@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-2A2KM5DU.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/isoformExpression.ts"],
+  "sourcesContent": ["import { Menu, addGeneSearchbox, sayerror, isoformSelect } from '#dom'\nimport type { GeneModel, IsoformTerm, IsoformCollectionTerm } from '#dom/types/isoformSelect'\nimport type { Div } from '../../types/d3'\nimport { dofetch3 } from '#common/dofetch'\nimport { ISOFORM_EXPRESSION } from '#shared/terms.js'\n\nexport class SearchHandler {\n\tcallback!: (term: IsoformTerm | IsoformCollectionTerm) => void\n\tapp: any\n\tdom!: { errDiv: Div; isoformDiv?: Div }\n\tcurrentGene: string | null = null\n\n\tinit(opts) {\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tconst holder = opts.holder.append('div').style('padding', '10px 0px')\n\t\tthis.dom = {\n\t\t\terrDiv: holder.append('div').style('margin', '5px 0px').style('display', 'none')\n\t\t}\n\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: opts.genomeObj,\n\t\t\trow: holder,\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\ttry {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'none')\n\t\t\t\t\tif (!geneSearch.geneSymbol) throw new Error('No gene selected')\n\t\t\t\t\t// guard against duplicate fires for the same gene\n\t\t\t\t\tif (geneSearch.geneSymbol === this.currentGene) return\n\t\t\t\t\tthis.currentGene = geneSearch.geneSymbol\n\t\t\t\t\t// isoformDiv is created after the search box so results appear below\n\t\t\t\t\tif (this.dom.isoformDiv) this.dom.isoformDiv.remove()\n\t\t\t\t\tthis.dom.isoformDiv = holder.append('div')\n\t\t\t\t\tawait this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj)\n\t\t\t\t} catch (e: unknown) {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'block')\n\t\t\t\t\tsayerror(this.dom.errDiv, 'Error: ' + (e instanceof Error ? e.message : String(e)))\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tasync showIsoforms(gene: string, genomeObj: any) {\n\t\tif (!gene) throw new Error('No gene selected')\n\n\t\t// deep lookup to get all isoforms for this gene\n\t\tconst data = await dofetch3('genelookup', { body: { genome: genomeObj.name, input: gene, deep: 1 } })\n\t\tif (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`)\n\n\t\t// filter to ENST isoforms, then check which have data via server-side lookup\n\t\tconst enstCandidates = data.gmlst.filter((gm: any) => gm.isoform?.startsWith('ENST'))\n\t\tif (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`)\n\n\t\tconst { available } = await dofetch3('termdb/isoformAvailability', {\n\t\t\tbody: {\n\t\t\t\tgenome: genomeObj.name,\n\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\tisoforms: enstCandidates.map((gm: any) => gm.isoform)\n\t\t\t}\n\t\t})\n\t\tconst availableSet = new Set(available || [])\n\t\tconst enstModels = enstCandidates.filter((gm: any) => availableSet.has(gm.isoform))\n\t\tif (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`)\n\n\t\t// bail if the user already searched a different gene while we were fetching\n\t\tif (gene !== this.currentGene) return\n\n\t\tconst div = this.dom.isoformDiv!\n\t\tdiv.append('div').style('margin-bottom', '8px').style('opacity', 0.65).text(`${gene} \u2014 select isoform(s):`)\n\n\t\tisoformSelect({\n\t\t\tholder: div,\n\t\t\tallgm: enstModels,\n\t\t\tmultiSelect: true,\n\t\t\tsubmitLabel: 'Create Collection',\n\t\t\tonMultiSelect: (selected: GeneModel[]) => {\n\t\t\t\tif (selected.length === 1) {\n\t\t\t\t\t// Single isoform: create individual isoformExpression term\n\t\t\t\t\tthis.selectIsoform(selected[0].isoform, gene)\n\t\t\t\t} else {\n\t\t\t\t\t// Multiple isoforms: create a custom termCollection\n\t\t\t\t\tthis.selectCollection(selected, gene)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tgetUnit() {\n\t\treturn this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || 'TPM'\n\t}\n\n\tselectIsoform(isoform: string, gene: string) {\n\t\tconst name = `${isoform} ${this.getUnit()}`\n\t\tthis.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION })\n\t}\n\n\tselectCollection(gms: GeneModel[], gene: string) {\n\t\tconst unit = this.getUnit()\n\t\tconst termlst = gms.map(gm => ({\n\t\t\tid: gm.isoform,\n\t\t\tname: gm.isoform,\n\t\t\ttype: ISOFORM_EXPRESSION as 'isoformExpression',\n\t\t\tisoform: gm.isoform\n\t\t}))\n\t\tthis.callback({\n\t\t\ttype: 'termCollection',\n\t\t\tisCustom: true,\n\t\t\tmemberType: 'numeric',\n\t\t\tname: `${gene} Isoforms (${unit})`,\n\t\t\ttermlst,\n\t\t\tpropsByTermId: {},\n\t\t\tisleaf: true\n\t\t})\n\t}\n}\n\n/** Filter gene models to ENST isoforms that exist in the available items list.