@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-EGPNRSPF.js

@@ -0,0 +1,292 @@
+import {
+  getSortOptions
+} from "./chunk-R6NM2HSH.js";
+import {
+  defaultUiLabels,
+  fillTermWrapper
+} from "./chunk-TKW5TW4Z.js";
+import {
+  isDictionaryType
+} from "./chunk-7JRDJNLR.js";
+import {
+  copyMerge
+} from "./chunk-M3J4MINX.js";
+import {
+  CNVClasses,
+  dtcnv,
+  mclass,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-6PNPHACF.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
+        // 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-EGPNRSPF.js.map

package/dist/chunk-FACITNG5.js

@@ -0,0 +1,142 @@
+import {
+  runproteinpaint
+} from "./chunk-BNAO6N5X.js";
+
+// test/front.helpers.js
+var serverData = /* @__PURE__ */ Object.create(null);
+function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
+  const host = window.testHost || _host;
+  const arg = {
+    host: window.testHost || _host,
+    noheader: 1,
+    nobox: true,
+    debug: 1,
+    norecover: true
+  };
+  if (appname == "mass" || appname == "termdb") {
+    defaultArgs.debounceInterval = 0;
+  }
+  if (appname) arg[appname] = defaultArgs;
+  else copyMerge(arg, defaultArgs);
+  const argStr = JSON.stringify(arg);
+  return function runpp(overrides = {}) {
+    const argCopy = JSON.parse(argStr);
+    if (appname) copyMerge(argCopy[appname], overrides);
+    else copyMerge(argCopy, overrides);
+    if (appname && defaultArgs.fetchOpts) {
+      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
+    }
+    return runproteinpaint(Object.assign(argCopy, { serverData }));
+  };
+}
+function copyMerge(base, ...args) {
+  const target = typeof base == "string" ? JSON.parse(base) : base;
+  for (const arg of args) {
+    if (arg) {
+      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
+      for (const key in source) {
+        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
+        else copyMerge(target[key], source[key]);
+      }
+    }
+  }
+  return target;
+}
+function rideInit(opts = {}) {
+  const self = new Ride(opts);
+  const rideApi = {
+    // ride on the default event bus
+    to(callback, sub = {}) {
+      self.addToThen(callback, Object.assign({}, opts, sub));
+      return rideApi;
+    },
+    use(triggerFxn, sub = {}) {
+      self.addUseThen(triggerFxn, Object.assign({}, opts, sub));
+      return rideApi;
+    },
+    change(sub = {}) {
+      Object.assign(opts, sub);
+      return rideApi;
+    },
+    // run callback without using bus, with or without timeout
+    run(callback, after = 0) {
+      self.addRunThen(callback, after, opts);
+      return rideApi;
+    },
+    // close the event bus
+    done(test) {
+      if (opts.bus) self.resolved.then(() => opts.bus.on(opts.eventType, null));
+      self.resolved.then(() => {
+        test.end();
+        if (!opts.preserve && test._ok && opts.arg.Inner.app && typeof opts.arg.Inner.app.destroy == "function") {
+          opts.arg.Inner.app.destroy();
+        }
+      }).catch(console.log);
+      return rideApi;
+    }
+  };
+  return Object.freeze(rideApi);
+}
+var Ride = class {
+  // mutable but private access props and methods
+  // when used inside rideInit()
+  constructor(opts) {
+    this.validateOpts(opts);
+    this.resolved = Promise.resolve();
+  }
+  validateOpts(opts) {
+    try {
+      if (opts.eventType && !opts.bus) {
+        if (!opts.arg) throw "must specify opts.bus or opts.arg for rideInit() argument";
+        opts.bus = opts.arg;
+      }
+      if (opts.bus) {
+        if (typeof opts.eventType !== "string") throw "invalid default.eventType";
+        opts.bus.on(opts.eventType, null);
+        return opts;
+      }
+    } catch (e) {
+      console.log(e);
+    }
+  }
+  addToThen(callback, opts) {
+    this.resolved = this.resolved.then(async (triggerFxn) => {
+      opts.bus.on(opts.eventType, null);
+      return new Promise(async (resolve, reject) => {
+        opts.bus.on(opts.eventType, async () => {
+          await sleep(opts.wait);
+          callback(opts.arg);
+          resolve();
+        });
+        if (triggerFxn) await triggerFxn();
+      });
+    });
+  }
+  // prepare a trigger function for use in the pattern
+  // rideInit().use(triggerFxn).to(...)
+  //
+  // .use() enables setting a different opts.arg to be used for triggerFxn
+  //
+  addUseThen(triggerFxn, opts) {
+    this.resolved = this.resolved.then(async (prevTriggerFxn) => {
+      if (typeof prevTriggerFxn == "function") await prevTriggerFxn();
+      await sleep(isNaN(opts.wait) ? 0 : opts.wait);
+      return () => triggerFxn(opts.arg);
+    });
+  }
+  addRunThen(callback, after, opts) {
+    this.resolved = this.resolved.then(async () => {
+      await sleep(typeof after == "number" ? after : 0);
+      callback(opts.arg);
+    });
+  }
+};
+function sleep(ms) {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+export {
+  getRunPp,
+  rideInit
+};
+//# sourceMappingURL=chunk-FACITNG5.js.map

