@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/chunk-DNVSEW6P.js

@@ -0,0 +1,170 @@
+import {
+  getEmptyCell,
+  maySetEmptyCell,
+  setCellProps
+} from "./chunk-VDIVDU3T.js";
+import {
+  TermTypeGroups
+} from "./chunk-7KRS7L4U.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.serieses.js
+var matrix_serieses_exports = {};
+__export(matrix_serieses_exports, {
+  getSerieses: () => getSerieses
+});
+function getSerieses(data) {
+  const s = this.settings.matrix;
+  const serieses = [];
+  const { colw, dx, dy, xMin, xMax } = this.dimensions;
+  const dvt = this.config.divideBy || {};
+  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
+  const legendGroups = {};
+  this.colorScaleByTermId = {};
+  for (const t of this.termOrder) {
+    const $id = t.tw.$id;
+    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
+    const isDivideByTerm = termid === divideByTermId;
+    const emptyGridCells = [];
+    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
+    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
+    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
+    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
+    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
+    const series = {
+      t,
+      tw: t.tw,
+      cells: [],
+      y,
+      hoverY0,
+      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
+    };
+    for (const so of this.unfilteredSampleOrder) {
+      const { totalIndex, grpIndex, row } = so;
+      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
+      const anno = row[$id];
+      const cellTemplate = {
+        s: so,
+        sample: row.sample,
+        tw: t.tw,
+        term: t.tw.term,
+        termid,
+        $id,
+        totalIndex,
+        grpIndex,
+        row,
+        t,
+        seriesY: y
+      };
+      if (!anno) {
+        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
+          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
+          series.cells.push(cell);
+        }
+        continue;
+      }
+      const key = anno.key;
+      const values = anno.filteredValues || anno.values || [anno.value];
+      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
+      const height = !s.transpose ? s.rowh / numRects : colw;
+      const width = !s.transpose ? colw : colw / values.length;
+      const siblingCells = [];
+      if (!anno || !anno.renderedValues?.length) {
+        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
+          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
+          series.cells.push(cell);
+        }
+        continue;
+      }
+      for (const [i, value] of values.entries()) {
+        const cell = Object.assign({ key, siblingCells }, cellTemplate);
+        cell.valueIndex = i;
+        let legend;
+        if (typeof t.tw.setCellProps == "function") {
+          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
+        } else {
+          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
+          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
+        }
+        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
+        if (legend) {
+          for (const l of [legendGroups, so.grp.legendGroups]) {
+            if (!l) continue;
+            if (!l[legend.group]) {
+              l[legend.group] = {
+                ref: legend.ref,
+                values: {},
+                order: legend.order,
+                $id,
+                origin: legend.entry.origin
+              };
+              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
+            }
+            const lg = l[legend.group];
+            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
+            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
+            if (!lg.values[legendK]) {
+              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
