@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-RAJZYWFN.js

@@ -1,95 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-NYX4B5CO.js";
-import {
-  fillTermWrapper
-} from "./chunk-LN3QYBGI.js";
-import {
-  copyMerge
-} from "./chunk-MVTCBVSX.js";
-import {
-  TermTypes,
-  numericTypes
-} from "./chunk-EGWVYY7K.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const hierClusterSubTypeOverrides = app.vocabApi.termdbConfig[`${config.dataType}Cluster`] || {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    hierClusterSubTypeOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType == TermTypes.GENE_EXPRESSION || config.dataType == TermTypes.METABOLITE_INTENSITY || config.dataType == TermTypes.PROTEOME_ABUNDANCE) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (grpType == "numericDictTerm") {
-    if (twType == "float" || twType == "integer") return true;
-  }
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-RAJZYWFN.js.map

package/dist/chunk-ROLVOPVR.js

@@ -1,252 +0,0 @@
-import {
-  getMclassSorter,
-  getSampleGroupSorter,
-  getSampleSorter,
-  getTermSorter
-} from "./chunk-IABWKPRK.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel,
-  sample_match_termvaluesetting
-} from "./chunk-AMYSEKPF.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.groups.js
-var matrix_groups_exports = {};
-__export(matrix_groups_exports, {
-  classifyValues: () => classifyValues,
-  getSampleGroups: () => getSampleGroups,
-  getSampleOrder: () => getSampleOrder,
-  getTermOrder: () => getTermOrder,
-  stackSiblingCellsByClass: () => stackSiblingCellsByClass
-});
-function getTermOrder(data) {
-  const s = this.settings.matrix;
-  this.termSorter = getTermSorter(this, s);
-  const termOrder = [];
-  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
-  this.mclassSorter = getMclassSorter(this);
-  for (const [grpIndex, grp] of this.termGroups.entries()) {
-    const lst = [];
-    for (const [index, tw] of grp.lst.entries()) {
-      const counts = { samples: 0, hits: 0 };
-      const countedSamples = /* @__PURE__ */ new Set();
-      for (const sd of data.lst) {
-        if (countedSamples.has(sd.sample)) continue;
-        countedSamples.add(sd.sample);
-        const anno = sd[tw.$id];
-        if (anno) {
-          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
-          anno.filteredValues = filteredValues;
-          anno.countedValues = countedValues;
-          anno.renderedValues = renderedValues;
-          if (anno.countedValues?.length) {
-            const v = tw.term.values?.[anno.value];
-            if (v?.uncountable) continue;
-            counts.samples += 1;
-            counts.hits += anno.countedValues.length;
-            if (tw.q?.mode == "continuous") {
-              const v2 = anno.value;
-              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
-              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
-            }
-          }
-        }
-      }
-      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
-      if (grp.type == "hierCluster") numClusterTerms++;
-    }
-    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
-    const processedLst = lst.filter((t) => {
-      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
-      if (!grp.settings) return true;
-      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
-    }).sort(termSorter);
-    if (!processedLst.length) continue;
-    for (const [index, t] of processedLst.entries()) {
-      const { tw, counts } = t;
-      const ref = data.refs.byTermId[t.tw.$id] || {};
-      termOrder.push({
-        grp,
-        grpIndex,
-        visibleGrpIndex,
-        tw,
-        index,
-        // rendered index
-        lstIndex: t.index,
-        // as-listed index, before applying term filters
-        processedLst,
-        prevGrpTotalIndex: totalIndex,
-        totalIndex: totalIndex + index,
-        ref,
-        allCounts: counts
-        // note: term label will be assigned after sample counts are known
-        // label: t.tw.label || t.tw.term.name,
-      });
-    }
-    totalIndex += processedLst.length;
-    visibleGrpIndex += 1;
-  }
-  this.numTerms = termOrder.length;
-  this.numClusterTerms = numClusterTerms;
-  return termOrder;
-}
-function getSampleGroups(data) {
-  const s = this.settings.matrix;
-  const defaultSampleGrp = {
-    id: this.config.divideBy?.$id,
-    name: this.config.divideBy ? "Not annotated" : "",
-    lst: []
-  };
-  const sampleGroups = /* @__PURE__ */ new Map();
-  const term = this.config.divideBy?.term || {};
-  const $id = this.config.divideBy?.$id || "-";
-  const exclude = this.config.divideBy?.exclude || [];
-  const values = term.values || {};
-  const ref = data.refs.byTermId[$id] || {};
-  for (const row of data.lst) {
-    if ($id in row) {
-      const key = row[$id].key;