\n *  If availableItems is empty, all ENST isoforms are returned (no filtering). */\nexport function filterIsoforms(gmlst: GeneModel[], availableItems: string[]) {\n\tconst itemSet = new Set(availableItems)\n\treturn gmlst.filter(gm => gm.isoform?.startsWith('ENST') && (itemSet.size === 0 || itemSet.has(gm.isoform)))\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;AAMO,IAAM,gBAAN,MAAoB;AAAA,EAApB;AAIN,uBAA6B;AAAA;AAAA,EAE7B,KAAK,MAAM;AACV,SAAK,WAAW,KAAK;AACrB,SAAK,MAAM,KAAK;AAChB,UAAM,SAAS,KAAK,OAAO,OAAO,KAAK,EAAE,MAAM,WAAW,UAAU;AACpE,SAAK,MAAM;AAAA,MACV,QAAQ,OAAO,OAAO,KAAK,EAAE,MAAM,UAAU,SAAS,EAAE,MAAM,WAAW,MAAM;AAAA,IAChF;AAEA,UAAM,aAAa,iBAAiB;AAAA,MACnC,KAAK,IAAI,KAAK,EAAE,SAAS,MAAM,CAAC;AAAA,MAChC,QAAQ,KAAK;AAAA,MACb,KAAK;AAAA,MACL,YAAY;AAAA,MACZ,UAAU,YAAY;AACrB,YAAI;AACH,eAAK,IAAI,OAAO,MAAM,WAAW,MAAM;AACvC,cAAI,CAAC,WAAW,WAAY,OAAM,IAAI,MAAM,kBAAkB;AAE9D,cAAI,WAAW,eAAe,KAAK,YAAa;AAChD,eAAK,cAAc,WAAW;AAE9B,cAAI,KAAK,IAAI,WAAY,MAAK,IAAI,WAAW,OAAO;AACpD,eAAK,IAAI,aAAa,OAAO,OAAO,KAAK;AACzC,gBAAM,KAAK,aAAa,WAAW,YAAY,KAAK,SAAS;AAAA,QAC9D,SAAS,GAAY;AACpB,eAAK,IAAI,OAAO,MAAM,WAAW,OAAO;AACxC,mBAAS,KAAK,IAAI,QAAQ,aAAa,aAAa,QAAQ,EAAE,UAAU,OAAO,CAAC,EAAE;AAAA,QACnF;AAAA,MACD;AAAA,IACD,CAAC;AAAA,EACF;AAAA,EAEA,MAAM,aAAa,MAAc,WAAgB;AAChD,QAAI,CAAC,KAAM,OAAM,IAAI,MAAM,kBAAkB;AAG7C,UAAM,OAAO,MAAM,SAAS,cAAc,EAAE,MAAM,EAAE,QAAQ,UAAU,MAAM,OAAO,MAAM,MAAM,EAAE,EAAE,CAAC;AACpG,QAAI,CAAC,KAAK,OAAO,OAAQ,OAAM,IAAI,MAAM,yBAAyB,IAAI,EAAE;AAGxE,UAAM,iBAAiB,KAAK,MAAM,OAAO,CAAC,OAAY,GAAG,SAAS,WAAW,MAAM,CAAC;AACpF,QAAI,eAAe,WAAW,EAAG,OAAM,IAAI,MAAM,4CAA4C,IAAI,EAAE;AAEnG,UAAM,EAAE,UAAU,IAAI,MAAM,SAAS,8BAA8B;AAAA,MAClE,MAAM;AAAA,QACL,QAAQ,UAAU;AAAA,QAClB,SAAS,KAAK,IAAI,SAAS,MAAM;AAAA,QACjC,UAAU,eAAe,IAAI,CAAC,OAAY,GAAG,OAAO;AAAA,MACrD;AAAA,IACD,CAAC;AACD,UAAM,eAAe,IAAI,IAAI,aAAa,CAAC,CAAC;AAC5C,UAAM,aAAa,eAAe,OAAO,CAAC,OAAY,aAAa,IAAI,GAAG,OAAO,CAAC;AAClF,QAAI,WAAW,WAAW,EAAG,OAAM,IAAI,MAAM,mCAAmC,IAAI,EAAE;AAGtF,QAAI,SAAS,KAAK,YAAa;AAE/B,UAAM,MAAM,KAAK,IAAI;AACrB,QAAI,OAAO,KAAK,EAAE,MAAM,iBAAiB,KAAK,EAAE,MAAM,WAAW,IAAI,EAAE,KAAK,GAAG,IAAI,4BAAuB;AAE1G,kBAAc;AAAA,MACb,QAAQ;AAAA,MACR,OAAO;AAAA,MACP,aAAa;AAAA,MACb,aAAa;AAAA,MACb,eAAe,CAAC,aAA0B;AACzC,YAAI,SAAS,WAAW,GAAG;AAE1B,eAAK,cAAc,SAAS,CAAC,EAAE,SAAS,IAAI;AAAA,QAC7C,OAAO;AAEN,eAAK,iBAAiB,UAAU,IAAI;AAAA,QACrC;AAAA,MACD;AAAA,IACD,CAAC;AAAA,EACF;AAAA,EAEA,UAAU;AACT,WAAO,KAAK,IAAI,SAAS,aAAa,QAAQ,mBAAmB,QAAQ;AAAA,EAC1E;AAAA,EAEA,cAAc,SAAiB,MAAc;AAC5C,UAAM,OAAO,GAAG,OAAO,IAAI,KAAK,QAAQ,CAAC;AACzC,SAAK,SAAS,EAAE,SAAS,MAAM,MAAM,MAAM,mBAAmB,CAAC;AAAA,EAChE;AAAA,EAEA,iBAAiB,KAAkB,MAAc;AAChD,UAAM,OAAO,KAAK,QAAQ;AAC1B,UAAM,UAAU,IAAI,IAAI,SAAO;AAAA,MAC9B,IAAI,GAAG;AAAA,MACP,MAAM,GAAG;AAAA,MACT,MAAM;AAAA,MACN,SAAS,GAAG;AAAA,IACb,EAAE;AACF,SAAK,SAAS;AAAA,MACb,MAAM;AAAA,MACN,UAAU;AAAA,MACV,YAAY;AAAA,MACZ,MAAM,GAAG,IAAI,cAAc,IAAI;AAAA,MAC/B;AAAA,MACA,eAAe,CAAC;AAAA,MAChB,QAAQ;AAAA,IACT,CAAC;AAAA,EACF;AACD;AAIO,SAAS,eAAe,OAAoB,gBAA0B;AAC5E,QAAM,UAAU,IAAI,IAAI,cAAc;AACtC,SAAO,MAAM,OAAO,QAAM,GAAG,SAAS,WAAW,MAAM,MAAM,QAAQ,SAAS,KAAK,QAAQ,IAAI,GAAG,OAAO,EAAE;AAC5G;",
+  "names": []
+}

package/dist/chunk-2K5DSRBJ.js

@@ -0,0 +1,84 @@
+// ../shared/utils/src/tree.js
+var hardcode_root = "root";
+var hierarchy_spacer = "...";
+function stratinput(lst, levels) {
+  const lp = /* @__PURE__ */ Object.create(null);
+  const nodes = /* @__PURE__ */ Object.create(null);
+  const size = /* @__PURE__ */ Object.create(null);
+  for (const m of lst) {
+    for (const [i, lev] of levels.entries()) {
+      const thisv = getkey(m, i, levels);
+      const pav = getkey(m, i - 1, levels);
+      if (!m[lev.k]) {
+        if (i > 0) {
+          size[pav] += 1;
+        }
+        break;
+      }
+      lp[thisv] = pav;
+      if (!(thisv in size)) {
+        size[thisv] = 0;
+      }
+      if (!(thisv in nodes)) {
+        const n = {
+          lst: []
+        };
+        if (lev.full) {
+          n.full = m[lev.full];
+        }
+        n.id0 = levels[0].k;
+        n.v0 = m[levels[0].k];
+        if (i == 1) {
+          n.id1 = levels[1].k;
+          n.v1 = m[levels[1].k];
+        }
+        if (i == 2) {
+          n.id2 = levels[2].k;
+          n.v1 = m[levels[2].k];
+        }
+        nodes[thisv] = n;
+      }
+      nodes[thisv].lst.push(m);
+      if (i == levels.length - 1) {
+        size[thisv] += 1;
+      }
+    }
+  }
+  const nlst = [{ id: hardcode_root, name: hardcode_root }];
+  for (const chid in lp) {
+    const paid = lp[chid];
+    const n = nodes[chid];
+    const fields = chid.split(hierarchy_spacer);
+    nlst.push({
+      id: chid,
+      parentId: paid,
+      lst: n.lst,
+      value: size[chid],
+      name: fields[fields.length - 1],
+      // show this instead of chid
+      full: n.full,
+      id0: n.id0,
+      v0: n.v0,
+      id1: n.id1,
+      v1: n.v1,
+      id2: n.id2,
+      v2: n.v2
+    });
+  }
+  return nlst;
+}
+function getkey(m, i, levels) {
+  const klst = [hardcode_root];
+  for (let j = 0; j < i; j++) {
+    klst.push(m[levels[j].k]);
+  }
+  if (i >= 0) {
+    klst.push(m[levels[i].k]);
