@sjcrh/proteinpaint-client 2.79.0 → 2.79.1-0

package/dist/genomeBrowser-K6H3EAIS.js

@@ -0,0 +1,411 @@
+import {
+  filterJoin
+} from "./chunk-ZXNPSDVH.js";
+import {
+  gbControlsInit,
+  mayUpdateGroupTestMethodsIdx
+} from "./chunk-UVBIK7UU.js";
+import "./chunk-5ZNWPUUW.js";
+import {
+  getNormalRoot
+} from "./chunk-FSQCXBJK.js";
+import "./chunk-MHTF3ZP5.js";
+import "./chunk-CLHA5AEH.js";
+import "./chunk-AFUEQSU6.js";
+import "./chunk-KUUVHWOH.js";
+import "./chunk-B2WJXDDI.js";
+import "./chunk-GIHTT3NN.js";
+import "./chunk-WTM3GD2X.js";
+import "./chunk-XNRMTK2Y.js";
+import "./chunk-7KFEDC2T.js";
+import "./chunk-FCO47PWR.js";
+import "./chunk-L7QWRU5Z.js";
+import "./chunk-LBX7K73F.js";
+import {
+  addGeneSearchbox
+} from "./chunk-J5LFFSQ5.js";
+import "./chunk-FCPSU6WB.js";
+import "./chunk-PWTXVCZ4.js";
+import "./chunk-O32YEJMI.js";
+import "./chunk-6S4SHPQA.js";
+import "./chunk-PGCZMKZL.js";
+import "./chunk-MCXHNZHB.js";
+import "./chunk-JVUJSWZ2.js";
+import "./chunk-ALPXXDQD.js";
+import "./chunk-JV3G5Q3X.js";
+import "./chunk-SHYGLBEM.js";
+import {
+  sayerror
+} from "./chunk-RKJGIOIF.js";
+import "./chunk-P64DWRTC.js";
+import "./chunk-ROQ5WSLC.js";
+import {
+  first_genetrack_tolist
+} from "./chunk-TRWKFVMG.js";
+import {
+  Menu
+} from "./chunk-7YY2KB6H.js";
+import "./chunk-2BM5YZ6X.js";
+import {
+  dofetch3
+} from "./chunk-H56REZKF.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-BT2NCQ7T.js";
+import "./chunk-KSBNOE4E.js";
+import "./chunk-WMK7VUYQ.js";
+import "./chunk-ZRUQHHLI.js";
+import "./chunk-JASS6SUY.js";
+import "./chunk-NUYFQ7WK.js";
+import "./chunk-P7BTNMOS.js";
+import "./chunk-5IJCZCP7.js";
+import "./chunk-CKF26VJ7.js";
+import "./chunk-Y6SKTI7D.js";
+import "./chunk-F3OQE4AZ.js";
+
+// plots/genomeBrowser.js
+var geneTip = new Menu({ padding: "0px" });
+var genomeBrowser = class {
+  constructor() {
+    this.type = "genomeBrowser";
+  }
+  async init() {
+    const holder = this.opts.holder.append("div");
+    this.opts.header.append("div").style("opacity", 0.6).style("padding-left", "10px").style("font-size", "0.75em").text("GENOME BROWSER");
+    const errDiv = holder.append("div");
+    const messageRow = holder.append("div").style("margin-left", "25px");
+    messageRow.append("span").html(" ");
+    this.dom = {
+      tip: new Menu(),
+      holder,
+      errDiv,
+      /*
+      skipMcountWithoutAltDiv: messageRow
+      	.append('span')
+      	.style('opacity', 0.5)
+      	.style('margin-right', '10px'),
+      	*/
+      loadingDiv: messageRow.append("span").text("Loading..."),
+      controlsDiv: holder.append("div").style("margin-left", "25px"),
+      blockHolder: holder.append("div")
+    };
+    this.components = {
+      gbControls: await gbControlsInit({
+        app: this.app,
+        id: this.id,
+        holder: this.dom.controlsDiv
+      })
+    };
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config)
+      throw `No plot with id='${this.id}' found`;
+    return {
+      config,
+      termdbConfig: appState.termdbConfig,
+      filter: getNormalRoot(appState.termfilter.filter)
+    };
+  }
+  async main() {
+    this.dom.loadingDiv.style("display", "inline");
+    try {
+      if (this.state.config?.snvindel?.details) {
+        await this.launchCustomMds3tk();
+      } else if (this.state.config?.trackLst) {
+        await this.launchBlockWithTracks(this.state.config.trackLst);
+      } else {
+        const tk = {
+          type: "mds3",
+          dslabel: this.app.opts.state.vocab.dslabel,
+          // for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu
+          newChartHolder: this.opts.plotDiv
+        };
+        if (this.state.filter?.lst?.length > 0) {
+          tk.filterObj = structuredClone(this.state.filter);
+        }
+        const tklst = [tk];
+        if (this.state.config?.subTkFilters) {
+          for (const subFilter of this.state.config.subTkFilters) {
+            const t2 = {
+              type: "mds3",
+              dslabel: this.app.opts.state.vocab.dslabel,
+              // for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu
+              newChartHolder: this.opts.plotDiv
+            };
