@sjcrh/proteinpaint-client 2.146.4-1 → 2.147.1

package/dist/imagePlot-R7RPGREP.js

@@ -1,136 +0,0 @@
-import {
-  controlsInit
-} from "./chunk-L5RO3TWT.js";
-import "./chunk-T6FHPT3J.js";
-import "./chunk-KQKE3HWV.js";
-import "./chunk-DXNHQCWO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-PYGUZ75W.js";
-import "./chunk-GDVG55UR.js";
-import "./chunk-L7N5BOMJ.js";
-import "./chunk-RY7CVONT.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-QTAXM2J6.js";
-import "./chunk-MXMPAXMS.js";
-import "./chunk-4W3BORF5.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-SU6RBYZK.js";
-import "./chunk-2J7NXRQQ.js";
-import "./chunk-IVJWQYGG.js";
-import "./chunk-OPZUIS3Y.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/imagePlot.js
-var imagePlot = class {
-  constructor() {
-    this.type = "imagePlot";
-  }
-  async init(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    const state = this.getState(appState);
-    const holder = this.opts.holder.append("div");
-    this.dom = {
-      holder,
-      controlsHolder: holder.append("div").style("display", "inline-block"),
-      imageHolder: holder.append("div").style("display", "inline-block")
-    };
-    this.setControls();
-    const result = await this.app.vocabApi.getSampleImages(config.sample.sampleId);
-    if (result.error) throw result.error;
-    for (const img of result.images) {
-      this.dom.imageHolder.append("img").style("padding", "10px").attr("src", img.src).attr("width", config.settings.imagePlot.width).attr("height", config.settings.imagePlot.height);
-    }
-  }
-  async setControls() {
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsHolder,
-        inputs: [
-          {
-            label: "Chart width",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "width"
-          },
-          {
-            label: "Chart height",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "height"
-          }
-        ]
-      })
-    };
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      termfilter: appState.termfilter,
-      vocab: appState.vocab
-    };
-  }
-};
-async function getPlotConfig(opts, app) {
-  let settings = getDefaultImagePlotSettings();
-  if (opts.settings) copyMerge(settings, opts.settings);
-  const config = {
-    settings: {
-      controls: {
-        isOpen: false
-        // control panel is hidden by default
-      },
-      imagePlot: settings
-    }
-  };
-  const result = copyMerge(config, opts);
-  return result;
-}
-function getDefaultImagePlotSettings() {
-  return {
-    width: 500,
-    height: 500
-  };
-}
-var imagePlotInit = getCompInit(imagePlot);
-var componentInit = imagePlotInit;
-async function renderImagePlot(state, holder, sample) {
-  const opts = {
-    holder,
-    state: {
-      vocab: state.vocab,
-      plots: [
-        {
-          chartType: "imagePlot",
-          sample
-        }
-      ]
-    }
-  };
-  const plot = await import("./plot.app-BNLSZKBR.js");
-  const plotAppApi = await plot.appInit(opts);
-}
-export {
-  componentInit,
-  getDefaultImagePlotSettings,
-  getPlotConfig,
-  imagePlotInit,
-  renderImagePlot
-};
-//# sourceMappingURL=imagePlot-R7RPGREP.js.map

package/dist/importPlot-G6NBPNHI.js

@@ -1,8 +0,0 @@
-import {
-  importPlot
-} from "./chunk-PYGUZ75W.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  importPlot
-};
-//# sourceMappingURL=importPlot-G6NBPNHI.js.map

package/dist/launch.adhoc-LT6NJTIU.js