package/dist/chunk-GNS6CQMA.js

@@ -0,0 +1,119 @@
+import {
+  GENE_EXPRESSION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-6PNPHACF.js";
+
+// common/termutils.js
+function sample_match_termvaluesetting(row, filter, geneVariant$ids) {
+  const lst = !filter ? [] : filter.type == "tvslst" ? filter.lst : [filter];
+  let numberofmatchedterms = 0;
+  for (const item of lst) {
+    if (item.type == "tvslst") {
+      if (sample_match_termvaluesetting(row, item)) {
+        numberofmatchedterms++;
+      }
+    } else {
+      const t = item.tvs;
+      let samplevalue;
+      if (t.term.type == "geneVariant") {
+        samplevalue = geneVariant$ids.map((g) => row[g]).filter((s) => s);
+      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
+        samplevalue = row[t.term.id] || row[t.term.$id]?.key;
+      } else if (t.term.type == "survival") {
+        samplevalue = row[t.term.$id]?.key;
+      } else {
+        samplevalue = row[t.term.id] || row[t.term.$id]?.value;
+      }
+      let thistermmatch;
+      if (t.term.type == "categorical") {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
+        thistermmatch = valueset.has(samplevalue);
+      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        for (const range of t.ranges) {
+          if ("value" in range) {
+            thistermmatch = samplevalue === range.value;
+            if (thistermmatch) break;
+          } else if (samplevalue == range.name) {
+            thistermmatch = true;
+            break;
+          } else {
+            if (t.term.values) {
+              const v = t.term.values[samplevalue.toString()];
+              if (v && v.uncomputable) {
+                continue;
+              }
+            }
+            let left, right;
+            if (range.startunbounded) {
+              left = true;
+            } else if ("start" in range) {
+              if (range.startinclusive) {
+                left = samplevalue >= range.start;
+              } else {
+                left = samplevalue > range.start;
+              }
+            }
+            if (range.stopunbounded) {
+              right = true;
+            } else if ("stop" in range) {
+              if (range.stopinclusive) {
+                right = samplevalue <= range.stop;
+              } else {
+                right = samplevalue < range.stop;
+              }
+            }
+            thistermmatch = left && right;
+          }
+          if (thistermmatch) break;
+        }
+      } else if (t.term.type == "condition") {
+        const key = getPrecomputedKey(t);
+        const anno = samplevalue && samplevalue[key];
+        if (anno) {
+          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
+        }
+      } else if (t.term.type == "survival") {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
+        thistermmatch = valueset.has(samplevalue);
+      } else if (t.term.type == "geneVariant" && t.legendFilterType == "geneVariant_hard") {
+        const f = t.values[0];
+        thistermmatch = samplevalue.find((s) => {
+          for (const v of s.values) {
+            if (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true;
+          }
+        }) && true;
+      } else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {
+      } else {
+        throw "unknown term type";
+      }
+      if (t.isnot) {
+        thistermmatch = !thistermmatch;
+      }
+      if (thistermmatch) numberofmatchedterms++;
+    }
+    if (filter.join == "or" && numberofmatchedterms) return true;
+  }
+  if (numberofmatchedterms == lst.length) return true;
+}
+
+export {
+  sample_match_termvaluesetting
+};
+//# sourceMappingURL=chunk-GNS6CQMA.js.map

