@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-QRIRWDIW.js

@@ -1,252 +0,0 @@
-import {
-  getMclassSorter,
-  getSampleGroupSorter,
-  getSampleSorter,
-  getTermSorter
-} from "./chunk-5UMPBVA6.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel,
-  sample_match_termvaluesetting
-} from "./chunk-XYFDBYOY.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-QRIRWDIW.js.map

package/dist/chunk-R6L6NVEC.js

@@ -1,14 +0,0 @@
-// src/block.lazyload.js
-var Block;
-async function blocklazyload(arg) {
-  if (!Block) {
-    const b = await import("./block-2MABX5QO.js");
-    Block = b.Block;
-  }
-  return new Block(arg);
-}
-
-export {
-  blocklazyload
-};
-//# sourceMappingURL=chunk-R6L6NVEC.js.map

package/dist/chunk-RLTLYKHO.js

@@ -1,34 +0,0 @@
-import {
-  appInit
-} from "./chunk-OXJ2TWDO.js";
-import {
-  TermTypes
-} from "./chunk-6ITDJ5UR.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-RLTLYKHO.js.map

package/dist/chunk-S5ZI6N2I.js

@@ -1,293 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-OXJ2TWDO.js";
-import {
-  dofetch3
-} from "./chunk-7RN3L2BX.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-XYFDBYOY.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-2MABX5QO.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-PBCPC5I7.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-2MABX5QO.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-S5ZI6N2I.js.map