@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

package/dist/chunk-NBGVEZNX.js

@@ -0,0 +1,56 @@
+import {
+  sayerror
+} from "./chunk-QJ3HYZH3.js";
+import {
+  TermTypeGroups
+} from "./chunk-4EZLVENZ.js";
+
+// termdb/handlers/singleCellCellType.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
+    if (!scctTerms?.length) {
+      sayerror(
+        holder,
+        `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
+      );
+      return;
+    }
+    const usecaseConfig = opts.usecase?.specialCase?.config;
+    const plots = usecaseConfig?.sample?.plots;
+    const isMeta = usecaseConfig?.sample?.isMetaResult;
+    const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
+    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
+    const filteredTerms = new Set(
+      plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
+    );
+    for (const t of Array.from(filteredTerms)) {
+      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
+        const term = this.makeTerm(t, usecaseConfig);
+        this.callback(term);
+      });
+    }
+  }
+  makeTerm(_term, usecaseConfig) {
+    const term = { ..._term };
+    if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
+    return term;
+  }
+  validateOpts(opts) {
+    if (opts.callback == null) throw new Error("callback is required");
+    if (opts.app == null) throw new Error("app is required");
+    if (opts.holder == null) throw new Error("holder is required");
+    if (opts.usecase == null) throw new Error("usecase is required");
+    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
+      throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-NBGVEZNX.js.map