+              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
+            }
+            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
+            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
+              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
+            } else lg.values[legendK].samples.add(row.sample);
+            if (isDivideByTerm) {
+              lg.values[legend.value].isExcluded = so.grp.isExcluded;
+            }
+          }
+        }
+        if (!so.grp.isExcluded) {
+          if (anno.renderedValues.includes(value)) series.cells.push(cell);
+          siblingCells.push(cell);
+        }
+      }
+      if (s.showGrid == "rect" && !so.grp.isExcluded) {
+        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
+        if (cell) emptyGridCells.push(cell);
+      }
+    }
+    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
+    if (series.cells.length) serieses.push(series);
+  }
+  addAllHiddenLegendGroups(legendGroups, this);
+  this.legendData = this.getLegendData(legendGroups, data.refs, this);
+  for (const grp of this.sampleGroups) {
+    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
+  }
+  return serieses;
+}
+function addAllHiddenLegendGroups(legendGroups, self) {
+  for (const valueFilter of self.config.legendValueFilter.lst) {
+    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
+      legendGroups[valueFilter.tvs.term.$id] = {
+        ref: {},
+        values: {},
+        $id: valueFilter.tvs.term.$id
+      };
+    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
+      legendGroups[valueFilter.legendGrpName] = {
+        ref: {},
+        values: {},
+        dt: [valueFilter.tvs.values[0].dt],
+        origin: valueFilter.tvs.values[0].origin
+      };
+    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
+      legendGroups[valueFilter.tvs.term.$id] = {
+        ref: {},
+        values: {},
+        $id: valueFilter.tvs.term.$id
+      };
+    }
+  }
+}
+
+export {
+  getSerieses,
+  matrix_serieses_exports
+};
+//# sourceMappingURL=chunk-DNVSEW6P.js.map

package/dist/chunk-E6XLLQCG.js

@@ -0,0 +1,299 @@
+import {
+  first_genetrack_tolist,
+  gmmode,
+  sayerror
+} from "./chunk-L7VDSIM7.js";
+import {
+  dofetch3
+} from "./chunk-6G4YOMWW.js";
+import {
+  codon_stop,
+  nt2aa,
+  proteinDomainColorScale
+} from "./chunk-7KRS7L4U.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.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-TCWYUB4R.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.hidePdomain) {
+        for (const i of a.pdomains) {
+          m.domain_hidden[i.name + i.description] = 1;
+        }
+      }
+    }
+  }
+  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-TNIIJABK.js");
+      _.validate_oldds(ds);
+      delete ds.legacyDsIsUninitiated;
+    }
+  }
+  const b = await import("./block-TCWYUB4R.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,
+    aarange: arg.aarange,
+    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-E6XLLQCG.js.map

package/dist/chunk-E6XLLQCG.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../common/snp.js", "../src/block.init.js"],
+  "sourcesContent": ["import { dofetch3 } from './dofetch'\n\n/*\ngenome={}: client-side genome object\nstr=str: query string to match with dbSNP accession\n\nreturns {chr,start,stop}\nthrows exception if no match\n*/\nexport async function string2snp(genome, str) {\n\tconst data = await dofetch3('snp', {\n\t\tmethod: 'POST',\n\t\tbody: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })\n\t})\n\tif (data.error) throw data.error\n\tif (!data.results || data.results.length == 0) throw str + ': not a SNP'\n\t// start/stop are ucsc bed format, include start, not stop\n\t// return hit on major if any\n\tfor (const i of data.results) {\n\t\tconst chr = genome.chrlookup[i.chrom.toUpperCase()]\n\t\tif (chr && chr.major) {\n\t\t\treturn {\n\t\t\t\tchr: i.chrom,\n\t\t\t\tstart: i.chromStart,\n\t\t\t\tstop: i.chromEnd\n\t\t\t}\n\t\t}\n\t}\n\t// no hit on major chr, just return the first one\n\tconst r = data.results[0]\n\treturn {\n\t\tchr: r.chrom,\n\t\tstart: r.chromStart,\n\t\tstop: r.chromEnd\n\t}\n}\n", "import { scaleOrdinal } from 'd3-scale'\nimport { gmmode } from './client'\nimport { nt2aa, codon_stop, bplen, proteinDomainColorScale } from '#shared/common.js'\nimport { select } from 'd3-selection'\nimport { dofetch3 } from '#common/dofetch'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport { sayerror } from '#dom'\nimport { string2snp } from '#common/snp'\n\n/*\nfor processing requests from entry point (app.js ui, embedding)\nmainly for launching gene view\nalso for browser view if search term is position/snp\n\nquick fix: arg.__blockInstance is attached\n*/\n\nexport default async function (arg) {\n\tif (!arg.holder) throw 'No holder for block.init'\n\tif (!arg.genome) throw 'no genome'\n\tif (arg.holder instanceof Element) arg.holder = select(arg.holder)\n\tif (!arg.tklst) arg.tklst = []\n\n\tif (arg.query) {\n\t\t/*\n\t\tquery=str, run step1() to match it with gene or snp\n\t\tif match with gene, adds arg.model{} and arg.allmodels[], and run step2()\n\t\tif match with snp, load block and exit\n\t\t*/\n\t\tawait step1_findgm(arg)\n\t\treturn\n\t}\n\n\tif (arg.model && arg.allmodels) {\n\t\tawait step2_getseq(arg)\n\t\treturn\n\t}\n\n\t// TODO if to throw\n\t//throw '.query and (.model, .allmodels) are both missing'\n}\n\nasync function step1_findgm(arg) {\n\t/* arg.query=str is given\n\tsearch it against gene or snp name\n\t*/\n\tconst wait = arg.holder\n\t\t.append('p')\n\t\t.style('font-size', '2em')\n\t\t.style('color', '#858585')\n\t\t.text('Searching for ' + arg.query + ' ...')\n\n\tconst data = await dofetch3('genelookup', {\n\t\tbody: { deep: 1, input: arg.query, genome: arg.genome.name }\n\t})\n\tif (!data) throw 'querying genes: server error'\n\tif (data.error) throw 'error querying genes: ' + data.error\n\n\tif (!data.gmlst || data.gmlst.length == 0) {\n\t\t// not a gene\n\t\tif (arg.genome.hasSNP) {\n\t\t\ttry {\n\t\t\t\t// throws exception if not matching a snp\n\t\t\t\tconst r = await string2snp(arg.genome, arg.query)\n\t\t\t\twait.remove()\n\t\t\t\t// TODO automatically add SNP track\n\t\t\t\tconst par = {\n\t\t\t\t\tgenome: arg.genome,\n\t\t\t\t\tholder: arg.holder,\n\t\t\t\t\tchr: r.chr,\n\t\t\t\t\tstart: Math.max(0, r.start - 300),\n\t\t\t\t\tstop: r.start + 300,\n\t\t\t\t\tnobox: true,\n\t\t\t\t\ttklst: arg.tklst,\n\t\t\t\t\tdebugmode: arg.debugmode\n\t\t\t\t}\n\t\t\t\tfirst_genetrack_tolist(arg.genome, par.tklst)\n\t\t\t\tconst b = await import('./block')\n\t\t\t\tconst block = new b.Block(par)\n\t\t\t\tblock.addhlregion(r.chr, r.start, r.stop - 1)\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Not a gene or SNP: ' + arg.query)\n\t\t\t}\n\t\t} else {\n\t\t\twait.text('No match to gene: ' + arg.query)\n\t\t}\n\t\treturn\n\t}\n\n\t// match to a gene\n\n\twait.remove()\n\targ.allmodels = data.gmlst\n\n\t// if query string matches with an isoform\n\tfor (const m of arg.allmodels) {\n\t\tif (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {\n\t\t\t// query string is an isoform\n\t\t\targ.model = m\n\t\t\tawait step2_getseq(arg)\n\t\t\treturn\n\t\t}\n\t}\n\n\t// query string is not an isoform\n\t// from the list of returned isoforms, find a canonical one and use as paint.model\n\n\tconst defaultisoforms = []\n\n\tfor (const m of arg.allmodels) {\n\t\tif (!m.isoform) throw 'isoform missing from one gene model: ' + JSON.stringify(m)\n\t\t// cache\n\t\tconst n = m.isoform.toUpperCase()\n\t\tif (arg.genome.isoformcache.has(n)) {\n\t\t\tlet nothas = true\n\t\t\tfor (const m2 of arg.genome.isoformcache.get(n)) {\n\t\t\t\tif (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {\n\t\t\t\t\tnothas = false\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (nothas) {\n\t\t\t\targ.genome.isoformcache.get(n).push(m)\n\t\t\t}\n\t\t} else {\n\t\t\targ.genome.isoformcache.set(n, [m])\n\t\t}\n\t\tif (m.isoform.toUpperCase() == arg.query.toUpperCase()) {\n\t\t\tdefaultisoforms.push(m)\n\t\t\tbreak\n\t\t}\n\t\tif (m.isdefault) {\n\t\t\tdefaultisoforms.push(m)\n\t\t}\n\t}\n\n\tif (defaultisoforms.length == 1) {\n\t\targ.model = defaultisoforms[0]\n\t} else if (defaultisoforms.length > 1) {\n\t\tfor (const m of defaultisoforms) {\n\t\t\tif (m.chr == 'chrY') {\n\t\t\t\t// hardcoded to avoid for CRLF2\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst chr = arg.genome.chrlookup[m.chr.toUpperCase()]\n\t\t\tif (!chr) {\n\t\t\t\t// unknown chr\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (!chr.major) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\targ.model = m\n\t\t\t/* in human, canonical isoforms are marked out in both refseq and gencode\n\t\t\tas in the \"genes\" table, refseq is loaded before gencode\n\t\t\tthis loop will encounter refseq canonical isoform first\n\t\t\tbreak here so that it won't override it with gencode\n\t\t\tand maintain the old behavior of showing refseq by searching a gene symbol\n\t\t\t*/\n\t\t\tbreak\n\t\t}\n\t\tif (!arg.model) {\n\t\t\targ.model = defaultisoforms[0]\n\t\t}\n\t}\n\tif (!arg.model) {\n\t\targ.model = arg.allmodels[0]\n\t}\n\tawait step2_getseq(arg)\n}\n\nasync function step2_getseq(arg) {\n\tif (arg.model.genomicseq) {\n\t\tchecker()\n\t\tstep2_getpdomain(arg)\n\t\treturn\n\t}\n\tconst par = {\n\t\tgenome: arg.genome.name,\n\t\tcoord: arg.model.chr + ':' + (arg.model.start + 1) + '-' + arg.model.stop\n\t}\n\tconst data = await dofetch3('ntseq', { method: 'POST', body: JSON.stringify(par) })\n\tif (!data) throw 'getting sequence: server error'\n\tif (data.error) throw 'getting sequence: ' + data.error\n\tif (!data.seq) throw 'no nt seq???'\n\targ.model.genomicseq = data.seq.toUpperCase()\n\targ.model.aaseq = nt2aa(arg.model)\n\tchecker()\n\tawait step2_getpdomain(arg)\n\n\tfunction checker() {\n\t\tif (arg.model.aaseq) {\n\t\t\t// stop codon check\n\t\t\tconst stop = arg.model.aaseq.indexOf(codon_stop)\n\t\t\tconst cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0) // subtrack non-translating nt from cds\n\t\t\tif (stop != -1 && stop < cdslen / 3 - 1) {\n\t\t\t\tsayerror(arg.holder, 'Translating ' + arg.model.isoform + ' ends at ' + stop + ' AA, expecting ' + cdslen / 3)\n\t\t\t}\n\t\t\t/*\n\t\t\tif (paint.model.aaseq[0] != 'M') {\n\t\t\t\tpaint.error('Translated protein does not start with \"M\" in ' + paint.model.isoform)\n\t\t\t}\n\t\t\t*/\n\t\t}\n\t}\n}\n\nasync function step2_getpdomain(arg) {\n\t/*\n\tblock.init special treatment:\n\twill get pdomain for all isoforms, not just the isoform that's used\n\t*/\n\tconst isoform2gm = new Map()\n\t// k: isoform name, v: [{}]\n\n\tfor (const m of arg.allmodels) {\n\t\tif (!m.pdomains) {\n\t\t\tm.pdomains = [] // empty for no domain\n\t\t\tm.domain_hidden = {}\n\t\t\tif (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, [])\n\t\t\tisoform2gm.get(m.isoform).push(m)\n\t\t}\n\t}\n\tif (isoform2gm.size == 0) {\n\t\tawait step3(arg)\n\t\treturn\n\t}\n\n\tconst data = await dofetch3('pdomain', {\n\t\tmethod: 'POST',\n\t\tbody: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })\n\t})\n\tif (data.error) throw 'error getting protein domain: ' + data.error\n\tif (!Array.isArray(data.lst)) throw '.lst[] not array'\n\t// apply server-returned domains\n\tfor (const a of data.lst) {\n\t\tfor (const m of isoform2gm.get(a.name)) {\n\t\t\tm.pdomains = a.pdomains\n\t\t\tif (arg.hidePdomain) {\n\t\t\t\tfor (const i of a.pdomains) {\n\t\t\t\t\tm.domain_hidden[i.name + i.description] = 1\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tif (arg.geneDomains) {\n\t\t// runpp-supplied