@@ -1,35 +0,0 @@
-import {
-  launch
-} from "./chunk-3DEQO2QU.js";
-import "./chunk-SLGI2XIJ.js";
-import "./chunk-I3ZL6SGL.js";
-import "./chunk-FPWU6QAA.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-DXNHQCWO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-PYGUZ75W.js";
-import "./chunk-GDVG55UR.js";
-import "./chunk-L7N5BOMJ.js";
-import "./chunk-RY7CVONT.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-QTAXM2J6.js";
-import "./chunk-MXMPAXMS.js";
-import "./chunk-4W3BORF5.js";
-import "./chunk-SU6RBYZK.js";
-import "./chunk-2J7NXRQQ.js";
-import "./chunk-IVJWQYGG.js";
-import "./chunk-OPZUIS3Y.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  launch
-};
-//# sourceMappingURL=launch.adhoc-LT6NJTIU.js.map

package/dist/leftlabel.sample-YXXZZ7H7.js

@@ -1,243 +0,0 @@
-import {
-  displaySampleTable,
-  getFilterName,
-  makelabel
-} from "./chunk-VELHP2RM.js";
-import "./chunk-Y5ZUEHEQ.js";
-import "./chunk-MYMDKREO.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-RS3G3HE7.js";
-import "./chunk-A6UVM6Q5.js";
-import {
-  Tabs,
-  fillbar,
-  filterInit,
-  getNormalRoot,
-  renderTable
-} from "./chunk-DXNHQCWO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-PYGUZ75W.js";
-import "./chunk-GDVG55UR.js";
-import "./chunk-L7N5BOMJ.js";
-import "./chunk-RY7CVONT.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-QTAXM2J6.js";
-import "./chunk-MXMPAXMS.js";
-import "./chunk-4W3BORF5.js";
-import "./chunk-SU6RBYZK.js";
-import "./chunk-2J7NXRQQ.js";
-import "./chunk-IVJWQYGG.js";
-import {
-  violinRenderer
-} from "./chunk-OPZUIS3Y.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// mds3/leftlabel.sample.js
-function makeSampleLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.samples) {
-    tk.leftlabels.doms.samples = makelabel(tk, block, laby);
-  }
-  if (data.sampleTotalNumber) {
-    tk.leftlabels.doms.samples.attr("class", "sja_clbtext2").style("opacity", 1).text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("data-testid", "sjpp_mds3tk_samples_label").on("click", async (event) => {
-      tk.menutip.clear().showunder(event.target);
-      await mayShowSummary(tk, block);
-      const buttonrow = tk.menutip.d.append("div").style("margin", "10px");
-      menu_listSamples(buttonrow, data, tk, block);
-    });
-  } else {
-    tk.leftlabels.doms.samples.text("No samples").attr("class", "").style("opacity", 0.5).on("click", null);
-  }
-}
-function makeSampleFilterLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.filterObj) {
-    tk.leftlabels.doms.filterObj = makelabel(tk, block, laby);
-  }
-  tk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on("click", async (event) => {
-    tk.menutip.clear().showunder(event.target);
-    const arg = {
-      holder: tk.menutip.d.append("div").style("margin", "10px"),
-      vocabApi: tk.mds.termdb.vocabApi,
-      callback: (f) => {
-        tk.filterObj = f;
-        tk.load();
-      }
-    };
-    mayAddGetCategoryArgs(arg, block);
-    filterInit(arg).main(tk.filterObj);
-  });
-}
-function mayAddGetCategoryArgs(arg, block) {
-  if (block.usegm) {
-    arg.getCategoriesArguments = { currentGeneNames: [block.usegm.name] };
-  } else {
-    arg.getCategoriesArguments = { rglst: structuredClone(block.rglst) };
-  }
-}
-async function mayShowSummary(tk, block) {
-  if (!tk.mds.variant2samples.twLst) {
-    return;
-  }