package/dist/chunk-NBGVEZNX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/singleCellCellType.ts"],
+  "sourcesContent": ["import type { AppApi } from '#rx'\nimport { TermTypeGroups } from '#shared/terms.js'\nimport { sayerror } from '#dom'\n\nexport class SearchHandler {\n\tcallback?: (f?: any) => void\n\tapp?: AppApi\n\n\tasync init(opts) {\n\t\tthis.validateOpts(opts)\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\n\t\tconst holder = opts.holder.append('div').style('padding', '10px 0px')\n\t\tconst scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE]\n\t\tif (!scctTerms?.length) {\n\t\t\tsayerror(\n\t\t\t\tholder,\n\t\t\t\t`termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`\n\t\t\t)\n\t\t\treturn\n\t\t}\n\t\tconst usecaseConfig = opts.usecase?.specialCase?.config\n\t\tconst plots = usecaseConfig?.sample?.plots\n\t\tconst isMeta = usecaseConfig?.sample?.isMetaResult\n\n\t\t/** Use either the usecase.config.sample.plots:[] or usecase.config.name (i.e.\n\t\t * plot name) to filter the terms OR display all. If displaying all terms,\n\t\t * append the plot name to the label. Only display a term once. */\n\t\tconst filtered = plots\n\t\t\t? scctTerms.filter(t => plots.includes(t.plot))\n\t\t\t: usecaseConfig?.name\n\t\t\t? scctTerms.filter(t => t.plot === usecaseConfig.name)\n\t\t\t: scctTerms\n\n\t\tconst getLabel = t => ((isMeta || plots?.length == 1) ? t.name : `${t.name} (${t.plot})`)\n\n\t\tconst filteredTerms: Set<any> = new Set(\n\t\t\tplots || !usecaseConfig?.name ? filtered.map(t => ({ ...t, label: getLabel(t)})) : filtered\n\t\t)\n\n\t\tfor (const t of Array.from(filteredTerms)) {\n\t\t\tholder\n\t\t\t\t/** The divs and styling duplicates the appearance of the\n\t\t\t\t * tree terms. The tree is NOT called for this handler. */\n\t\t\t\t.append('div')\n\t\t\t\t.classed('termdiv', true)\n\t\t\t\t.style('padding', '0px 5px')\n\t\t\t\t.append('div')\n\t\t\t\t.classed('termlabel sja_filter_tag_btn sja_tree_click_term ts_pill', true)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '5px 8px')\n\t\t\t\t.style('margin', '1px 0px')\n\t\t\t\t.style('border-radius', '6px')\n\t\t\t\t//End duplicated pill styling\n\t\t\t\t.text(t.label || t.name)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst term = this.makeTerm(t, usecaseConfig)\n\t\t\t\t\tthis.callback!(term)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tmakeTerm(_term, usecaseConfig) {\n\t\tconst term = { ..._term }\n\t\tif (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample\n\t\treturn term\n\t}\n\n\tvalidateOpts(opts) {\n\t\tif (opts.callback == null) throw new Error('callback is required')\n\t\tif (opts.app == null) throw new Error('app is required')\n\t\tif (opts.holder == null) throw new Error('holder is required')\n\t\tif (opts.usecase == null) throw new Error('usecase is required')\n\t\tif (!opts.app.vocabApi.termdbConfig?.termType2terms)\n\t\t\tthrow new Error('termType2terms is required in termdbConfig for singleCellCellType handler')\n\t}\n}\n"],
+  "mappings": ";;;;;;;;AAIO,IAAM,gBAAN,MAAoB;AAAA,EAI1B,MAAM,KAAK,MAAM;AAChB,SAAK,aAAa,IAAI;AACtB,SAAK,WAAW,KAAK;AACrB,SAAK,MAAM,KAAK;AAEhB,UAAM,SAAS,KAAK,OAAO,OAAO,KAAK,EAAE,MAAM,WAAW,UAAU;AACpE,UAAM,YAAY,KAAK,IAAI,SAAS,cAAc,iBAAiB,eAAe,mBAAmB;AACrG,QAAI,CAAC,WAAW,QAAQ;AACvB;AAAA,QACC;AAAA,QACA,kBAAkB,eAAe,mBAAmB;AAAA,MACrD;AACA;AAAA,IACD;AACA,UAAM,gBAAgB,KAAK,SAAS,aAAa;AACjD,UAAM,QAAQ,eAAe,QAAQ;AACrC,UAAM,SAAS,eAAe,QAAQ;AAKtC,UAAM,WAAW,QACd,UAAU,OAAO,OAAK,MAAM,SAAS,EAAE,IAAI,CAAC,IAC5C,eAAe,OACf,UAAU,OAAO,OAAK,EAAE,SAAS,cAAc,IAAI,IACnD;AAEH,UAAM,WAAW,OAAO,UAAU,OAAO,UAAU,IAAK,EAAE,OAAO,GAAG,EAAE,IAAI,KAAK,EAAE,IAAI;AAErF,UAAM,gBAA0B,IAAI;AAAA,MACnC,SAAS,CAAC,eAAe,OAAO,SAAS,IAAI,QAAM,EAAE,GAAG,GAAG,OAAO,SAAS,CAAC,EAAC,EAAE,IAAI;AAAA,IACpF;AAEA,eAAW,KAAK,MAAM,KAAK,aAAa,GAAG;AAC1C,aAGE,OAAO,KAAK,EACZ,QAAQ,WAAW,IAAI,EACvB,MAAM,WAAW,SAAS,EAC1B,OAAO,KAAK,EACZ,QAAQ,4DAA4D,IAAI,EACxE,MAAM,WAAW,cAAc,EAC/B,MAAM,WAAW,SAAS,EAC1B,MAAM,UAAU,SAAS,EACzB,MAAM,iBAAiB,KAAK,EAE5B,KAAK,EAAE,SAAS,EAAE,IAAI,EACtB,GAAG,SAAS,MAAM;AAClB,cAAM,OAAO,KAAK,SAAS,GAAG,aAAa;AAC3C,aAAK,SAAU,IAAI;AAAA,MACpB,CAAC;AAAA,IACH;AAAA,EACD;AAAA,EAEA,SAAS,OAAO,eAAe;AAC9B,UAAM,OAAO,EAAE,GAAG,MAAM;AACxB,QAAI,CAAC,KAAK,UAAU,eAAe,OAAQ,MAAK,SAAS,cAAc;AACvE,WAAO;AAAA,EACR;AAAA,EAEA,aAAa,MAAM;AAClB,QAAI,KAAK,YAAY,KAAM,OAAM,IAAI,MAAM,sBAAsB;AACjE,QAAI,KAAK,OAAO,KAAM,OAAM,IAAI,MAAM,iBAAiB;AACvD,QAAI,KAAK,UAAU,KAAM,OAAM,IAAI,MAAM,oBAAoB;AAC7D,QAAI,KAAK,WAAW,KAAM,OAAM,IAAI,MAAM,qBAAqB;AAC/D,QAAI,CAAC,KAAK,IAAI,SAAS,cAAc;AACpC,YAAM,IAAI,MAAM,2EAA2E;AAAA,EAC7F;AACD;",
+  "names": []
+}