custom domains for specific isoforms https://github.com/stjude/proteinpaint/wiki/Embedding#Gene-view\n\t\tif (typeof arg.geneDomains != 'object') throw 'geneDomains not object'\n\t\tfor (const isoform in arg.geneDomains) {\n\t\t\tconst lst = isoform2gm.get(isoform)\n\t\t\tif (!lst) throw `unknown isoform ${isoform} from geneDomains{}`\n\t\t\tfor (const g of lst) {\n\t\t\t\tif (!g.pdomains) g.pdomains = [] // a genemodel may be missing this array (no server-returned domains)\n\t\t\t\tif (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`\n\t\t\t\tfor (const b of arg.geneDomains[isoform]) {\n\t\t\t\t\tif (typeof b != 'object') throw 'element from geneDomains[] not object'\n\t\t\t\t\tif (!Number.isInteger(b.start)) throw 'start not integer from geneDomains[]'\n\t\t\t\t\tif (!Number.isInteger(b.stop)) throw 'stop not integer from geneDomains[]'\n\t\t\t\t\tif (b.start > b.stop) throw 'start>stop from geneDomains[]'\n\t\t\t\t\tif (!b.name) b.name = 'Custom domain'\n\t\t\t\t\t// g.pdomains is a reference to shared array. the custom domain may have been added before and avoid adding twice\n\t\t\t\t\tif (!g.pdomains.find(a => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tconst s = proteinDomainColorScale() // important to declare color getter outside of loop so that a domain appearing in multiple isoforms can get same color\n\tfor (const lst of isoform2gm.values()) {\n\t\tfor (const g of lst) {\n\t\t\tfor (const d of g.pdomains || []) {\n\t\t\t\tif (!d.color) d.color = s(d.name + d.description)\n\t\t\t}\n\t\t}\n\t}\n\n\tawait step3(arg)\n}\n\nasync function step3(arg) {\n\t// mode\n\tlet mode = arg.gmmode\n\tif (!mode) {\n\t\tif (arg.model.cdslen) {\n\t\t\tmode = gmmode.protein\n\t\t} else {\n\t\t\tmode = gmmode.exononly\n\t\t}\n\t}\n\n\tif (arg.dataset) {\n\t\t/*\n\t\tfor legacy ds\n\t\twhen migrated to mds3, can delete this step\n\t\tsince mds3 ds is loaded from mds3/makeTk, when initiating a track\n\t\t*/\n\t\tif (!Array.isArray(arg.dataset)) throw 'dataset is not array'\n\n\t\t// load dataset client-side object, register in genome\n\t\tfor (const dsname of arg.dataset) {\n\t\t\t// potentially problematic logic: only skip the dataset when that flag is false\n\t\t\t// if the flag is true, tells the legacy ds is uninitiated\n\t\t\tif (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue\n\t\t\tconst d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`)\n\t\t\tif (d.error) throw `invalid name from dataset[]: ${d.error}`\n\t\t\tif (!d.ds) throw '.ds missing'\n\n\t\t\t// dataset is already registered under genome by ds.label\n\t\t\tconst ds = arg.genome.datasets[d.ds.label]\n\t\t\tObject.assign(ds, d.ds)\n\t\t\tconst _ = await import('./legacyDataset')\n\t\t\t_.validate_oldds(ds)\n\n\t\t\tdelete ds.legacyDsIsUninitiated\n\t\t}\n\t}\n\n\tconst b = await import('./block')\n\n\t// quick fix to make block instance available to caller\n\targ.__blockInstance = new b.Block({\n\t\tgenome: arg.genome,\n\t\tholder: arg.holder,\n\t\tnobox: true,\n\t\tusegm: arg.model,\n\t\tgmstackheight: 37,\n\t\tallgm: arg.allmodels,\n\t\tdatasetlst: arg.dataset,\n\t\tlegacyDsFilter: arg.legacyDsFilter,\n\t\tmset: arg.mset,\n\t\thlaachange: arg.hlaachange,\n\t\thlvariants: arg.hlvariants,\n\t\thlregions: arg.hlregions,\n\t\taarange: arg.aarange,\n\t\tgmmode: mode,\n\t\thidedatasetexpression: arg.hidedatasetexpression,\n\t\thidegenecontrol: arg.hidegenecontrol,\n\t\thidegenelegend: arg.hidegenelegend,\n\t\tvariantPageCall_snv: arg.variantPageCall_snv,\n\t\tdatasetqueries: arg.datasetqueries,\n\t\tsamplecart: arg.samplecart,\n\t\tdebugmode: arg.debugmode,\n\t\ttklst: arg.tklst,\n\t\tmclassOverride: arg.mclassOverride,\n\t\thide_dsHandles: arg.hide_dsHandles,\n\t\tonloadalltk_always: arg.onloadalltk_always,\n\t\tonAddRemoveTk: arg.onAddRemoveTk\n\t})\n}\n"],
+  "mappings": 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