+            t2.filterObj = tk.filterObj ? filterJoin(tk.filterObj, subFilter) : structuredClone(subFilter);
+            tklst.push(t2);
+          }
+        }
+        await this.launchBlockWithTracks(tklst);
+      }
+      this.updateLDtrack();
+    } catch (e) {
+      sayerror(this.dom.errDiv, e.message || e);
+      if (e.stack)
+        console.log(e.stack);
+    }
+    this.dom.loadingDiv.style("display", "none");
+  }
+  //////////////////////////////////////////////////
+  //       rest of methods are app-specific       //
+  //////////////////////////////////////////////////
+  async launchCustomMds3tk() {
+    const data = await this.preComputeData();
+    this.mayDisplaySampleCountInControls(data);
+    if (this.blockInstance) {
+      const t2 = this.blockInstance.tklst.find((i) => i.type == "mds3");
+      t2.custom_variants = data.mlst;
+      furbishViewModeWithSnvindelComputeDetails(
+        this,
+        t2.skewer.viewModes.find((i) => i.type == "numeric")
+      );
+      t2.load();
+      return;
+    }
+    const nm = {
+      // numeric mode object; to fill in based on snvindel.details{}
+      type: "numeric",
+      inuse: true,
+      byAttribute: "nm_axis_value"
+    };
+    furbishViewModeWithSnvindelComputeDetails(this, nm);
+    const tk = {
+      type: "mds3",
+      // despite having custom data, still provide dslabel for the mds3 tk to function as an official dataset
+      dslabel: this.app.opts.state.vocab.dslabel,
+      name: "Variants",
+      custom_variants: data.mlst,
+      skewerModes: [nm]
+    };
+    await this.launchBlockWithTracks([tk]);
+  }
+  mayDisplaySampleCountInControls(data) {
+    if (Number.isInteger(data.totalSampleCount_group1) || Number.isInteger(data.totalSampleCount_group2)) {
+      const current = {
+        appState: {
+          plots: [
+            {
+              id: this.components.gbControls.id,
+              _partialData: {
+                groupSampleCounts: [data.totalSampleCount_group1, data.totalSampleCount_group2],
+                pop2average: data.pop2average
+              }
+            }
+          ]
+        }
+      };
+      this.components.gbControls.update(current);
+    }
+  }
+  async preComputeData() {
+    const body = {
+      genome: this.app.opts.state.vocab.genome,
+      dslabel: this.app.opts.state.vocab.dslabel,
+      for: "mds3variantData",
+      chr: this.state.config.geneSearchResult.chr,
+      start: this.state.config.geneSearchResult.start,
+      stop: this.state.config.geneSearchResult.stop,
+      details: this.state.config.snvindel.details,
+      filter: this.state.filter,
+      variantFilter: this.state.config.variantFilter?.filter
+    };
+    const data = await dofetch3("termdb", { body });
+    if (data.error)
+      throw data.error;
+    return data;
+  }
+  async launchBlockWithTracks(tklst) {
+    this.dom.blockHolder.selectAll("*").remove();
+    const arg = {
+      holder: this.dom.blockHolder,
+      genome: this.app.opts.genome,
+      // genome obj
+      nobox: true,
+      tklst: await this.getTracks2show(tklst),
+      debugmode: this.app.opts.debug,
+      onloadalltk_always: (bb) => {
+        this.maySaveMds3SubtkToState(bb);
+      }
+    };
+    if (this.state.termdbConfig?.queries.defaultBlock2GeneMode && this.state.config.geneSearchResult.geneSymbol) {
+      arg.query = this.state.config.geneSearchResult.geneSymbol;
+      const _2 = await import("./block.init-KP4HQEIL.js");
+      await _2.default(arg);
+      this.blockInstance = arg.__blockInstance;
+      this.opts.header.text(arg.query);
+      return;
+    }
+    arg.chr = this.state.config.geneSearchResult.chr;
+    arg.start = this.state.config.geneSearchResult.start;
+    arg.stop = this.state.config.geneSearchResult.stop;
+    first_genetrack_tolist(this.app.opts.genome, arg.tklst);
+    arg.onCoordinateChange = async (rglst) => {
+      await this.app.dispatch({
+        type: "plot_edit",
+        id: this.id,
+        config: { geneSearchResult: { chr: rglst[0].chr, start: rglst[0].start, stop: rglst[0].stop } }
+      });
+    };
+    const _ = await import("./block-OJMSUBGJ.js");
+    this.blockInstance = new _.Block(arg);
+  }