-  const div = tk.menutip.d.append("div").style("margin", "10px");
-  const wait = div.append("div").text("Loading...");
-  try {
-    const { summary } = await tk.mds.getSamples({ isSummary: true });
-    tk.leftlabels.__samples_data = summary;
-    wait.remove();
-    await showSummary4terms(summary, div.append("div").attr("class", "sja_mds3samplesummarydiv"), tk, block);
-  } catch (e) {
-    wait.text(`Error: ${e.message || e}`);
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function showSummary4terms(data, div, tk, block) {
-  const tabs = [];
-  for (const { termid, numbycategory } of data) {
-    tabs.push({
-      label: tk.mds.variant2samples.twLst.find((i) => i.term.id == termid).term.name + (numbycategory ? `<span style="font-size:.8em;float:right;margin-left: 5px;">n=${numbycategory.length}</span>` : ""),
-      keydownCallback: function(event) {
-        setTimeout(() => {
-          const tr = this.contentHolder.select("tbody").select("tr").node();
-          if (!tr) return;
-          tr.focus();
-        }, 100);
-      }
-    });
-  }
-  new Tabs({
-    holder: div,
-    tabsPosition: "vertical",
-    linePosition: "right",
-    tabs
-  }).main();
-  for (const [i, d] of data.entries()) {
-    const holder = tabs[i].contentHolder.style("padding-left", "20px");
-    if (d.numbycategory) {
-      holder.append("div").text("Click a category to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block);
-      continue;
-    }
-    if (d.density_data) {
-      if (!Number.isFinite(d.density_data.minvalue) || !Number.isFinite(d.density_data.maxvalue)) {
-        holder.append("div").text("No data");
-        continue;
-      }
-      holder.append("div").text("Select a range to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showDensity4oneTerm(d.termid, holder, d, tk, block);
-      continue;
-    }
-    throw "unknown summary data";
-  }
-}
-function showSummary4oneTerm(termid, div, numbycategory, tk, block) {
-  const tw = tk.mds.variant2samples.twLst.find((i) => i.term.id == termid);
-  if (!tw) throw "showSummary4oneTerm(): tw not found from variant2samples.twLst";
-  const rows = [];
-  for (const [category_key, count, total] of numbycategory) {
-    const row = [
-      { value: tw.term.values?.[category_key]?.label || category_key },
-      { html: total == void 0 ? "" : fillbar(null, { f: count / total, v1: count, v2: total }) },
-      { html: count + (total ? ' <span style="font-size:.8em">/ ' + total + "</span>" : "") }
-    ];
-    rows.push(row);
-  }
-  renderTable({
-    div,
-    rows,
-    columns: [
-      {
-        nowrap: true
-        // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed
-      },
-      {},
-      {}
-    ],
-    showHeader: false,
-    singleMode: true,
-    noRadioBtn: true,
-    noButtonCallback: (i) => {
-      clickCategory(numbycategory[i][0]);
-    }
-  });
-  async function clickCategory(category) {
-    tk.menutip.clear();
-    const term = await tk.mds.termdb.vocabApi.getterm(termid);
-    if (!term.values || Object.keys(term.values).length == 0) {
-      term.values = {};
-      for (const c of numbycategory) {
-        term.values[c[0]] = { label: c[0], samplecount: c[1] };
-      }
-    }
-    const tvs = {
-      type: "tvs",
-      tvs: { term, values: [{ key: category }] }
-    };
-    createSubTk(tk, block, tvs);
-  }
-}
-function getNewFilter(tk, tvs) {
-  if (tk.filterObj) {
-    return getNormalRoot({