+  }
+  return klst.join(hierarchy_spacer);
+}
+
+export {
+  stratinput
+};
+//# sourceMappingURL=chunk-2K5DSRBJ.js.map

package/dist/chunk-2K5DSRBJ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/tree.js"],
+  "sourcesContent": ["/*\ninput:\n1. list of leaf nodes, e.g. mutation cases, each with a set of key-value pairs\n2. levels of hierarchy in an ordered list\n   each item: { k, full }\n   \"k\" and \"full\" are two attribute keys\n\noutput:\na list of items, as input for d3-hierarchy.stratify\none item for each child-parent relationship in the hierarchy\n{\n\tid:\n\tparentId:\n\tlst:\n\tvalue:\n\tname:\n\tfull:\n\tid0:\n\tv0:\n\tid1:\n\tv1:\n\tid2:\n\tv2:\n}\n\nstrange issue: https://github.com/stjude/proteinpaint/commit/c36004d47d4374d2ade719c6ef9e2b848f0850dc\nusing Map for lp, nodes etc will cause memory issue, thus the use of simple objects\n\nto-do: verify this works after a reorg\n*/\n\nconst hardcode_root = \"root\"\nconst hierarchy_spacer = \"...\"\n\nexport function stratinput(lst, levels) {\n\tconst lp = Object.create(null)\n\t// leaf to parent\n\t// k: HM...BALL...sub\n\t// v: HM...BALL\n\n\tconst nodes = Object.create(null)\n\t/*\n\tk: string id of node, e.g. HM...BALL\n\tv: node\n\t\t.full\n\t\t.lst[]\n\t\t\titems from input\n\t*/\n\n\tconst size = Object.create(null)\n\t// only increment size to leaf nodes, so that root.sum() will work\n\t// k: string id of a node, e.g. HM...BALL\n\t// v: number of items\n\n\tfor (const m of lst) {\n\t\tfor (const [i, lev] of levels.entries()) {\n\t\t\tconst thisv = getkey(m, i, levels)\n\t\t\tconst pav = getkey(m, i - 1, levels)\n\n\t\t\t// as mutations can come as {\"subtype\":\"\"}\n\t\t\t// in the sunburst chart at the subtype level, this mutation should not be counted\n\t\t\t// thus the test with !m[lev.k] rather than !(lev.k in m)\n\t\t\tif (!m[lev.k]) {\n\t\t\t\t// stop at this level\n\t\t\t\t// add count to prev level\n\t\t\t\tif (i > 0) {\n\t\t\t\t\tsize[pav] += 1\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\n\t\t\tlp[thisv] = pav\n\t\t\tif (!(thisv in size)) {\n\t\t\t\tsize[thisv] = 0\n\t\t\t}\n\t\t\tif (!(thisv in nodes)) {\n\t\t\t\tconst n = {\n\t\t\t\t\tlst: [],\n\t\t\t\t}\n\t\t\t\tif (lev.full) {\n\t\t\t\t\tn.full = m[lev.full]\n\t\t\t\t}\n\n\t\t\t\tn.id0 = levels[0].k\n\t\t\t\tn.v0 = m[levels[0].k]\n\t\t\t\tif (i == 1) {\n\t\t\t\t\tn.id1 = levels[1].k\n\t\t\t\t\tn.v1 = m[levels[1].k]\n\t\t\t\t}\n\t\t\t\tif (i == 2) {\n\t\t\t\t\tn.id2 = levels[2].k\n\t\t\t\t\tn.v1 = m[levels[2].k]\n\t\t\t\t}\n\n\t\t\t\tnodes[thisv] = n\n\t\t\t}\n\t\t\tnodes[thisv].lst.push(m)\n\t\t\tif (i == levels.length - 1) {\n\t\t\t\tsize[thisv] += 1\n\t\t\t}\n\t\t}\n\t}\n\n\tconst nlst = [{ id: hardcode_root, name: hardcode_root }]\n\n\tfor (const chid in lp) {\n\t\tconst paid = lp[chid]\n\t\tconst n = nodes[chid]\n\t\tconst fields = chid.split(hierarchy_spacer)\n\t\tnlst.push({\n\t\t\tid: chid,\n\t\t\tparentId: paid,\n\t\t\tlst: n.lst,\n\t\t\tvalue: size[chid],\n\t\t\tname: fields[fields.length - 1], // show this instead of chid\n\t\t\tfull: n.full,\n\t\t\tid0: n.id0,\n\t\t\tv0: n.v0,\n\t\t\tid1: n.id1,\n\t\t\tv1: n.v1,\n\t\t\tid2: n.id2,\n\t\t\tv2: n.v2,\n\t\t})\n\t}\n\treturn nlst\n}\n\nfunction getkey(m, i, levels) {\n\t// if i is 0, return 'root'\n\tconst klst = [hardcode_root]\n\tfor (let j = 0; j < i; j++) {\n\t\tklst.push(m[levels[j].k])\n\t}\n\tif (i >= 0) {\n\t\tklst.push(m[levels[i].k])\n\t}\n\treturn klst.join(hierarchy_spacer)\n}\n"],
+  "mappings": ";AA+BA,IAAM,gBAAgB;AACtB,IAAM,mBAAmB;AAElB,SAAS,WAAW,KAAK,QAAQ;AACvC,QAAM,KAAK,uBAAO,OAAO,IAAI;AAK7B,QAAM,QAAQ,uBAAO,OAAO,IAAI;AAShC,QAAM,OAAO,uBAAO,OAAO,IAAI;AAK/B,aAAW,KAAK,KAAK;AACpB,eAAW,CAAC,GAAG,GAAG,KAAK,OAAO,QAAQ,GAAG;AACxC,YAAM,QAAQ,OAAO,GAAG,GAAG,MAAM;AACjC,YAAM,MAAM,OAAO,GAAG,IAAI,GAAG,MAAM;AAKnC,UAAI,CAAC,EAAE,IAAI,CAAC,GAAG;AAGd,YAAI,IAAI,GAAG;AACV,eAAK,GAAG,KAAK;AAAA,QACd;AACA;AAAA,MACD;AAEA,SAAG,KAAK,IAAI;AACZ,UAAI,EAAE,SAAS,OAAO;AACrB,aAAK,KAAK,IAAI;AAAA,MACf;AACA,UAAI,EAAE,SAAS,QAAQ;AACtB,cAAM,IAAI;AAAA,UACT,KAAK,CAAC;AAAA,QACP;AACA,YAAI,IAAI,MAAM;AACb,YAAE,OAAO,EAAE,IAAI,IAAI;AAAA,QACpB;AAEA,UAAE,MAAM,OAAO,CAAC,EAAE;AAClB,UAAE,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC;AACpB,YAAI,KAAK,GAAG;AACX,YAAE,MAAM,OAAO,CAAC,EAAE;AAClB,YAAE,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC;AAAA,QACrB;AACA,YAAI,KAAK,GAAG;AACX,YAAE,MAAM,OAAO,CAAC,EAAE;AAClB,YAAE,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC;AAAA,QACrB;AAEA,cAAM,KAAK,IAAI;AAAA,MAChB;AACA,YAAM,KAAK,EAAE,IAAI,KAAK,CAAC;AACvB,UAAI,KAAK,OAAO,SAAS,GAAG;AAC3B,aAAK,KAAK,KAAK;AAAA,MAChB;AAAA,IACD;AAAA,EACD;AAEA,QAAM,OAAO,CAAC,EAAE,IAAI,eAAe,MAAM,cAAc,CAAC;AAExD,aAAW,QAAQ,IAAI;AACtB,UAAM,OAAO,GAAG,IAAI;AACpB,UAAM,IAAI,MAAM,IAAI;AACpB,UAAM,SAAS,KAAK,MAAM,gBAAgB;AAC1C,SAAK,KAAK;AAAA,MACT,IAAI;AAAA,MACJ,UAAU;AAAA,MACV,KAAK,EAAE;AAAA,MACP,OAAO,KAAK,IAAI;AAAA,MAChB,MAAM,OAAO,OAAO,SAAS,CAAC;AAAA;AAAA,MAC9B,MAAM,EAAE;AAAA,MACR,KAAK,EAAE;AAAA,MACP,IAAI,EAAE;AAAA,MACN,KAAK,EAAE;AAAA,MACP,IAAI,EAAE;AAAA,MACN,KAAK,EAAE;AAAA,MACP,IAAI,EAAE;AAAA,IACP,CAAC;AAAA,EACF;AACA,SAAO;AACR;AAEA,SAAS,OAAO,GAAG,GAAG,QAAQ;AAE7B,QAAM,OAAO,CAAC,aAAa;AAC3B,WAAS,IAAI,GAAG,IAAI,GAAG,KAAK;AAC3B,SAAK,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC;AAAA,EACzB;AACA,MAAI,KAAK,GAAG;AACX,SAAK,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC;AAAA,EACzB;AACA,SAAO,KAAK,KAAK,gBAAgB;AAClC;",