+  async getTracks2show(tklst) {
+    const showLst = [];
+    for (const i of tklst) {
+      if (i.isfacet) {
+        const j = JSON.parse(JSON.stringify(i));
+        if (!this.app.opts.genome.tkset)
+          this.app.opts.genome.tkset = [];
+        if (!j.tklst)
+          throw ".tklst[] missing from a facet table";
+        if (!Array.isArray(j.tklst))
+          throw ".tklst[] not an array from a facet table";
+        for (const t of j.tklst) {
+          if (!t.assay)
+            throw ".assay missing from a facet track";
+          if (!t.sample)
+            throw ".sample missing from a facet track";
+          t.tkid = Math.random().toString();
+          if (t.defaultShown)
+            showLst.push(t);
+        }
+        this.app.opts.genome.tkset.push(j);
+      } else {
+        showLst.push(i);
+      }
+    }
+    return showLst;
+  }
+  updateLDtrack() {
+    if (!this.state.config.ld)
+      return;
+    if (!this.blockInstance)
+      return;
+    for (const tk of this.state.config.ld.tracks) {
+      const tkidx = this.blockInstance.tklst.findIndex((j) => j.file == tk.file0);
+      if (tk.shown) {
+        if (tkidx == -1) {
+          const arg = {
+            type: "ld",
+            name: tk.name,
+            file: tk.file0
+          };
+          const t = this.blockInstance.block_addtk_template(arg);
+          this.blockInstance.tk_load(t);
+        }
+        continue;
+      }
+      if (tkidx == -1)
+        continue;
+      this.blockInstance.tk_remove(tkidx);
+    }
+  }
+  async maySaveMds3SubtkToState(bb) {
+    const config = structuredClone(this.state.config);
+    config.subTkFilters = [];
+    for (const t of bb.tklst) {
+      if (t.filterObj) {
+        config.subTkFilters.push(t.filterObj);
+      }
+    }
+    await this.app.save({
+      type: "plot_edit",
+      id: this.id,
+      config
+    });
+  }
+};
+var genomeBrowserInit = getCompInit(genomeBrowser);
+var componentInit = genomeBrowserInit;
+async function getPlotConfig(opts, app) {
+  try {
+    return await getDefaultConfig(app.vocabApi, opts);
+  } catch (e) {
+    throw `${e} [genomeBrowser getPlotConfig()]`;
+  }
+}
+function makeChartBtnMenu(holder, chartsInstance) {
+  const genomeObj = chartsInstance.app.opts.genome;
+  if (typeof genomeObj != "object")
+    throw "chartsInstance.app.opts.genome not an object and needed for gene search box";
+  const arg = {
+    tip: geneTip,
+    genome: genomeObj,
+    row: holder.append("div").style("margin", "10px"),
+    callback: async () => {
+      try {
+        const config = await getDefaultConfig(chartsInstance.app.vocabApi);
+        config.chartType = "genomeBrowser";
+        config.geneSearchResult = result;
+        const chart = { config };
+        chartsInstance.prepPlot(chart);
+      } catch (e) {
+        holder.append("div").text("Error: " + (e.message || e));
+        console.log(e);
+      }
+    }
+  };
+  if (!chartsInstance.state.termdbConfig.queries.defaultBlock2GeneMode) {
+    arg.defaultCoord = chartsInstance.state.termdbConfig.queries.defaultCoord;
+  } else {
+    arg.searchOnly = "gene";
+  }
+  const result = addGeneSearchbox(arg);
+}
+async function getDefaultConfig(vocabApi, override) {
+  const config = await vocabApi.getMds3queryDetails();
+  const vf = await vocabApi.get_variantFilter();
+  if (vf?.filter) {
+    config.variantFilter = vf;
+  }
+  const c2 = override ? copyMerge(config, override) : config;
+  if (c2.snvindel?.details) {
+    mayUpdateGroupTestMethodsIdx({ state: { config: c2 } }, c2.snvindel.details);
+  }
+  return c2;
+}
+function furbishViewModeWithSnvindelComputeDetails(self, viewmode) {
+  delete viewmode.tooltipPrintValue;
+  const [g1, g2] = self.state.config.snvindel.details.groups;
+  if (g1 && g2) {
+    if (g1.type == "info" || g2.type == "info") {
+      viewmode.label = "Value difference";
+      return;
+    }
+    const testMethod = self.state.config.snvindel.details.groupTestMethods[self.state.config.snvindel.details.groupTestMethodsIdx];
+    viewmode.label = testMethod.axisLabel || testMethod.name;
+    if (testMethod.name == "Allele frequency difference") {
+      viewmode.tooltipPrintValue = (m) => [{ k: "AF diff", v: m.nm_axis_value }];