package/dist/chunk-OBBR4UYN.js

@@ -0,0 +1,54 @@
+import {
+  getColors
+} from "./chunk-4EZLVENZ.js";
+
+// termdb/handlers/junction.customTerm.ts
+var junctionCustomTermSource = "junction";
+function makeJunctionCustomTerm(junctions, eventlabel) {
+  if (!junctions.length) throw new Error("junctions[] is empty");
+  if (!eventlabel) {
+    const term = junctions[0];
+    return {
+      id: `junction:${term.id}`,
+      name: term.name,
+      source: junctionCustomTermSource,
+      tw: {
+        term,
+        q: { mode: "continuous" }
+      }
+    };
+  }
+  const termlst = [...new Map(junctions.map((term) => [term.id, term])).values()];
+  const colorScale = getColors(termlst.length);
+  const termIds = termlst.map((term) => term.id);
+  return {
+    id: `junction-event:${eventlabel}`,
+    name: eventlabel,
+    source: junctionCustomTermSource,
+    eventlabel,
+    tw: {
+      term: {
+        type: "termCollection",
+        isCustom: true,
+        memberType: "numeric",
+        name: eventlabel,
+        termIds,
+        termlst,
+        propsByTermId: Object.fromEntries(termlst.map((term) => [term.id, { color: colorScale(term.id) }])),
+        isleaf: true
+      },
+      q: {
+        mode: "continuous",
+        type: "values",
+        lst: termIds,
+        numerators: termIds
+      }
+    }
+  };
+}
+
+export {
+  junctionCustomTermSource,
+  makeJunctionCustomTerm
+};
+//# sourceMappingURL=chunk-OBBR4UYN.js.map

package/dist/chunk-PQA3C2NY.js

@@ -0,0 +1,294 @@
+import {
+  getSortOptions
+} from "./chunk-U45R6QNT.js";
+import {
+  defaultUiLabels,
+  fillTermWrapper
+} from "./chunk-QJ3HYZH3.js";
+import {
+  isDictionaryType
+} from "./chunk-GMRIEUBW.js";
+import {
+  CNVClasses,
+  dtcnv,
+  mclass,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-4EZLVENZ.js";
+import {
+  copyMerge
+} from "./chunk-WINIL2KN.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
+        // 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-PQA3C2NY.js.map