+  "names": []
+}

package/dist/chunk-2LULD7RN.js

@@ -0,0 +1,31 @@
+import {
+  IN_frame,
+  OUT_frame
+} from "./chunk-XYFDBYOY.js";
+
+// src/spliceevent.exonskip.getdefault.js
+function spliceevent_exonskip_getdefault_default(events) {
+  let evt2showidx = 0;
+  for (let i = 1; i < events.length; i++) {
+    const e = events[i];
+    const e2show = events[evt2showidx];
+    if (e.isskipexon && e2show.isaltexon) {
+      evt2showidx = i;
+      continue;
+    }
+    if (e.frame == OUT_frame && e2show.framenocheck) {
+      evt2showidx = i;
+      continue;
+    }
+    if (e.frame == IN_frame && e2show.frame != IN_frame) {
+      evt2showidx = i;
+      continue;
+    }
+  }
+  return evt2showidx;
+}
+
+export {
+  spliceevent_exonskip_getdefault_default
+};
+//# sourceMappingURL=chunk-2LULD7RN.js.map

package/dist/chunk-36DYWBU7.js

@@ -0,0 +1,514 @@
+import {
+  colorDelta,
+  getInterpolatedDomainRange,
+  removeOutliers
+} from "./chunk-OXJ2TWDO.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.js";
+import {
+  roundValueAuto
+} from "./chunk-L4QG7XZE.js";
+import {
+  dtcnv
+} from "./chunk-XYFDBYOY.js";
+import {
+  Blues_default,
+  Reds_default
+} from "./chunk-IH7ILDJS.js";
+import {
+  axisBottom,
+  axisLeft,
+  axisRight,
+  axisTop
+} from "./chunk-LOZEKOES.js";
+import {
+  linear
+} from "./chunk-OAWQ6LOO.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.layout.js
+var matrix_layout_exports = {};
+__export(matrix_layout_exports, {
+  getMaxGrpLabelWidth: () => getMaxGrpLabelWidth,
+  setAutoDimensions: () => setAutoDimensions,
+  setLabelsAndScales: () => setLabelsAndScales,
+  setLayout: () => setLayout
+});
+var MINCOLWSPACED = 7;
+function setAutoDimensions(xOffset) {
+  const m = this.state.config.settings.matrix;
+  if (!this.autoDimensions) this.autoDimensions = /* @__PURE__ */ new Set();
+  if (!m.colw) this.autoDimensions.add("colw");
+  else this.autoDimensions.delete("colw");
+  if (!m.rowh) this.autoDimensions.add("rowh");
+  else this.autoDimensions.delete("rowh");
+  const s = this.settings.matrix;
+  this.computedSettings = {
+    useCanvas: this.sampleOrder.length > m.svgCanvasSwitch
+  };
+  if (s.availContentWidth) {
+    this.availContentWidth = s.availContentWidth;
+  } else {
+    let boundingWidth = this.dom.contentNode.getBoundingClientRect().width;
+    if (boundingWidth < 600) {
+      boundingWidth = window.document.body.clientWidth;
+    }
+    const maxGrpLabelWidth = this.getMaxGrpLabelWidth();
+    const padding = Math.max(65, maxGrpLabelWidth);
+    const hcw = this.state.config.settings.hierCluster?.xDendrogramHeight || 0;
+    this.availContentWidth = boundingWidth - padding - s.margin.right - xOffset - hcw;
+  }
+  let colwSpaced, colwNoSpace;
+  if (this.autoDimensions.has("colw")) {
+    const totalColgspace = s.colgspace * Math.max(0, this.visibleSampleGrps.size - 1);
+    const tentativeGaps = this.sampleOrder.length * s.colspace + totalColgspace;
+    const spacedColw = (this.availContentWidth - tentativeGaps) / this.sampleOrder.length;
+    const constrainedMINCOLWSPACED = Math.max(s.colwMin, Math.min(MINCOLWSPACED, s.colwMax));
+    colwSpaced = Math.max(constrainedMINCOLWSPACED, Math.min(spacedColw, s.colwMax));
+    const noSpacedColw = (this.availContentWidth - totalColgspace) / this.sampleOrder.length;
+    colwNoSpace = Math.max(s.colwMin, Math.min(noSpacedColw, s.colwMax));
+    this.computedSettings.colw = colwSpaced <= MINCOLWSPACED ? colwNoSpace : colwSpaced;
+    this.computedSettings.zoomMin = s.colwMin / this.computedSettings.colw;
+    this.computedSettings.zoomMax = s.colwMax / this.computedSettings.colw;
+  } else {
+    colwSpaced = m.colw;
+    colNoSpace = m.colw;
+    this.computedSettings.colw = m.colw;
+    this.computedSettings.zoomMin = s.colwMin / m.colw;
+    this.computedSettings.zoomMax = s.colwMax / m.colw;
+  }
+  const { colw } = this.computedSettings;
+  this.computedSettings.colspace = colw === colwNoSpace && colwSpaced < colwNoSpace || colw * s.zoomLevel < MINCOLWSPACED ? 0 : s.colspace;
+  const hch = this.state.config.settings.hierCluster?.yDendrogramHeight || 0;
+  const availHeight = s.availContentHeight || screen.availHeight - hch;
+  this.computedSettings.clusterRowh = Math.min(