+    } else if (testMethod.name == "Fisher's exact test") {
+      viewmode.tooltipPrintValue = (m) => [{ k: "p-value", v: m.p_value }];
+    } else {
+    }
+    return;
+  }
+  if (g1.type == "info") {
+    const f = self.state.config.variantFilter?.terms?.find((i) => i.id == g1.infoKey);
+    viewmode.label = f?.name || g1.infoKey;
+    viewmode.tooltipPrintValue = (m) => [{ k: viewmode.label, v: m.info[g1.infoKey] }];
+    return;
+  }
+  if (g1.type == "filter") {
+    viewmode.label = "Allele frequency";
+    viewmode.tooltipPrintValue = (m) => [{ k: "Allele frequency", v: m.nm_axis_value }];
+    return;
+  }
+  if (g1.type == "population") {
+    viewmode.label = "Allele frequency";
+    viewmode.tooltipPrintValue = (m) => [{ k: "Allele frequency", v: m.nm_axis_value }];
+    return;
+  }
+  throw "unknown type of the only group";
+}
+export {
+  componentInit,
+  genomeBrowserInit,
+  getPlotConfig,
+  makeChartBtnMenu
+};
+//# sourceMappingURL=genomeBrowser-K6H3EAIS.js.map

package/dist/genomeBrowser-K6H3EAIS.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/genomeBrowser.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge } from '#rx'\nimport { addGeneSearchbox } from '../dom/genesearch.ts'\nimport { Menu } from '#dom/menu'\nimport { sayerror } from '../dom/sayerror.ts'\nimport { dofetch3 } from '#common/dofetch'\nimport { getNormalRoot } from '#filter/filter'\nimport { filterJoin } from '#shared/filter.js'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport { gbControlsInit, mayUpdateGroupTestMethodsIdx } from './genomeBrowser.controls'\n\n/*\n//////////////// instance structure\n\nthis{}\n\tvocabApi{}\n\tapp {}\n\t\topts {}\n\t\t\tgenome{} // client-side genome obj\n\t\t\tstate {}\n\t\t\t\tvocab {}\n\t\t\t\t\tdslabel:str\n\t\t\t\t\tgenome:str\n\t\tdispatch()\n\t\tsave()\n\topts{}\n\t\tapp{}\n\t\theader\n\t\tholder\n\t\tplotDiv\n\t\tid\n\tstate {}\n\t\tconfig {}\n\t\t\tfilter{} // mass filter\n\t\t\tvariantFilter{}\n\t\t\t\tfilter{}\n\t\t\t\topts{ joinWith }\n\t\t\t\tterms[]\n\t\t\tgeneSearchResult{}\n\t\t\tsnvindel {}\n\t\t\t\tdetails {}\n\t\t\t\t\tgroupTypes[]\n\t\t\t\t\tgroups:[]\n\t\t\t\t\t\t// each element is a group object\n\t\t\t\t\t\t{type='info', infoKey=str}\n\t\t\t\t\t\t{type='filter', filter={}}\n\t\t\t\t\t\t{type='population', key, label, ..}\n\t\t\t\t\tgroupTestMethod{}\n\t\t\t\t\tgroupTestMethodsIdx\n\t\t\t\tpopulations [{key,label}] // might not be part of state\n\t\t\tld {}\n\t\t\t\ttracks[]\n\t\t\tsubTkFilters[] // list of sub tk filter objects created on mds3 tk sample summary ui\n\t\ttermdbConfig{}\n\tblockInstance // exists when block has been launched; one block in each plot\n\n\n////////////////// functions\n\ninit\nmain\n\tlaunchCustomMds3tk\n\t\tpreComputeData\n\t\t\tdofetch3\n\t\tfurbishViewModeWithSnvindelComputeDetails\n\t\tlaunchBlockWithTracks\n\t\t\tgetTracks2show\ngetPlotConfig\n\tgetDefaultConfig\nmakeChartBtnMenu\n*/\n\nconst geneTip = new Menu({ padding: '0px' })\n\nclass genomeBrowser {\n\tconstructor() {\n\t\tthis.type = 'genomeBrowser'\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div')\n\t\tthis.opts.header\n\t\t\t.append('div')\n\t\t\t.style('opacity', 0.6)\n\t\t\t.style('padding-left', '10px')\n\t\t\t.style('font-size', '0.75em')\n\t\t\t.text('GENOME BROWSER')\n\t\t// layout rows from top to bottom\n\t\tconst errDiv = holder.append('div')\n\t\tconst messageRow = holder.append('div').style('margin-left', '25px')\n\t\tmessageRow.append('span').html(' ') // to not to collapse row when empty\n\n\t\tthis.dom = {\n\t\t\ttip: new Menu(),\n\t\t\tholder,\n\t\t\terrDiv,\n\t\t\t/*\n\t\t\tskipMcountWithoutAltDiv: messageRow\n\t\t\t\t.append('span')\n\t\t\t\t.style('opacity', 0.5)\n\t\t\t\t.style('margin-right', '10px'),\n\t\t\t\t*/\n\t\t\tloadingDiv: messageRow.append('span').text('Loading...'),\n\t\t\tcontrolsDiv: holder.append('div').style('margin-left', '25px'),\n\t\t\tblockHolder: holder.append('div')\n\t\t}\n\n\t\tthis.components = {\n\t\t\tgbControls: await gbControlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsDiv\n\t\t\t})\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\t// {plots[], termdbConfig{}, termfilter{}}\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tfilter: getNormalRoot(appState.termfilter.filter)\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.loadingDiv.style('display', 'inline')\n\t\ttry {\n\t\t\tif (this.state.config?.snvindel?.details) {\n\t\t\t\t// pre-compute variant data in the app here, e.g. fisher test etc, but not in mds3 backend as the official track does\n\t\t\t\t// and launch custom mds3 tk to show the variants\n\t\t\t\tawait this.launchCustomMds3tk()\n\t\t\t} else if (this.state.config?.trackLst) {\n\t\t\t\tawait this.launchBlockWithTracks(this.state.config.trackLst)\n\t\t\t} else {\n\t\t\t\t// launch official mds3 tk, same way as mds3/tk.js\n\t\t\t\tconst tk = {\n\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\t\t\t// for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu\n\t\t\t\t\tnewChartHolder: this.opts.plotDiv\n\t\t\t\t}\n\t\t\t\tif (this.state.filter?.lst?.length > 0) {\n\t\t\t\t\t// state has a non-empty filter, register at tk obj to pass to mds3 data queries\n\t\t\t\t\ttk.filterObj = structuredClone(this.state.filter)\n\t\t\t\t\t// TODO this will cause mds3 tk to show a leftlabel to indicate the filtering, which should be hidden\n\t\t\t\t}\n\t\t\t\tconst tklst = [tk]\n\n\t\t\t\tif (this.state.config?.subTkFilters) {\n\t\t\t\t\tfor (const subFilter of this.state.config.subTkFilters) {\n\t\t\t\t\t\t// for every element, create a new subtk\n\t\t\t\t\t\tconst t2 = {\n\t\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\t\t\t\t\t// for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu\n\t\t\t\t\t\t\tnewChartHolder: this.opts.plotDiv\n\t\t\t\t\t\t}\n\t\t\t\t\t\tt2.filterObj = tk.filterObj ? filterJoin(tk.filterObj, subFilter) : structuredClone(subFilter)\n\t\t\t\t\t\ttklst.push(t2)\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tawait this.launchBlockWithTracks(tklst)\n\t\t\t}\n\t\t\tthis.updateLDtrack()\n\t\t} catch (e) {\n\t\t\tsayerror(this.dom.errDiv, e.message || e)\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t}\n\t\tthis.dom.loadingDiv.style('display', 'none')\n\t}\n\n\t//////////////////////////////////////////////////\n\t//       rest of methods are app-specific       //\n\t//////////////////////////////////////////////////\n\n\tasync launchCustomMds3tk() {\n\t\tconst data = await this.preComputeData()\n\t\tthis.mayDisplaySampleCountInControls(data)\n\n\t\tif (this.blockInstance) {\n\t\t\t// block already launched. update data on the tk and rerender\n\t\t\tconst t2 = this.blockInstance.tklst.find(i => i.type == 'mds3')\n\t\t\tt2.custom_variants = data.mlst\n\n\t\t\t// details.groups[] may have changed. update label and tooltip callback etc, of tk numeric axis view mode object\n\t\t\tfurbishViewModeWithSnvindelComputeDetails(\n\t\t\t\tthis,\n\t\t\t\tt2.skewer.viewModes.find(i => i.type == 'numeric')\n\t\t\t)\n\n\t\t\tt2.load()\n\t\t\treturn\n\t\t}\n\n\t\tconst nm = {\n\t\t\t// numeric mode object; to fill in based on snvindel.details{}\n\t\t\ttype: 'numeric',\n\t\t\tinuse: true,\n\t\t\tbyAttribute: 'nm_axis_value'\n\t\t}\n\t\tfurbishViewModeWithSnvindelComputeDetails(this, nm)\n\t\tconst tk = {\n\t\t\ttype: 'mds3',\n\t\t\t// despite having custom data, still provide dslabel for the mds3 tk to function as an official dataset\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tname: 'Variants',\n\t\t\tcustom_variants: data.mlst,\n\t\t\tskewerModes: [nm]\n\t\t}\n\t\tawait this.launchBlockWithTracks([tk])\n\t}\n\n\tmayDisplaySampleCountInControls(data) {\n\t\t/* quick fix\n\t\tgroup sample count returned by server is not part of state and is not accessible to controls component\n\t\thas to synthesize a \"current\" object with the _partialData special attribute\n\t\tand pass it to api.update() for component instance to receive it via getState()\n\t\t*/\n\t\tif (Number.isInteger(data.totalSampleCount_group1) || Number.isInteger(data.totalSampleCount_group2)) {\n\t\t\tconst current = {\n\t\t\t\tappState: {\n\t\t\t\t\tplots: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tid: this.components.gbControls.id,\n\t\t\t\t\t\t\t_partialData: {\n\t\t\t\t\t\t\t\tgroupSampleCounts: [data.totalSampleCount_group1, data.totalSampleCount_group2],\n\t\t\t\t\t\t\t\tpop2average: data.pop2average\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t}\n\t\t\tthis.components.gbControls.update(current)\n\t\t}\n\t}\n\n\tasync preComputeData() {\n\t\t// analysis details including cohorts and compute methods are in state.config.snvindel.details{}\n\t\t// send to back to compute and get results back\n\n\t\tconst body = {\n\t\t\tgenome: this.app.opts.state.vocab.genome,\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tfor: 'mds3variantData',\n\t\t\tchr: this.state.config.geneSearchResult.chr,\n\t\t\tstart: this.state.config.geneSearchResult.start,\n\t\t\tstop: this.state.config.geneSearchResult.stop,\n\t\t\tdetails: this.state.config.snvindel.details,\n\t\t\tfilter: this.state.filter,\n\t\t\tvariantFilter: this.state.config.variantFilter?.filter\n\t\t}\n\n\t\t// using dofetch prevents the app from working with custom dataset; may change to vocab method later\n\n\t\tconst data = await dofetch3('termdb', { body })\n\t\tif (data.error) throw data.error\n\t\t/*\n\t\tif (data.skipMcountWithoutAlt) {\n\t\t\tthis.dom.skipMcountWithoutAltDiv.text(\n\t\t\t\t`${data.skipMcountWithoutAlt} variant${\n\t\t\t\t\tdata.skipMcountWithoutAlt > 1 ? 's' : ''\n\t\t\t\t} skipped for absence of ALT allele from the cohort.`\n\t\t\t)\n\t\t} else {\n\t\t\tthis.dom.skipMcountWithoutAltDiv.text('')\n\t\t}\n\t\t*/\n\t\treturn data\n\t}\n\n\tasync launchBlockWithTracks(tklst) {\n\t\t// when state changes, delete existing block and relaunch new one\n\t\t// since block/tk is not state-controlled\n\t\t// attaches this.blockInstance\n\t\tthis.dom.blockHolder.selectAll('*').remove()\n\n\t\tconst arg = {\n\t\t\tholder: this.dom.blockHolder,\n\t\t\tgenome: this.app.opts.genome, // genome obj\n\t\t\tnobox: true,\n\t\t\ttklst: await this.getTracks2show(tklst),\n\t\t\tdebugmode: this.app.opts.debug,\n\t\t\tonloadalltk_always: bb => {\n\t\t\t\t// TODO on any tk update, collect tk config and save to state so they are recoverable from session\n\t\t\t\tthis.maySaveMds3SubtkToState(bb)\n\t\t\t}\n\t\t}\n\t\tif (this.state.termdbConfig?.queries.defaultBlock2GeneMode && this.state.config.geneSearchResult.geneSymbol) {\n\t\t\t// dataset config wants to default to gene view, and gene symbol is available\n\t\t\t// call block.init to launch gene view\n\t\t\targ.query = this.state.config.geneSearchResult.geneSymbol\n\t\t\tconst _ = await import('#src/block.init')\n\t\t\tawait _.default(arg)\n\t\t\tthis.blockInstance = arg.__blockInstance\n\n\t\t\t// update sandbox header with gene name\n\t\t\tthis.opts.header.text(arg.query)\n\t\t\treturn\n\t\t}\n\t\t// launch locus\n\t\targ.chr = this.state.config.geneSearchResult.chr\n\t\targ.start = this.state.config.geneSearchResult.start\n\t\targ.stop = this.state.config.geneSearchResult.stop\n\t\tfirst_genetrack_tolist(this.app.opts.genome, arg.tklst)\n\n\t\targ.onCoordinateChange = async rglst => {\n\t\t\tawait this.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig: { geneSearchResult: { chr: rglst[0].chr, start: rglst[0].start, stop: rglst[0].stop } }\n\t\t\t})\n\t\t}\n\n\t\tconst _ = await import('#src/block')\n\t\tthis.blockInstance = new _.Block(arg)\n\t}\n\n\tasync getTracks2show(tklst) {\n\t\tconst showLst = []\n\t\tfor (const i of tklst) {\n\t\t\tif (i.isfacet) {\n\t\t\t\t// legacy method to insert facet table into genome.tkset[]\n\n\t\t\t\t// must duplicate as i is frozen\n\t\t\t\tconst j = JSON.parse(JSON.stringify(i))\n\n\t\t\t\tif (!this.app.opts.genome.tkset) this.app.opts.genome.tkset = []\n\t\t\t\tif (!j.tklst) throw '.tklst[] missing from a facet table'\n\t\t\t\tif (!Array.isArray(j.tklst)) throw '.tklst[] not an array from a facet table'\n\t\t\t\tfor (const t of j.tklst) {\n\t\t\t\t\tif (!t.assay) throw '.assay missing from a facet track'\n\t\t\t\t\tif (!t.sample) throw '.sample missing from a facet track'\n\t\t\t\t\t// must assign tkid otherwise the tk buttons from facet table won't work\n\t\t\t\t\tt.tkid = Math.random().toString()\n\t\t\t\t\tif (t.defaultShown) showLst.push(t)\n\t\t\t\t}\n\t\t\t\tthis.app.opts.genome.tkset.push(j)\n\t\t\t} else {\n\t\t\t\t// must be a track\n\t\t\t\tshowLst.push(i)\n\t\t\t}\n\t\t}\n\t\treturn showLst\n\t}\n\n\tupdateLDtrack() {\n\t\t/* based on ld.tracks[] whether each track is shown, to