-      const name = key in values && values[key].label ? values[key].label : key;
-      if (!sampleGroups.has(key)) {
-        const grp = {
-          name: `${name}`,
-          // convert to a string
-          id: key,
-          lst: [],
-          tw: this.config.divideBy,
-          legendGroups: {},
-          isExcluded: exclude.includes(key)
-        };
-        if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
-        else delete grp.order;
-        sampleGroups.set(key, grp);
-      }
-      sampleGroups.get(key).lst.push(row);
-    } else {
-      defaultSampleGrp.lst.push(row);
-    }
-  }
-  const sampleGrpsArr = [...sampleGroups.values()];
-  const n = sampleGroups.size;
-  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
-    const l = s.controlLabels;
-    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
-  }
-  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
-    sampleGroups.set(void 0, defaultSampleGrp);
-    sampleGrpsArr.push(...sampleGroups.values());
-  }
-  this.asListedSampleOrder = [];
-  for (const grp of sampleGrpsArr) {
-    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
-  }
-  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
-  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
-    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
-  });
-  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
-  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
-  const dataFilter = (d) => allowedSamples.includes(d);
-  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
-  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
-  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
-  for (const grp of sampleGrpsArr) {
-    grp.lst = grp.lst.filter(dataFilter);
-    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
-    grp.lst.sort(grpLstSampleSorter);
-  }
-  const sampleGrpSorter = getSampleGroupSorter(this);
-  return sampleGrpsArr.sort(sampleGrpSorter);
-}
-function getSampleOrder(data) {
-  const s = this.settings.matrix;
-  this.visibleSampleGrps = /* @__PURE__ */ new Set();
-  const sampleOrder = [];
-  let total = 0, numHiddenGrps = 0;
-  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
-    if (!grp.lst.length) continue;
-    if (grp.isExcluded) numHiddenGrps++;
-    let processedLst = grp.lst;
-    for (const [index, row] of processedLst.entries()) {
-      sampleOrder.push({
-        grp,
-        grpIndex: grpIndex - numHiddenGrps,
-        // : this.sampleGroups.length,
-        row,
-        index,
-        prevGrpTotalIndex: total,
-        totalIndex: total + index,
-        totalHtAdjustments: 0,
-        // may be required when transposed???
-        grpTotals: { htAdjustment: 0 },
-        // may be required when transposed???
-        processedLst
-      });
-    }
-    if (!grp.isExcluded) total += processedLst.length;
-    this.visibleSampleGrps.add(grp);
-  }
-  this.unfilteredSampleOrder = sampleOrder;
-  return sampleOrder.filter((so) => !so.grp.isExcluded);
-}
-function classifyValues(anno, tw, grp, s, sample) {
-  const values = "value" in anno ? [anno.value] : anno.values;
-  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
-  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
-  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
-    throw `unknown matrix value filter type='${isSpecific.type}'`;
-  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
-  const renderedValues = [];
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
-    filteredValues.sort(this.mclassSorter);
-    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
-    else {
-      const sortedFilteredValues = [];
-      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
-        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
-        if (v) renderedValues.push(v);
-        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
-        sortedFilteredValues.push(...oneDtV);
-      }
-      filteredValues = sortedFilteredValues;
-    }
-  } else {
-    renderedValues.push(...filteredValues);
-  }
-  return {
-    filteredValues,
-    countedValues: filteredValues.filter((v) => {
-      if (tw.term.type == "geneVariant") {
-        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
-          if (!groupset) throw "groupset not found";
-          const group = groupset.groups[0];
-          if (v != group.name) return false;
-        } else {
-          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
-            return false;
-        }
-      }
-      return true;
-    }),
-    renderedValues
-  };
-}
-function stackSiblingCellsByClass(a, b) {
-  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
-}
-
-export {
-  getTermOrder,
-  getSampleGroups,
-  getSampleOrder,
-  classifyValues,
-  stackSiblingCellsByClass,
-  matrix_groups_exports
-};
-//# sourceMappingURL=chunk-ROLVOPVR.js.map