+    s.rowhMax,
+    Math.max(s.rowhMin, Math.floor(availHeight / this.numClusterTerms))
+  );
+  copyMerge(this.settings.matrix, this.computedSettings);
+}
+function getMaxGrpLabelWidth() {
+  const s = this.settings.matrix;
+  const g = this.dom.svg.append("g").attr("opacity", 0.01);
+  let maxWidth = 0;
+  for (const grp of this.termGroups) {
+    const grpLabel = !grp.name ? "" : grp.name.length <= s.termGrpLabelMaxChars ? grp.name : grp.name.slice(0, s.termGrpLabelMaxChars) + "\u2026";
+    const text = g.append("text").text(grpLabel).attr("font-size", 12);
+    const box = text.node().getBBox();
+    if (maxWidth < box.width) maxWidth = box.width;
+  }
+  g.remove();
+  return maxWidth;
+}
+function setLabelsAndScales() {
+  const s = this.settings.matrix;
+  this.cnvValues = [];
+  const ht = s.transpose ? s.colw : s.rowh;
+  const grpTotals = {};
+  const processedLabels = { sampleGrpByName: {}, termGrpByName: {} };
+  let totalHtAdjustments = 0;
+  for (const t of this.termOrder) {
+    const countedSamples = /* @__PURE__ */ new Set();
+    t.counts = { samples: 0, hits: 0 };
+    const renderedContinuousVs = [];
+    let hasMixedValues = false;
+    if (t.tw.term.type == "termCollection") {
+      t.counts.minval = 0;
+      t.counts.maxval = 0;
+    }
+    t.counts.subGroupCounts = {};
+    for (const group of this.sampleGroups) {
+      t.counts.subGroupCounts[group.name] = {
+        samplesTotal: 0,
+        // number of counted (not Blank or WT) samples
+        classes: {}
+        // number of each class
+      };
+      if (t.tw.term.type == "geneVariant") {
+        t.counts.subGroupCounts[group.name].samplesNotTested = 0;
+      }
+    }
+    if (!processedLabels.termGrpByName[t.grp.name || ""]) {
+      const name = t.grp.name || "";
+      t.grp.label = name.length <= s.termGrpLabelMaxChars ? name : name.slice(0, s.termGrpLabelMaxChars) + "\u2026";
+      processedLabels.termGrpByName[name] = t.grp.label;
+    }
+    for (const sample of this.sampleOrder) {
+      if (countedSamples.has(sample.row.sample)) continue;
+      const name = sample.grp.name || "";
+      if (!(name in processedLabels.sampleGrpByName)) {
+        sample.grp.label = name.length <= s.sampleGrpLabelMaxChars ? name : name.slice(0, s.sampleGrpLabelMaxChars) + "\u2026";
+        if (this.config.divideBy) sample.grp.label += ` (${sample.grp.lst.length})`;
+        processedLabels.sampleGrpByName[name] = sample.grp.label;
+      }
+      const sampleName = sample.row._ref_.label || "";
+      sample.label = sampleName.length <= s.collabelmaxchars ? sampleName : sampleName.slice(0, s.collabelmaxchars) + "\u2026";
+      const anno = sample.row[t.tw.$id];
+      if (!anno) continue;
+      if (t.tw.term.type == "termCollection" && anno.hasMixedValues) {
+        hasMixedValues = true;
+      }
+      if (t.tw.term.type == "termCollection" && anno.values) {
+        for (const val of anno.values) {
+          const pct = val.value;
+          if (pct > 0) {
+            const cumSum = val.pre_val_sum + pct;
+            if (!("maxval" in t.counts) || t.counts.maxval < cumSum) {
+              t.counts.maxval = cumSum;
+            }
+          } else if (pct < 0) {
+            const cumSum = val.pre_val_sum + pct;
+            if (!("minval" in t.counts) || t.counts.minval > cumSum) {
+              t.counts.minval = cumSum;
+            }
+          }
+        }
+      }
+      const { filteredValues, countedValues, renderedValues } = this.classifyValues(
+        anno,
+        t.tw,
+        t.grp,
+        this.settings.matrix,
+        sample.row
+      );
+      anno.filteredValues = filteredValues;
+      anno.countedValues = countedValues;
+      anno.renderedValues = renderedValues;
+      if (anno.countedValues?.length) {
+        t.counts.samples += 1;
+        t.counts.hits += anno.countedValues.length;
+        if (t.tw.q?.mode == "continuous") {
+          const v = anno.value;
+          if (!t.tw.term.values?.[v]?.uncomputable) {
+            if (!("minval" in t.counts) || t.counts.minval > v) t.counts.minval = v;
+            if (!("maxval" in t.counts) || t.counts.maxval < v) t.counts.maxval = v;
+          }
+        }
+        if (t.tw.term.type == "geneVariant" && anno.values) {
+          for (const val of anno.values) {
+            if (val.dt == dtcnv && "value" in val && !s.ignoreCnvValues) {
+              const v = val.value;
+              this.cnvValues.push(v);
+            }
+          }
+        }
+      }
+      if (t.tw.q?.mode == "continuous" && renderedValues?.length && t.grp.type != "hierCluster") {
+        renderedContinuousVs.push(
+          t.tw.term.valueConversion ? t.tw.term.valueConversion.scaleFactor * (renderedValues[0].value || renderedValues[0]) : renderedValues[0].value || renderedValues[0]