-      type: "tvslst",
-      join: "and",
-      in: true,
-      lst: [tk.filterObj, tvs]
-    });
-  }
-  return {
-    type: "tvslst",
-    in: true,
-    join: "",
-    lst: [tvs]
-  };
-}
-async function showDensity4oneTerm(termid, div, data, tk, block) {
-  const term = await tk.mds.termdb.vocabApi.getterm(termid);
-  const callback = async (range) => {
-    tk.menutip.clear();
-    const tvs = {
-      type: "tvs",
-      tvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }
-    };
-    createSubTk(tk, block, tvs);
-  };
-  const scaleFactor = term.valueConversion ? term.valueConversion.scaleFactor : 1;
-  const vr = new violinRenderer(div, data.density_data, 400, 100, 10, 20, callback, scaleFactor);
-  vr.render();
-}
-function createSubTk(tk, block, tvs) {
-  const tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)));
-  block.tk_load(tk2);
-}
-function menu_listSamples(buttonrow, data, tk, block) {
-  buttonrow.append("div").text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("class", "sja_menuoption sja_mds3_slb_sampletablebtn").on("click", async () => {
-    tk.menutip.clear();
-    const wait = tk.menutip.d.append("div").text("Loading...").style("margin", "15px");
-    try {
-      const { samples } = await tk.mds.getSamples();
-      await displaySampleTable(samples, {
-        div: tk.menutip.d,
-        tk,
-        block
-      });
-      wait.remove();
-    } catch (e) {
-      wait.text(e.message || e);
-      console.log(e);
-    }
-  });
-}
-export {
-  makeSampleFilterLabel,
-  makeSampleLabel
-};
-//# sourceMappingURL=leftlabel.sample-YXXZZ7H7.js.map

package/dist/leftlabel.sample-YXXZZ7H7.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../mds3/leftlabel.sample.js"],
-  "sourcesContent": ["import { makelabel } from './leftlabel'\nimport { Tabs, fillbar, renderTable, violinRenderer } from '#dom'\nimport { displaySampleTable } from './sampletable'\nimport { filterInit, getNormalRoot } from '../filter/filter'\nimport { getFilterName } from './filterName'\n\n/*\nmakeSampleLabel()\n\tmakes the \"# samples\" sub label on the left.\n\tclick label to view summaries about samples that have mutation data in the view range\n\nmakeSampleFilterLabel()\ncreateSubTk()\n*/\n\nexport function makeSampleLabel(data, tk, block, laby) {\n\tif (!tk.leftlabels.doms.samples) {\n\t\t// \"Samples\" label is missing. create\n\t\ttk.leftlabels.doms.samples = makelabel(tk, block, laby)\n\t}\n\n\tif (data.sampleTotalNumber) {\n\t\t// current data has samples, activate label\n\t\ttk.leftlabels.doms.samples\n\t\t\t.attr('class', 'sja_clbtext2')\n\t\t\t.style('opacity', 1)\n\t\t\t.text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? 's' : ''}`)\n\t\t\t.attr('data-testid', 'sjpp_mds3tk_samples_label')\n\t\t\t.on('click', async event => {\n\t\t\t\ttk.menutip.clear().showunder(event.target)\n\n\t\t\t\tawait mayShowSummary(tk, block)\n\n\t\t\t\tconst buttonrow = tk.menutip.d.append('div').style('margin', '10px')\n\n\t\t\t\tmenu_listSamples(buttonrow, data, tk, block)\n\t\t\t\t// TODO new button \"Customize variables\", launch tree in submit_lst mode to update tk.mds.variant2samples.twLst\n\t\t\t})\n\t} else {\n\t\t// current data has no sample, disable label\n\t\ttk.leftlabels.doms.samples.text('No samples').attr('class', '').style('opacity', 0.5).on('click', null)\n\t}\n}\n\nexport function makeSampleFilterLabel(data, tk, block, laby) {\n\t// track