add/remove ld tracks from blockInstance\n\t\t */\n\t\tif (!this.state.config.ld) return // no ld tracks\n\t\tif (!this.blockInstance) return // no block, cannot update ld\n\t\tfor (const tk of this.state.config.ld.tracks) {\n\t\t\tconst tkidx = this.blockInstance.tklst.findIndex(j => j.file == tk.file0)\n\t\t\tif (tk.shown) {\n\t\t\t\t// tk should be shown\n\t\t\t\tif (tkidx == -1) {\n\t\t\t\t\t// tk not in block, add\n\t\t\t\t\tconst arg = {\n\t\t\t\t\t\ttype: 'ld',\n\t\t\t\t\t\tname: tk.name,\n\t\t\t\t\t\tfile: tk.file0\n\t\t\t\t\t}\n\t\t\t\t\tconst t = this.blockInstance.block_addtk_template(arg)\n\t\t\t\t\tthis.blockInstance.tk_load(t)\n\t\t\t\t}\n\t\t\t\t// tk already in block\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// tk should be hidden\n\t\t\tif (tkidx == -1) continue\n\t\t\t// remove\n\t\t\tthis.blockInstance.tk_remove(tkidx)\n\t\t}\n\t}\n\n\tasync maySaveMds3SubtkToState(bb) {\n\t\t/* arg is block instance\n\t\twhen a mds3 subtk is created/updated, its tk.filterObj should be saved to state so it can be recovered from session\n\t\t*/\n\t\tconst config = structuredClone(this.state.config)\n\t\tconfig.subTkFilters = []\n\t\tfor (const t of bb.tklst) {\n\t\t\tif (t.filterObj) {\n\t\t\t\tconfig.subTkFilters.push(t.filterObj)\n\t\t\t\t// filter0?\n\t\t\t}\n\t\t}\n\t\tawait this.app.save({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig\n\t\t})\n\t}\n}\n\n///////////////////////////////////////////////////////\n//                  end of class                     //\n///////////////////////////////////////////////////////\n\nexport const genomeBrowserInit = getCompInit(genomeBrowser)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = genomeBrowserInit\n\nexport async function getPlotConfig(opts, app) {\n\ttry {\n\t\t// request default queries config from dataset, and allows opts to override\n\t\treturn await getDefaultConfig(app.vocabApi, opts)\n\t} catch (e) {\n\t\tthrow `${e} [genomeBrowser getPlotConfig()]`\n\t}\n}\n\n/*\ncalled in mass/charts.js, to render the menu upon clicking the chart button in the charts tray\n\nholder: the holder in the tooltip\nchartsInstance: MassCharts instance\n{\n\tapp {\n\t\tvocabApi\n\t\topts { // the mass ui options\n\t\t\tgenome{} // client-side genome object\n\t\t}\n\t}\n\tstate {\n\t\ttermdbConfig{}\n\t}\n}\n*/\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\tconst genomeObj = chartsInstance.app.opts.genome\n\tif (typeof genomeObj != 'object') throw 'chartsInstance.app.opts.genome not an object and needed for gene search box'\n\tconst arg = {\n\t\ttip: geneTip,\n\t\tgenome: genomeObj,\n\t\trow: holder.append('div').style('margin', '10px'),\n\t\tcallback: async () => {\n\t\t\t// found a gene {chr,start,stop,geneSymbol}\n\t\t\t// dispatch to create new plot\n\n\t\t\ttry {\n\t\t\t\t// must do this as 'plot_prep' does not call getPlotConfig()\n\t\t\t\t// request default queries config from dataset, and allows opts to override\n\t\t\t\t// this config{} will become this.state.config{}\n\t\t\t\tconst config = await getDefaultConfig(chartsInstance.app.vocabApi)\n\n\t\t\t\tconfig.chartType = 'genomeBrowser'\n\t\t\t\tconfig.geneSearchResult = result\n\t\t\t\tconst chart = { config }\n\t\t\t\tchartsInstance.prepPlot(chart)\n\t\t\t} catch (e) {\n\t\t\t\t// upon err, create div in chart button menu to display err\n\t\t\t\tholder.append('div').text('Error: ' + (e.message || e))\n\t\t\t\tconsole.log(e)\n\t\t\t}\n\t\t}\n\t}\n\tif (!chartsInstance.state.termdbConfig.queries.defaultBlock2GeneMode) {\n\t\t// block is not shown in gene mode, add default coord to arg\n\t\targ.defaultCoord = chartsInstance.state.termdbConfig.queries.defaultCoord\n\t} else {\n\t\targ.searchOnly = 'gene'\n\t}\n\tconst result = addGeneSearchbox(arg)\n}\n\n// get default config of the app from vocabApi\nasync function getDefaultConfig(vocabApi, override) {\n\tconst config = await vocabApi.getMds3queryDetails()\n\t// request default variant filter (against vcf INFO)\n\tconst vf = await vocabApi.get_variantFilter()\n\tif (vf?.filter) {\n\t\tconfig.variantFilter = vf\n\t}\n\tconst c2 = override ? copyMerge(config, override) : config\n\tif (c2.snvindel?.details) {\n\t\t// test method may be inconsistent with group