+        );
+      }
+      const subGroup = t.counts.subGroupCounts?.[sample.grp.name];
+      const countedValuesNoSkip = anno.filteredValues.filter((v) => {
+        if (t.tw.term.type == "geneVariant") {
+          if (v.class == "WT" || v.class == "Blank") return false;
+        }
+        return true;
+      });
+      if (countedValuesNoSkip.length) {
+        if (t.tw.term.type == "geneVariant") {
+          let sampleCounted = false;
+          for (const countedValue of countedValuesNoSkip) {
+            if (s.geneVariantCountSamplesSkipMclass.includes(countedValue.class)) {
+              if (!subGroup.notTestedClasses) subGroup.notTestedClasses = {};
+              if (!(countedValue.class in subGroup.notTestedClasses)) subGroup.notTestedClasses[countedValue.class] = 1;
+              else subGroup.notTestedClasses[countedValue.class] += 1;
+            } else if (!(countedValue.class in subGroup.classes)) {
+              if (!sampleCounted) {
+                subGroup.samplesTotal += 1;
+                sampleCounted = true;
+              }
+              subGroup.classes[countedValue.class] = 1;
+            } else {
+              if (!sampleCounted) {
+                subGroup.samplesTotal += 1;
+                sampleCounted = true;
+              }
+              subGroup.classes[countedValue.class] += 1;
+            }
+          }
+        } else {
+          subGroup.samplesTotal += 1;
+          for (const countedValue of countedValuesNoSkip) {
+            if (!(countedValue in subGroup.classes)) subGroup.classes[countedValue] = 1;
+            else subGroup.classes[countedValue] += 1;
+          }
+        }
+      }
+      if (anno.filteredValues?.length && t.tw.term.type == "geneVariant") {
+        const notTested = anno.filteredValues.every((v) => v.class == "Blank");
+        if (notTested) {
+          subGroup.samplesNotTested += 1;
+        }
+      }
+    }
+    if (t.tw.label) {
+      t.label = t.tw.label;
+    } else if (t.grp.type == "hierCluster") {
+      t.label = t.tw.term.gene || t.tw.term.name;
+    } else {
+      t.label = t.tw.term.name;
+    }
+    if (t.label.length > s.rowlabelmaxchars) t.label = t.label.slice(0, s.rowlabelmaxchars - 1) + "\u2026";
+    const termGroupName = this.config?.settings.hierCluster?.termGroupName;
+    if (s.samplecount4gene && t.tw.term.type.startsWith("gene") && (!termGroupName || t.grp.name !== termGroupName)) {
+      const count = s.samplecount4gene === "abs" ? t.counts.samples : (100 * t.counts.samples / this.sampleOrder.length).toFixed(1) + "%";
+      t.label = `${t.label} (${count})`;
+    }
+    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
+    if (!twSpecificSettings[t.tw.$id]) twSpecificSettings[t.tw.$id] = {};
+    const twSettings = twSpecificSettings[t.tw.$id];
+    if (t.grp.type !== "hierCluster" && t.tw.q?.mode == "continuous") {
+      const vc = t.tw.term.valueConversion;
+      if (vc) {
+        t.counts.minval *= vc.scaleFactor;
+        t.counts.maxval *= vc.scaleFactor;
+      }
+      if (renderedContinuousVs.length && t.tw.q.convert2ZScore) {
+        const mean = renderedContinuousVs.reduce((acc, val) => acc + val, 0) / renderedContinuousVs.length;
+        const std = Math.sqrt(
+          renderedContinuousVs.reduce((acc, val) => acc + Math.pow(val - mean, 2), 0) / renderedContinuousVs.length
+        );
+        t.mean = mean;
+        t.std = std;
+        t.counts.minval = (t.counts.minval - mean) / std;
+        t.counts.maxval = (t.counts.maxval - mean) / std;
+      }
+      if (!twSettings.contBarH) twSettings.contBarH = t.tw.term.type == "termCollection" ? 150 : s.barh;
+      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+      const barh = twSettings.contBarH;
+      if (t.tw.term.type == "termCollection") {
+        if (!("minval" in t.counts)) t.counts.minval = 0;
+        if (!("maxval" in t.counts)) t.counts.maxval = 0;
+      }
+      const absMin = Math.abs(t.counts.minval);
+      const rangeSpansZero = t.counts.minval < 0 && t.counts.maxval > 0;
+      const ratio = t.counts.minval >= 0 ? 1 : t.counts.maxval / (absMin + t.counts.maxval);
+      t.counts.posMaxHt = ratio * barh;
+      const tickValues = [t.counts.maxval, t.counts.minval];
+      t.scales = {
+        tickValues,
+        full: linear().domain(tickValues).range([1, barh])
+      };
+      if (t.counts.maxval >= 0) {
+        const domainMin = rangeSpansZero ? 0 : t.counts.minval;
+        t.scales.pos = linear().domain([domainMin, t.counts.maxval]).range([1, t.counts.posMaxHt]);
+      }
+      if (t.counts.minval < 0) {
+        const domainMax = rangeSpansZero ? 0 : t.counts.maxval;
+        t.scales.neg = linear().domain([domainMax, t.counts.minval]).range([1, barh - t.counts.posMaxHt]);
+      }
+    }