package/dist/chunk-GNS6CQMA.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../common/termutils.js"],
+  "sourcesContent": ["import { SINGLECELL_GENE_EXPRESSION, GENE_EXPRESSION, METABOLITE_INTENSITY, PROTEOME_ABUNDANCE } from '#types'\n// import { dofetch3 } from '../src/client'\n\n/*\nto retrieve the termjson object of one term, using its id\nonly works for a termdb-enabled dataset\n\nif the function is attached to an instance with .state{ dslabel, genome }, then simply call:\n\tawait instance.getterm( ? )\n\notherwise, do:\n\tawait getterm( id, dslabel, genome )\n\n*/\n\nconst cache = { serverData: {} }\n\n/*\n\tGiven data of a sample and a filter, return if the sample match the filter\n\t\trow:{} data of a sample\n\t\tfilter\n\t\tgeneVariant$ids: [] array of $id of the geneVariant terms (in the matrix)\n*/\nexport function sample_match_termvaluesetting(row, filter, geneVariant$ids) {\n\tconst lst = !filter ? [] : filter.type == 'tvslst' ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\n\t/* for AND, require all terms to match */\n\tfor (const item of lst) {\n\t\tif (item.type == 'tvslst') {\n\t\t\tif (sample_match_termvaluesetting(row, item)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst t = item.tvs\n\t\t\tlet samplevalue\n\t\t\tif (t.term.type == 'geneVariant') {\n\t\t\t\tsamplevalue = geneVariant$ids.map(g => row[g]).filter(s => s) // filter out the genes that are not annotated for the sample\n\t\t\t} else if (\n\t\t\t\tt.term.type == 'integer' ||\n\t\t\t\tt.term.type == 'float' ||\n\t\t\t\tt.term.type == GENE_EXPRESSION ||\n\t\t\t\tt.term.type == METABOLITE_INTENSITY ||\n\t\t\t\tt.term.type == PROTEOME_ABUNDANCE\n\t\t\t) {\n\t\t\t\tsamplevalue = row[t.term.id] || row[t.term.$id]?.key\n\t\t\t} else if (t.term.type == 'survival') {\n\t\t\t\tsamplevalue = row[t.term.$id]?.key\n\t\t\t} else {\n\t\t\t\tsamplevalue = row[t.term.id] || row[t.term.$id]?.value\n\t\t\t}\n\t\t\tlet thistermmatch\n\n\t\t\tif (t.term.type == 'categorical') {\n\t\t\t\tif (samplevalue === undefined) {\n\t\t\t\t\t// this sample has no anno for this term, check isnot\n\t\t\t\t\tif (t.isnot) thistermmatch = !thistermmatch\n\t\t\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t\t// t may be frozen, should not modify to attach valueset if missing\n\t\t\t\t}\n\t\t\t\tconst valueset = t.valueset ? t.valueset : new Set(t.values.map(i => i.key))\n\t\t\t\tthistermmatch = valueset.has(samplevalue)\n\t\t\t} else if (\n\t\t\t\tt.term.type == 'integer' ||\n\t\t\t\tt.term.type == 'float' ||\n\t\t\t\tt.term.type == GENE_EXPRESSION ||\n\t\t\t\tt.term.type == METABOLITE_INTENSITY ||\n\t\t\t\tt.term.type == PROTEOME_ABUNDANCE\n\t\t\t) {\n\t\t\t\tif (samplevalue === undefined) {\n\t\t\t\t\t// this sample has no anno for this term, check isnot\n\t\t\t\t\tif (t.isnot) thistermmatch = !thistermmatch\n\t\t\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif ('value' in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value // || \"\"+samplevalue == range.value || samplevalue == \"\"+range.value //; if (thistermmatch) console.log(i++)\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// actual range\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if ('start' in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if ('stop' in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'condition') {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find(d => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find(d => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'survival') {\n\t\t\t\tif (samplevalue === undefined) {\n\t\t\t\t\t// this sample has no anno for this term, check isnot\n\t\t\t\t\tif (t.isnot) thistermmatch = !thistermmatch\n\t\t\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t\t// t may be frozen, should not modify to attach valueset if missing\n\t\t\t\t}\n\t\t\t\tconst valueset = t.valueset ? t.valueset : new Set(t.values.map(i => i.key))\n\t\t\t\tthistermmatch = valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == 'geneVariant' && t.legendFilterType == 'geneVariant_hard') {\n\t\t\t\t// handle a matrix legend hard filter\n\t\t\t\t// values: [{ dt, origin, mclasslst:[key] }]\n\t\t\t\tconst f = t.values[0] //matrix geneVariant legend filter only has one item in tvs.values\n\t\t\t\tthistermmatch =\n\t\t\t\t\tsamplevalue.find(s => {\n\t\t\t\t\t\tfor (const v of s.values) {\n\t\t\t\t\t\t\tif (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true\n\t\t\t\t\t\t}\n\t\t\t\t\t}) && true\n\t\t\t} else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {\n\t\t\t} else {\n\t\t\t\tthrow 'unknown term type'\n\t\t\t}\n\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\n\t\t// if one tvslst is matched with an \"or\" (Set UNION), then sample is okay\n\t\tif (filter.join == 'or' && numberofmatchedterms) return true\n\t}\n\n\t// for join=\"and\" (Set intersection)\n\tif (numberofmatchedterms == lst.length) return true\n}\n"],
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+}