configuration (e.g. no fisher for INFO fields), update test method here\n\t\t// 1st arg is a fake \"self\"\n\t\tmayUpdateGroupTestMethodsIdx({ state: { config: c2 } }, c2.snvindel.details)\n\t}\n\treturn c2\n}\n\n//////////////////////////////////////////////////\n//                  helpers                     //\n//////////////////////////////////////////////////\n\n/* given group configuration, determine: numeric track axis label\n- viewmode.label as axis label of numeric mode\n- viewmode.tooltipPrintValue()\n*/\nfunction furbishViewModeWithSnvindelComputeDetails(self, viewmode) {\n\tdelete viewmode.tooltipPrintValue\n\n\tconst [g1, g2] = self.state.config.snvindel.details.groups\n\tif (g1 && g2) {\n\t\tif (g1.type == 'info' || g2.type == 'info') {\n\t\t\t// either group is info field. value type can only be value difference\n\t\t\tviewmode.label = 'Value difference'\n\t\t\treturn\n\t\t}\n\t\t// none of the group is info field. each group should derive AF and there can be different ways of comparing it from two groups\n\t\tconst testMethod =\n\t\t\tself.state.config.snvindel.details.groupTestMethods[self.state.config.snvindel.details.groupTestMethodsIdx]\n\t\tviewmode.label = testMethod.axisLabel || testMethod.name\n\t\tif (testMethod.name == 'Allele frequency difference') {\n\t\t\t// callback returns value separated by ' = ', which allows this to be also displayed in itemtable.js\n\t\t\tviewmode.tooltipPrintValue = m => [{ k: 'AF diff', v: m.nm_axis_value }]\n\t\t} else if (testMethod.name == \"Fisher's exact test\") {\n\t\t\tviewmode.tooltipPrintValue = m => [{ k: 'p-value', v: m.p_value }]\n\t\t} else {\n\t\t}\n\t\treturn\n\t}\n\n\t// only 1 group\n\tif (g1.type == 'info') {\n\t\tconst f = self.state.config.variantFilter?.terms?.find(i => i.id == g1.infoKey)\n\t\tviewmode.label = f?.name || g1.infoKey\n\t\tviewmode.tooltipPrintValue = m => [{ k: viewmode.label, v: m.info[g1.infoKey] }]\n\t\treturn\n\t}\n\tif (g1.type == 'filter') {\n\t\tviewmode.label = 'Allele frequency'\n\t\tviewmode.tooltipPrintValue = m => [{ k: 'Allele frequency', v: m.nm_axis_value }]\n\t\treturn\n\t}\n\tif (g1.type == 'population') {\n\t\tviewmode.label = 'Allele frequency'\n\t\tviewmode.tooltipPrintValue = m => [{ k: 'Allele frequency', v: m.nm_axis_value }]\n\t\treturn\n\t}\n\tthrow 'unknown type of the only group'\n}\n"],
+  "mappings": 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+  "names": ["_"]
+}

package/dist/genomeBrowser.controls-NJYECYTP.js

@@ -0,0 +1,52 @@
+import {
+  gbControlsInit,
+  mayUpdateGroupTestMethodsIdx
+} from "./chunk-UVBIK7UU.js";
+import "./chunk-5ZNWPUUW.js";
+import "./chunk-FSQCXBJK.js";
+import "./chunk-MHTF3ZP5.js";
+import "./chunk-CLHA5AEH.js";
+import "./chunk-AFUEQSU6.js";
+import "./chunk-KUUVHWOH.js";
+import "./chunk-B2WJXDDI.js";
+import "./chunk-GIHTT3NN.js";
+import "./chunk-WTM3GD2X.js";
+import "./chunk-XNRMTK2Y.js";
+import "./chunk-7KFEDC2T.js";
+import "./chunk-FCO47PWR.js";
+import "./chunk-L7QWRU5Z.js";
+import "./chunk-LBX7K73F.js";
+import "./chunk-J5LFFSQ5.js";
+import "./chunk-FCPSU6WB.js";
+import "./chunk-PWTXVCZ4.js";
+import "./chunk-O32YEJMI.js";
+import "./chunk-6S4SHPQA.js";
+import "./chunk-PGCZMKZL.js";
+import "./chunk-MCXHNZHB.js";
+import "./chunk-JVUJSWZ2.js";
+import "./chunk-ALPXXDQD.js";
+import "./chunk-JV3G5Q3X.js";
+import "./chunk-SHYGLBEM.js";
+import "./chunk-RKJGIOIF.js";
+import "./chunk-P64DWRTC.js";
+import "./chunk-ROQ5WSLC.js";
+import "./chunk-TRWKFVMG.js";
+import "./chunk-7YY2KB6H.js";
+import "./chunk-2BM5YZ6X.js";
+import "./chunk-H56REZKF.js";
+import "./chunk-BT2NCQ7T.js";
+import "./chunk-KSBNOE4E.js";
+import "./chunk-WMK7VUYQ.js";
+import "./chunk-ZRUQHHLI.js";
+import "./chunk-JASS6SUY.js";
+import "./chunk-NUYFQ7WK.js";
+import "./chunk-P7BTNMOS.js";
+import "./chunk-5IJCZCP7.js";
+import "./chunk-CKF26VJ7.js";
+import "./chunk-Y6SKTI7D.js";
+import "./chunk-F3OQE4AZ.js";
+export {
+  gbControlsInit,
+  mayUpdateGroupTestMethodsIdx
+};
+//# sourceMappingURL=genomeBrowser.controls-NJYECYTP.js.map

package/dist/genomeBrowser.controls-NJYECYTP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": [],
+  "sourcesContent": [],
+  "mappings": "",
+  "names": []
+}