package/dist/chunk-QJ2VBXFB.js

@@ -0,0 +1,134 @@
+import {
+  addGeneSearchbox,
+  isoformSelect,
+  pickCollectionFraction,
+  sayerror
+} from "./chunk-QJ3HYZH3.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  dofetch3
+} from "./chunk-VMRO6DMC.js";
+import {
+  ISOFORM_EXPRESSION,
+  getColors
+} from "./chunk-4EZLVENZ.js";
+
+// termdb/handlers/isoformExpression.ts
+var SearchHandler = class {
+  constructor() {
+    this.currentGene = null;
+  }
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    this.termCollectionSelectionMode = opts.termCollectionSelectionMode;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.dom = {
+      errDiv: holder.append("div").style("margin", "5px 0px").style("display", "none")
+    };
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          if (!geneSearch.geneSymbol) throw new Error("No gene selected");
+          if (geneSearch.geneSymbol === this.currentGene) return;
+          this.currentGene = geneSearch.geneSymbol;
+          if (this.dom.isoformDiv) this.dom.isoformDiv.remove();
+          this.dom.isoformDiv = holder.append("div");
+          await this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e instanceof Error ? e.message : String(e)));
+        }
+      }
+    });
+  }
+  async showIsoforms(gene, genomeObj) {
+    if (!gene) throw new Error("No gene selected");
+    const data = await dofetch3("genelookup", { body: { genome: genomeObj.name, input: gene, deep: 1 } });
+    if (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`);
+    const enstCandidates = data.gmlst.filter((gm) => gm.isoform?.startsWith("ENST"));
+    if (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`);
+    const { available } = await dofetch3("termdb/isoformAvailability", {
+      body: {
+        genome: genomeObj.name,
+        dslabel: this.app.vocabApi.vocab.dslabel,
+        isoforms: enstCandidates.map((gm) => gm.isoform)
+      }
+    });
+    const availableSet = new Set(available || []);
+    const enstModels = enstCandidates.filter((gm) => availableSet.has(gm.isoform));
+    if (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`);
+    if (gene !== this.currentGene) return;
+    const div = this.dom.isoformDiv;
+    div.append("div").style("margin-bottom", "8px").style("opacity", 0.65).text(`${gene} \u2014 select isoform(s):`);
+    isoformSelect({
+      holder: div,
+      allgm: enstModels,
+      multiSelect: true,
+      // a single checked isoform yields an individual term, 2+ yield a collection
+      getSubmitLabel: (selectedCount) => selectedCount === 1 ? "Select One Isoform" : `Create Collection (${selectedCount})`,
+      onMultiSelect: (selected) => {
+        if (selected.length === 1) {
+          this.selectIsoform(selected[0].isoform, gene);
+        } else {
+          this.selectCollection(selected, gene);
+        }
+      }
+    });
+  }
+  getUnit() {
+    return this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "TPM";
+  }
+  selectIsoform(isoform, gene) {
+    const name = `${isoform} ${this.getUnit()}`;
+    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
+  }
+  selectCollection(gms, gene) {
+    const unit = this.getUnit();
+    const termlst = gms.map((gm) => ({
+      id: gm.isoform,
+      name: gm.isoform,
+      type: ISOFORM_EXPRESSION,
+      isoform: gm.isoform
+    }));
+    const colorScale = getColors(termlst.length);
+    const term = {
+      type: "termCollection",
+      isCustom: true,
+      memberType: "numeric",
+      name: `${gene} Isoforms (${unit})`,
+      termlst,
+      propsByTermId: Object.fromEntries(termlst.map((term2) => [term2.id, { color: colorScale(term2.id) }])),
+      isleaf: true
+    };
+    if (this.termCollectionSelectionMode === "fraction") {
+      if (!this.dom?.isoformDiv) throw new Error("isoform result holder is missing");
+      this.dom.fractionDiv?.remove();
+      this.dom.fractionDiv = this.dom.isoformDiv.append("div").style("margin-top", "10px");
+      pickCollectionFraction({
+        holder: this.dom.fractionDiv,
+        term,
+        callback: (tw) => this.callback(tw)
+      });
+      return;
+    }
+    this.callback(term);
+  }
+};
+function filterIsoforms(gmlst, availableItems) {
+  const itemSet = new Set(availableItems);
+  return gmlst.filter((gm) => gm.isoform?.startsWith("ENST") && (itemSet.size === 0 || itemSet.has(gm.isoform)));
+}
+
+export {
+  SearchHandler,
+  filterIsoforms
+};
+//# sourceMappingURL=chunk-QJ2VBXFB.js.map