has a modifiable sample filter. add a new label to access the filter UI\n\tif (!tk.leftlabels.doms.filterObj) {\n\t\ttk.leftlabels.doms.filterObj = makelabel(tk, block, laby)\n\t}\n\n\ttk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on('click', async event => {\n\t\ttk.menutip.clear().showunder(event.target)\n\n\t\t// display filter UI\n\n\t\tconst arg = {\n\t\t\tholder: tk.menutip.d.append('div').style('margin', '10px'),\n\t\t\tvocabApi: tk.mds.termdb.vocabApi,\n\t\t\tcallback: f => {\n\t\t\t\ttk.filterObj = f\n\t\t\t\ttk.load()\n\t\t\t}\n\t\t}\n\t\tmayAddGetCategoryArgs(arg, block)\n\t\tfilterInit(arg).main(tk.filterObj)\n\t})\n}\n\nfunction mayAddGetCategoryArgs(arg, block) {\n\tif (block.usegm) {\n\t\t/////////////////////////////////////\n\t\t//\n\t\t// GDC specific logic\n\t\t// in gene mode, supply the current gene name as a new parameter\n\t\t// for the vocabApi getCategories() query, so it can pull the number of mutated samples for a term\n\t\t// this parameter is used by some sneaky gdc-specific logic in termdb.matrix.js getData()\n\t\t// should not impact non-gdc datasets\n\t\t//\n\t\t/////////////////////////////////////\n\t\targ.getCategoriesArguments = { currentGeneNames: [block.usegm.name] }\n\t\t// TODO {name: block.usegm.name, isoform, q:{allowedDt}}\n\t} else {\n\t\t/////////////////////////////////////\n\t\t//\n\t\t// GDC specific logic\n\t\t// in genomic mode, pass rglst for pulling cases mutated in this region, handled in the same way as currentGeneNames\n\t\t//\n\t\t/////////////////////////////////////\n\t\targ.getCategoriesArguments = { rglst: structuredClone(block.rglst) }\n\t}\n}\n\nasync function mayShowSummary(tk, block) {\n\tif (!tk.mds.variant2samples.twLst) {\n\t\t// no terms to summarize for\n\t\treturn\n\t}\n\n\tconst div = tk.menutip.d.append('div').style('margin', '10px')\n\n\tconst wait = div.append('div').text('Loading...')\n\n\ttry {\n\t\tconst { summary } = await tk.mds.getSamples({ isSummary: true })\n\t\ttk.leftlabels.__samples_data = summary // for testing\n\t\twait.remove()\n\t\tawait showSummary4terms(summary, div.append('div').attr('class', 'sja_mds3samplesummarydiv'), tk, block)\n\t} catch (e) {\n\t\twait.text(`Error: ${e.message || e}`)\n\t\tif (e.stack) console.log(e.stack)\n\t}\n}\n\n/* show summaries over a list of terms\ndata is array, each ele: {termid, numbycategory}\n*/\nasync function showSummary4terms(data, div, tk, block) {\n\tconst tabs = []\n\tfor (const { termid, numbycategory } of data) {\n\t\ttabs.push({\n\t\t\tlabel:\n\t\t\t\ttk.mds.variant2samples.twLst.find(i => i.term.id == termid).term.name +\n\t\t\t\t(numbycategory\n\t\t\t\t\t? `<span style=\"font-size:.8em;float:right;margin-left: 5px;\">n=${numbycategory.length}</span>`\n\t\t\t\t\t: ''),\n\t\t\tkeydownCallback: function (event) {\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tconst tr = this.contentHolder.select('tbody').select('tr').node()\n\t\t\t\t\tif (!tr) return\n\t\t\t\t\t// to support keyboard navigation, automatically highlight the first table row\n\t\t\t\t\t// after this tab/button is clicked, use setTimeout() to ensure the table has\n\t\t\t\t\t// finished rendering\n\t\t\t\t\t//\n\t\t\t\t\t// TODO: support violin plot range selection, which does not use table rows,\n\t\t\t\t\t//       should use start-stop input there\n\t\t\t\t\t//\n\t\t\t\t\ttr.focus()\n\t\t\t\t}, 100)\n\t\t\t}\n\t\t})\n\t}\n\n\tnew Tabs({\n\t\tholder: div,\n\t\ttabsPosition: 'vertical',\n\t\tlinePosition: 'right',\n\t\ttabs\n\t}).main()\n\n\tfor (const [i, d] of data.entries()) {\n\t\tconst holder = tabs[i].contentHolder.style('padding-left', '20px')\n\t\tif (d.numbycategory) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Click a category to create new track.')