+    t.totalHtAdjustments = totalHtAdjustments;
+    t.rowHt = t.grp.type == "hierCluster" ? s.clusterRowh : twSettings.contBarH && t.tw.q?.mode == "continuous" ? twSettings.contBarH + 2 * twSettings.contBarGap : ht;
+    const adjustment = t.rowHt - ht - (t.grp.type == "hierCluster" ? s.rowspace : 0);
+    totalHtAdjustments += adjustment;
+    t.cumulativeAdjustment = totalHtAdjustments;
+    if (!(t.visibleGrpIndex in grpTotals)) grpTotals[t.visibleGrpIndex] = { htAdjustment: 0 };
+    grpTotals[t.visibleGrpIndex].htAdjustment += adjustment;
+    t.grpTotals = grpTotals[t.visibleGrpIndex];
+  }
+  let cnvLegendDomainRange;
+  if (this.cnvValues.length) {
+    if (s.cnvValues.cutoffMode == "fixed") {
+      this.cnvValues = this.cnvValues.filter((v) => v >= s.cnvValues.min && v <= s.cnvValues.max).sort((a, b) => a - b);
+      if (this.cnvValues[0] != s.cnvValues.min) this.cnvValues.unshift(s.cnvValues.min);
+      if (this.cnvValues[this.cnvValues.length - 1] != s.cnvValues.max) this.cnvValues.push(s.cnvValues.max);
+    } else if (s.cnvValues.cutoffMode == "percentile" || s.cnvValues.cutoffMode == "auto") {
+      let maxPercentile = s.cnvValues.cutoffMode == "auto" ? s.cnvValues.defaultPercentile : s.cnvValues.percentile;
+      maxPercentile = maxPercentile / 100;
+      const minPercentile = roundValueAuto(1 - maxPercentile);
+      this.cnvValues = removeOutliers(this.cnvValues, { minPercentile, maxPercentile, baseValue: 0 });
+    } else throw new Error(`Invalid cnvValues cutoffMode: ${s.cnvValues.cutoffMode}`);
+    const minLoss = this.cnvValues[0] <= 0 ? this.cnvValues[0] : void 0;
+    const maxGain = this.cnvValues[this.cnvValues.length - 1] >= 0 ? this.cnvValues[this.cnvValues.length - 1] : void 0;
+    let maxLoss, minGain, absMax;
+    for (const n of this.cnvValues) {
+      if (n < 0) maxLoss = n;
+      if (!minGain && n > 0) {
+        minGain = n;
+        break;
+      }
+    }
+    for (const t of this.termOrder) {
+      if (t.tw.term.type == "geneVariant") {
+        if (!cnvLegendDomainRange) {
+          const loss0color = Blues_default(0);
+          const gain0color = Reds_default(0);
+          const colorDiff = colorDelta(loss0color, gain0color);
+          if (minLoss !== void 0 && maxGain !== void 0 && colorDiff > 25)
+            console.warn(
+              `CNV loss and gain do not have the same middle color for value=0'${loss0color}' vs '${gain0color}', color difference=${colorDiff}`
+            );
+          absMax = minLoss !== void 0 && maxGain !== void 0 ? Math.max(Math.abs(minLoss), maxGain) : minLoss !== void 0 ? Math.abs(minLoss) : maxGain;
+          cnvLegendDomainRange = getInterpolatedDomainRange({
+            absMin: 0,
+            absMax,
+            totalNumSteps: 10,
+            negInterpolator: minLoss !== void 0 && Blues_default,
+            posInterpolator: maxGain !== void 0 && Reds_default,
+            // force this middleColor to white, knowing that interpolateBlues and interpolateReds,
+            // as hardcoded above and below, share similar white colors for their minimum abs values
+            middleColor: "white"
+          });
+        }
+        t.scales = {
+          loss: Blues_default,
+          gain: Reds_default,
+          maxLoss,
+          maxGain,
+          minLoss,
+          minGain,
+          absMax,
+          legend: cnvLegendDomainRange
+        };
+      }
+    }
+  }
+}
+function setLayout() {
+  const s = this.settings.matrix;
+  const [col, row] = !s.transpose ? ["sample", "term"] : ["term", "sample"];
+  const [_t_, _b_] = s.collabelpos == "top" ? ["", "Grp"] : ["Grp", ""];
+  const [_l_, _r_] = s.rowlabelpos == "left" ? ["", "Grp"] : ["Grp", ""];
+  const top = col + _t_;
+  const btm = col + _b_;
+  const left = row + _l_;
+  const right = row + _r_;
+  this.samples = this.sampleOrder;
+  this.sampleGrps = this.sampleOrder.filter((s2) => s2.index === 0);
+  this.terms = this.termOrder;
+  this.termGrps = this.termOrder.filter((t) => t.index === 0);
+  const layout = {};
+  const sides = { top, btm, left, right };
+  for (const direction in sides) {
+    const d = sides[direction];
+    const Direction = direction[0].toUpperCase() + direction.slice(1);
+    layout[direction] = {
+      prefix: d,
+      data: this[`${d}s`],
+      offset: s[`${d}LabelOffset`],
+      box: this.dom[`${d}LabelG`],
+      key: this[`${d}Key`],
+      label: this[`${d}Label`],
+      render: this[`render${Direction}Label`],
+      isGroup: sides[direction].includes("Grp")
+    };
+  }
+  const yOffset = layout.top.offset + s.margin.top + s.scrollHeight;
+  const xOffset = layout.left.offset + s.margin.left;
+  this.setAutoDimensions(xOffset);
+  this.setLabelsAndScales();
+  const colw = Math.max(s.colwMin, Math.min(s.colwMax, s.colw * s.zoomLevel));
