX = Math.round(this.xscale(this.displayMin));
-    const scaledMaxX = Math.round(this.xscale(this.displayMax));
-    const lines = [];
-    for (const [index, v] of boundaryOpts.values.entries()) {
-      lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
-    }
-    const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
-    const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
-    const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
-    this.dom.binsize_g.selectAll("line").remove();
-    this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
-      if (d.isDraggable) select_default(this).style("stroke-width", 3);
-    }).on("mouseout", function() {
-      select_default(this).style("stroke-width", 1);
-    }).each(function(d) {
-      if (d.isDraggable) select_default(this).call(dragger);
-    });
-    const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
-    function toBoundaryValue(x) {
-      const inverted = xscale.invert(x);
-      return Number(
-        scaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3)
-      );
-    }
-    function toLineValue(line) {
-      return line.draggedX === void 0 ? line.x : toBoundaryValue(line.draggedX);
-    }
-    function getNeighbors(d) {
-      const x = d.draggedX ?? d.scaledX;
-      let lower, upper;
-      for (const line of lines) {
-        if (line.index === d.index || !line.isDraggable) continue;
-        const lineX = line.draggedX ?? line.scaledX;
-        if (lineX <= x) {
-          if (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line;
-        } else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line;
-      }
-      return [lower, upper];
-    }
-    function onDrag(event, _d) {
-      const d = _d;
-      const [lower, upper] = getNeighbors(d);
-      const lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX);
-      const upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX);
-      if (upperX - lowerX < 2) return;
-      const draggedX = Math.min(Math.max(pointer_default(event, this)[0], lowerX + 1), upperX - 1);
-      const value = toBoundaryValue(draggedX);
-      if (lower && value === toLineValue(lower)) return;
-      if (upper && value === toLineValue(upper)) return;
-      d.draggedX = draggedX;
-      select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
-      const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
-      const xOffset = d.draggedX - d.scaledX;
-      if (xOffset) {
-        for (const elem of lineElems) {
-          const c = elem.__data__;
-          if (c.movesWithLineIndex !== d.index) continue;
-          c.draggedX = c.scaledX + xOffset;
-          select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
-        }
-        boundaryOpts.callback(d, value);
-      }
-    }
-  }
-  destroy() {
-    for (const [k, v] of Object.entries(this.dom)) {
-      delete this.dom[k];
-      if (typeof v.remove == "function") v.remove();
-    }
-  }
-};
-
-export {
-  NumericDensity
-};
-//# sourceMappingURL=chunk-WY3IORKG.js.map