\n\t\t\t\t.style('margin-bottom', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('opacity', 0.5)\n\t\t\tshowSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block)\n\t\t\tcontinue\n\t\t}\n\t\tif (d.density_data) {\n\t\t\tif (!Number.isFinite(d.density_data.minvalue) || !Number.isFinite(d.density_data.maxvalue)) {\n\t\t\t\tholder.append('div').text('No data')\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Select a range to create new track.')\n\t\t\t\t.style('margin-bottom', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('opacity', 0.5)\n\t\t\tshowDensity4oneTerm(d.termid, holder, d, tk, block)\n\t\t\tcontinue\n\t\t}\n\t\tthrow 'unknown summary data'\n\t}\n}\n\n/*\nshow categories and #case for one term\nclick a category to launch subtrack\nnumbycategory = []\n\teach element is array of length 3 representing one category, from a categorical term\n\t[0] = category name\n\t[1] = number of cases mutated in current gene\n\t[2] = total number of cases from this category\n*/\nfunction showSummary4oneTerm(termid, div, numbycategory, tk, block) {\n\tconst tw = tk.mds.variant2samples.twLst.find(i => i.term.id == termid)\n\tif (!tw) throw 'showSummary4oneTerm(): tw not found from variant2samples.twLst'\n\n\tconst rows = []\n\tfor (const [category_key, count, total] of numbycategory) {\n\t\t// in future tw may be in groupsetting mode\n\t\tconst row = [\n\t\t\t{ value: tw.term.values?.[category_key]?.label || category_key },\n\t\t\t{ html: total == undefined ? '' : fillbar(null, { f: count / total, v1: count, v2: total }) },\n\t\t\t{ html: count + (total ? ' <span style=\"font-size:.8em\">/ ' + total + '</span>' : '') }\n\t\t]\n\t\trows.push(row)\n\t}\n\trenderTable({\n\t\tdiv,\n\t\trows,\n\t\tcolumns: [\n\t\t\t{\n\t\t\t\tnowrap: true // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed\n\t\t\t},\n\t\t\t{},\n\t\t\t{}\n\t\t],\n\t\tshowHeader: false,\n\t\tsingleMode: true,\n\t\tnoRadioBtn: true,\n\t\tnoButtonCallback: i => {\n\t\t\tclickCategory(numbycategory[i][0])\n\t\t}\n\t})\n\n\tasync function clickCategory(category) {\n\t\t// for a selected category, launch subtrack\n\t\ttk.menutip.clear()\n\n\t\tconst term = await tk.mds.termdb.vocabApi.getterm(termid)\n\n\t\tif (!term.values || Object.keys(term.values).length == 0) {\n\t\t\t/////////////////////////////////////\n\t\t\t//\n\t\t\t// GDC specific logic:\n\t\t\t// a gdc term will have blank .values{}, fill in term.values{} so filter/tvs won't break\n\t\t\t//\n\t\t\t/////////////////////////////////////\n\t\t\tterm.values = {}\n\t\t\tfor (const c of numbycategory) {\n\t\t\t\tterm.values[c[0]] = { label: c[0], samplecount: c[1] }\n\t\t\t}\n\t\t}\n\n\t\tconst tvs = {\n\t\t\ttype: 'tvs',\n\t\t\ttvs: { term, values: [{ key: category }] }\n\t\t}\n\t\tcreateSubTk(tk, block, tvs)\n\t}\n}\n\nfunction getNewFilter(tk, tvs) {\n\tif (tk.filterObj) {\n\t\t// merge new tvs to current filter\n\t\treturn getNormalRoot({\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tin: true,\n\t\t\tlst: [tk.filterObj, tvs]\n\t\t})\n\t}\n\t// create new