+  const dx = colw + s.colspace;
+  const nx = this[`${col}s`].length;
+  const dy = s.rowh + s.rowspace;
+  const ny = this[`${row}s`].length;
+  const mainwByColDimensions = nx * (colw + s.colspace) + this[`${col}Grps`].length * s.colgspace + (this[`${col}s`].slice(-1)[0]?.totalHtAdjustments || 0);
+  const mainw = Math.min(mainwByColDimensions, this.availContentWidth);
+  const lastRow = this[`${row}s`].slice(-1)[0];
+  const mainh = ny * dy + (this[`${row}Grps`].length - 1) * s.rowgspace + (lastRow?.cumulativeAdjustment || 0);
+  const colLabelFontSize = Math.min(
+    Math.max(colw + s.colspace - 2 * s.collabelpad - s.colspace, s.minLabelFontSize),
+    s.maxLabelFontSize
+  );
+  const topFontSize = _t_ == "Grp" ? s.grpLabelFontSize : colLabelFontSize;
+  layout.top.attr = {
+    boxTransform: `translate(${xOffset}, ${yOffset - s.collabelgap})`,
+    adjustBoxTransform: (dx2) => layout.top.box.attr("transform", `translate(${xOffset + dx2}, ${yOffset - s.collabelgap})`),
+    labelTransform: "rotate(-90)",
+    labelAnchor: "start",
+    labelGY: 0,
+    labelGTransform: this[`col${_t_}LabelGTransform`],
+    fontSize: topFontSize,
+    textpos: { coord: "y", factor: -1 },
+    axisFxn: axisTop
+  };
+  if (layout.top.prefix == "sample")
+    layout.top.display = s.sampleLabelsToggle !== "hide" && colw >= s.minLabelFontSize ? "" : "none";
+  const btmFontSize = _b_ == "Grp" ? s.grpLabelFontSize : colLabelFontSize;
+  layout.btm.attr = {
+    boxTransform: `translate(${xOffset}, ${yOffset + mainh + s.collabelgap})`,
+    adjustBoxTransform: (dx2) => layout.btm.box.attr("transform", `translate(${xOffset + dx2}, ${yOffset + mainh + s.collabelgap})`),
+    labelTransform: "rotate(-90)",
+    labelAnchor: "end",
+    labelGY: 0,
+    labelGTransform: this[`col${_b_}LabelGTransform`],
+    fontSize: btmFontSize,
+    textpos: { coord: "y", factor: 1 },
+    axisFxn: axisBottom
+  };
+  if (layout.btm.prefix == "sample")
+    layout.btm.display = s.sampleLabelsToggle !== "hide" && colw >= s.minLabelFontSize ? "" : "none";
+  const leftFontSize = _l_ == "Grp" ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad - s.rowspace, s.minLabelFontSize);
+  layout.left.attr = {
+    boxTransform: `translate(${xOffset - s.rowlabelgap}, ${yOffset})`,
+    labelTransform: "",
+    labelAnchor: "end",
+    labelGX: 0,
+    labelGTransform: this[`row${_l_}LabelGTransform`],
+    fontSize: leftFontSize,
+    textpos: { coord: "x", factor: -1 },
+    axisFxn: axisLeft
+  };
+  const rtFontSize = _r_ == "Grp" ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad, s.minLabelFontSize);
+  layout.right.attr = {
+    boxTransform: `translate(${xOffset + mainw + s.rowlabelgap}, ${yOffset})`,
+    labelTransform: "",
+    labelAnchor: "start",
+    labelGX: 0,
+    labelGTransform: this[`row${_r_}LabelGTransform`],
+    fontSize: rtFontSize,
+    textpos: { coord: "x", factor: 1 },
+    axisFxn: axisRight
+  };
+  this.dom.sampleLabelsPG.attr("clip-path", s.transpose ? "" : `url(#${this.seriesClipId})`);
+  this.dom.termLabelsPG.attr("clip-path", s.transpose ? `url(#${this.seriesClipId})` : "");
+  this.layout = layout;
+  if (!s.zoomCenterPct) {
+    s.zoomCenterPct = 0.5;
+    s.zoomIndex = Math.round(s.zoomCenterPct * mainw / dx);
+    s.zoomGrpIndex = this.sampleOrder[s.zoomIndex]?.grpIndex || 0;
+  }
+  const zoomCenter = s.zoomCenterPct * mainw;
+  const centerCellX = s.zoomIndex * dx + s.zoomGrpIndex * s.colgspace;
+  const zoomedMainW = Math.max(0, nx * dx + (this[`${col}Grps`].length - 1) * s.colgspace);
+  const seriesXoffset = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : Math.max(zoomCenter - centerCellX, mainw - zoomedMainW);
+  const imgW = (s.imgWMax > zoomedMainW ? zoomedMainW : s.imgWMax) - 1e-7;
+  const halfImgW = 0.5 * imgW;
+  const unwantedRightOvershoot = Math.max(0, centerCellX + halfImgW - zoomedMainW);
+  const imgLeftMin = Math.max(0, centerCellX - Math.min(halfImgW, imgW) - unwantedRightOvershoot);
+  const xMin = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : imgLeftMin;
+  const xMax = imgW + xMin;
+  this.dimensions = {
+    xMin,
+    xMax,
+    dx,
+    dy,
+    xOffset,
+    yOffset,
+    mainw,
+    mainh,
+    colw,
+    zoomedMainW,
+    seriesXoffset: seriesXoffset > 0 ? 0 : seriesXoffset,
+    maxMainW: Math.max(mainwByColDimensions, this.availContentWidth),
+    imgW,
+    // recompute the resolvable "pixel width", in case the pixel ratio changes
+    // when moving the browser window to a different monitor,
+    // will be used to sharpen canvas shapes that are smaller than this pixel width
+    pxw: 1 / window.devicePixelRatio
+  };
+}
+
+export {
+  setAutoDimensions,
+  getMaxGrpLabelWidth,
+  setLabelsAndScales,
+  setLayout,
+  matrix_layout_exports
+};
+//# sourceMappingURL=chunk-36DYWBU7.js.map