package/dist/chunk-RQZJIBIH.js

@@ -1,34 +0,0 @@
-import {
-  appInit
-} from "./chunk-LN3QYBGI.js";
-import {
-  TermTypes
-} from "./chunk-EGWVYY7K.js";
-
-// termdb/handlers/ssGSEA.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const genesetDbName = Object.keys(opts.genomeObj.termdbs || {})[0];
-    if (!genesetDbName) throw "genesetDbName missing";
-    await appInit({
-      holder: opts.holder,
-      state: {
-        dslabel: genesetDbName,
-        genome: opts.genomeObj.name,
-        nav: { header_mode: "search_only" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback({ id: term.id, type: TermTypes.SSGSEA, name: term.name });
-        }
-      }
-    });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-RQZJIBIH.js.map

package/dist/chunk-RSE2FOKW.js

@@ -1,217 +0,0 @@
-import {
-  dofetch,
-  dofetch2
-} from "./chunk-YC6ZJ7RP.js";
-import {
-  contigNameNoChr2
-} from "./chunk-AMYSEKPF.js";
-
-// tracks/hic/data/parseData.ts
-async function hicParseFile(hic, debugmode, errList = []) {
-  if (debugmode) window["hic"] = hic;
-  if (hic.tklst) {
-    const lst = [];
-    for (const t of hic.tklst) {
-      if (!t.type) {
-        errList.push("type missing from one of the tracks accompanying HiC");
-      } else {
-        t.iscustom = true;
-        lst.push(t);
-      }
-    }
-    if (lst.length) {
-      hic.tklst = lst;
-    } else {
-      delete hic.tklst;
-    }
-  }
-  if (hic.enzyme) {
-    if (hic.genome.hicenzymefragment) {
-      let frag = null;
-      for (const f of hic.genome.hicenzymefragment) {
-        if (f.enzyme == hic.enzyme) {
-          frag = f;
-          break;
-        }
-      }
-      if (frag) {
-        hic.enzymefile = frag.file;
-      } else {
-        errList.push("unknown enzyme: " + hic.enzyme);
-        delete hic.enzyme;
-      }
-    } else {
-      errList.push("no enzyme fragment information available for this genome");
-      delete hic.enzyme;
-    }
-  }
-  try {
-    if (hic.sv && hic.sv.file) {
-      const re = await dofetch(hic.hostURL + "/textfile", {
-        method: "POST",
-        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
-      });
-      const data2 = re.json();
-      const [err2, header, items] = parseSV(data2.text);
-      if (err2) throw { message: "Error parsing SV: " + err2 };
-      hic.sv.header = header;
-      hic.sv.items = items;
-    }
-    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
-    if (data.error) {
-      errList.push(data.error);
-      return;
-    }
-    const err = hicparsestat(hic, data.out);
-    if (err) throw { message: err };
-  } catch (err) {
-    errList.push(err.message || err);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-  }
-  return hic;
-}
-function parseSV(txt) {
-  const lines = txt.trim().split(/\r?\n/);
-  const [err, header] = parseSVheader(lines[0]);
-  if (err) return ["header error: " + err];
-  const items = [];
-  for (let i = 1; i < lines.length; i++) {
-    const line = lines[i];
-    if (line[0] == "#") continue;
-    const [e, m] = parseSVline(line, header);
-    if (e) return ["line " + (i + 1) + " error: " + e];
-    items.push(m);
-  }
-  return [null, header, items];
-}
-function parseSVheader(line) {
-  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("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("strand_a", "orta", "orienta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb", "orientb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("numreadsa");
-  if (i != -1) header[i] = "reads1";
-  i = htry("numreadsb");
-  if (i != -1) header[i] = "reads2";
-  return [null, header];
-}
-function parseSVline(line, header) {
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) return ["missing chr1"];
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) return ["missing chr2"];
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  if (!m.position1) return ["missing position1"];
-  let v = Number.parseInt(m.position1);
-  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
-  m.position1 = v;
-  if (!m.position2) return ["missing position2"];
-  v = Number.parseInt(m.position2);
-  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
-  m.position2 = v;
-  if (m.reads1) {
-    v = Number.parseInt(m.reads1);
-    if (Number.isNaN(v)) return ["reads1 invalid value"];
-    m.reads1 = v;
-  }
-  if (m.reads2) {
-    v = Number.parseInt(m.reads2);
-    if (Number.isNaN(v)) return ["reads2 invalid value"];
-    m.reads2 = v;
-  }
-  return [null, m];
-}
-function hicparsestat(hic, j) {
-  if (!j) return "cannot stat hic file";
-  hic.normalization = j.normalization;
-  hic.version = j.version;
-  if (!j.Chromosomes) return "Chromosomes not found in file stat";
-  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
-  if (j.chrorder.length == 0) return ".chrorder[] empty array";
-  hic.chrorder = j.chrorder;
-  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
-  hic.bpresolution = j["Base pair-delimited resolutions"];
-  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
-  hic.fragresolution = j["Fragment-delimited resolutions"];
-  const chrlst = [];
-  for (const chr in j.Chromosomes) {
-    chrlst.push(chr);
-  }
-  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
-  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
-  if (nochrcount > 0) {
-    hic.nochr = true;
-    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
-  }
-  hic.chrlst = [];
-  for (const chr of hic.genome.majorchrorder) {
-    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
-    if (chrlst.indexOf(c2) != -1) {
-      hic.chrlst.push(chr);
-    }
-  }
-}
-function hicparsefragdata(items) {
-  const id2coord = /* @__PURE__ */ new Map();
-  let min = null, max;
-  for (const i of items) {
-    if (!i.rest || !i.rest[0]) {
-      return ["items[].rest data problem"];
-    }
-    const id = Number.parseInt(i.rest[0]);
-    if (Number.isNaN(id)) {
-      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
-    }
-    id2coord.set(id, [i.start, i.stop]);
-    if (min == null) {
-      min = id;
-      max = id;
-    } else {
-      min = Math.min(min, id);
-      max = Math.max(max, id);
-    }
-  }
-  return [null, id2coord, min, max];
-}
-
-export {
-  hicParseFile,
-  hicparsestat,
-  hicparsefragdata
-};
-//# sourceMappingURL=chunk-RSE2FOKW.js.map