filter\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: '',\n\t\tlst: [tvs]\n\t}\n}\n\n// will be nice if the data computing and rendering can both be replaced by violin\nasync function showDensity4oneTerm(termid, div, data, tk, block) {\n\tconst term = await tk.mds.termdb.vocabApi.getterm(termid)\n\tconst callback = async range => {\n\t\t// a range is selected\n\t\ttk.menutip.clear()\n\t\tconst tvs = {\n\t\t\ttype: 'tvs',\n\t\t\ttvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }\n\t\t}\n\t\tcreateSubTk(tk, block, tvs)\n\t}\n\tconst scaleFactor = term.valueConversion ? term.valueConversion.scaleFactor : 1\n\tconst vr = new violinRenderer(div, data.density_data, 400, 100, 10, 20, callback, scaleFactor)\n\tvr.render()\n}\n\nfunction createSubTk(tk, block, tvs) {\n\tconst tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)))\n\tblock.tk_load(tk2)\n}\n\nfunction menu_listSamples(buttonrow, data, tk, block) {\n\t// subject to change\n\n\tbuttonrow\n\t\t.append('div')\n\t\t.text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? 's' : ''}`)\n\t\t.attr('class', 'sja_menuoption sja_mds3_slb_sampletablebtn')\n\t\t.on('click', async () => {\n\t\t\ttk.menutip.clear()\n\t\t\tconst wait = tk.menutip.d.append('div').text('Loading...').style('margin', '15px')\n\t\t\ttry {\n\t\t\t\tconst { samples } = await tk.mds.getSamples()\n\t\t\t\tawait displaySampleTable(samples, {\n\t\t\t\t\tdiv: tk.menutip.d,\n\t\t\t\t\ttk,\n\t\t\t\t\tblock\n\t\t\t\t})\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text(e.message || e)\n\t\t\t\tconsole.log(e)\n\t\t\t}\n\t\t})\n}\n"],
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-  "names": []
-}

package/dist/lollipop-DA67ETKC.js

@@ -1,161 +0,0 @@
-import {
-  block_init_default
-} from "./chunk-Z3QJUOGM.js";
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist
-} from "./chunk-DXNHQCWO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-PYGUZ75W.js";
-import {
-  dofetch3
-} from "./chunk-GDVG55UR.js";
-import "./chunk-L7N5BOMJ.js";
-import "./chunk-RY7CVONT.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-QTAXM2J6.js";
-import "./chunk-MXMPAXMS.js";
-import "./chunk-4W3BORF5.js";
-import "./chunk-SU6RBYZK.js";
-import "./chunk-2J7NXRQQ.js";
-import {
-  Menu
-} from "./chunk-IVJWQYGG.js";
-import "./chunk-OPZUIS3Y.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// gdc/lollipop.js
-var gdcGenome = "hg38";
-var gdcDslabel = "GDC";
-var tip = new Menu({ padding: "" });
-async function init(arg, holder, genomes) {
-  const genome = genomes[gdcGenome];
-  if (!genome) throw gdcGenome + " missing";
-  if (arg.geneSearch4GDCmds3.onloadalltk_always && typeof arg.geneSearch4GDCmds3.onloadalltk_always != "function")
-    throw "arg.geneSearch4GDCmds3.onloadalltk_always not function";
-  if (arg.geneSearch4GDCmds3.postRender && typeof arg.geneSearch4GDCmds3.postRender != "function")
-    throw "arg.geneSearch4GDCmds3.postRender not function";
-  holder.selectAll(".sja_lollipop_holder").remove();
-  const mainDiv = holder.append("div").attr("class", "sja_lollipop_holder");
-  const geneInputDiv = mainDiv.append("div").style("margin-left", "20px");
-  geneInputDiv.append("div").text(
-    arg.geneSearch4GDCmds3.hardcodeCnvOnly ? "To view GDC CNV segments over a gene or region, enter genomic position (chr11:108195437-108267444), dbSNP accesion, or gene name (MYC)." : "To view GDC mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467)."
-  );
-  const graphDiv = mainDiv.append("div").attr("class", "sja_geneSearch4GDCmds3_blockdiv");
-  const searchOpt = {
-    genome,
-    tip,
-    row: geneInputDiv,
-    callback: launchView,
-    geneSymbol: arg.geneSymbol,
-    triggerSearch: arg.geneSymbol && arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true,
-    hideInputBeforeCallback: arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true
-  };
-  if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-    searchOpt.searchOnly = "gene";
-  }
-  const coordInput = addGeneSearchbox(searchOpt);
-  let userSelection;
-  await arg.geneSearch4GDCmds3.postRender?.({ tip });
-  if (arg.state) {
-    if (arg.state.userSelection) launchView(false, arg.state.userSelection);
-    delete arg.state;
-  }
-  async function launchView(triggeredByInput = true, userSelection2) {
-    const pa = {
-      // param for instantiating block
-      genome,
-      holder: graphDiv,
-      gmmode: "exon only",
-      nobox: 1,
-      hide_dsHandles: arg.hide_dsHandles,
-      onloadalltk_always: arg.geneSearch4GDCmds3.onloadalltk_always
-    };
-    if (arg.tracks) {
-      pa.tklst = arg.tracks;
-    } else {
-      const tk = {
-        type: "mds3",
-        dslabel: gdcDslabel,
-        allow2selectSamples: arg.allow2selectSamples,
-        filter0: arg.filter0
-      };
-      pa.tklst = [tk];
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        tk.hardcodeCnvOnly = 1;
-        delete pa.gmmode;
-        first_genetrack_tolist(pa.genome, pa.tklst);
-      }
-    }
-    if (userSelection2) {
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        if (typeof userSelection2 != "object") throw "userSelection not object when pa.block is true";
-        pa.chr = userSelection2.chr;
-        pa.start = userSelection2.start;
-        pa.stop = userSelection2.stop;
-        if (!pa.chr || !Number.isInteger(pa.start) || !Number.isInteger(pa.stop))
-          throw "userSelection not {chr,start,stop}";
-      } else {
-        if (typeof userSelection2 != "string") throw "userSelection should be string when pa.block is not true";
-        pa.query = userSelection2;
-      }
-    } else {
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        if (!coordInput.chr || !Number.isInteger(coordInput.start) || !Number.isInteger(coordInput.stop)) {
-          if (triggeredByInput) throw "coordInput.chr/start/stop missing";
-        }
-        pa.chr = coordInput.chr;
-        pa.start = coordInput.start;
-        pa.stop = coordInput.stop;
-      } else {
-        if (!coordInput.geneSymbol) {
-          if (triggeredByInput) throw "coordInput.geneSymbol missing";
-        }
-        const gmlst = (await dofetch3(`genelookup?deep=1&input=${coordInput.geneSymbol}&genome=${gdcGenome}`)).gmlst;
-        if (!Array.isArray(gmlst) || gmlst.length == 0) throw "gmlst is not non-empty array";
-        pa.query = getSelectedIsoform(coordInput, gmlst);
-        if (gmlst.some((i) => i.coding)) pa.gmmode = "protein";
-      }
-    }
-    graphDiv.selectAll("*").remove();
-    if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) return await block_init_default(pa);
-    const _ = await import("./block-5HOXOGQZ.js");
-    return new _.Block(pa);
-  }
-  const api = {
-    update: (_arg) => {
-      Object.assign(arg, _arg);
-      launchView(false);
-    },
-    getState: () => ({ userSelection })
-  };
-  return api;
-}
-function getSelectedIsoform(coordInput, gmlst) {
-  if (coordInput.fromWhat) {
-    if (gmlst.some((i) => i.isoform.toUpperCase() == coordInput.fromWhat.toUpperCase())) {
-      return coordInput.fromWhat;
-    }
-    if (coordInput.fromWhat.toUpperCase().startsWith("ENSG")) {
-      for (const i of gmlst) {
-        if (i.isdefault && i.isoform.startsWith("ENST")) return i.isoform;
-      }
-    }
-  }
-  const defaultIsoform = gmlst.find((i) => i.isdefault);
-  if (defaultIsoform) return defaultIsoform.isoform;
-  return gmlst[0].isoform;
-}
-export {
-  init
-};
-//# sourceMappingURL=lollipop-DA67ETKC.js.map