@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/geneVariant.integration.spec-Y2NPNTYX.js

@@ -1,198 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  sleep
-} from "./chunk-ECIBJXFT.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import {
-  SearchHandler,
-  vocabInit
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/test/geneVariant.integration.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-async function getVocabApi() {
-  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
-  if (!vocabApi2) throw "vocabApi is missing";
-  await vocabApi2.getTermdbConfig();
-  return vocabApi2;
-}
-var vocabApi = await getVocabApi();
-var handler = new SearchHandler();
-function getHolder() {
-  const holder = select_default("body").append("div");
-  return holder;
-}
-async function initializeSearchHandler(opts) {
-  const callback = opts.callback || (() => {
-  });
-  await handler.init({
-    holder: opts.holder,
-    app: { vocabApi },
-    genomeObj: hg38,
-    callback
-  });
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- geneVariant search handler -***-");
-  test.end();
-});
-(0, import_tape.default)("Search handler layout", async (test) => {
-  const holder = getHolder();
-  await initializeSearchHandler({ holder });
-  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
-  test.ok(
-    mutationTypeRadiosDiv.selectAll('input[type="radio"]').size() > 0,
-    "Mutation type radio buttons should be present"
-  );
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  test.equal(
-    inputTypeRadiosDiv.selectAll('input[type="radio"]').size(),
-    2,
-    "Input type radio buttons should be present"
-  );
-  const searchDiv = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]');
-  test.equal(searchDiv.selectAll('input[type="search"]').size(), 1, "Gene search input should be present");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single gene input", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(tw.term.type, "geneVariant", "term.type should be geneVariant");
-  test.equal(tw.q.type, "predefined-groupset", "q.type should be predefined-groupset");
-  test.equal(tw.q.predefined_groupset_idx, 0, "q.predefined_groupset_idx should be 0");
-  test.equal(tw.term.genes.length, 1, "term.genes[] should have length of 1");
-  test.deepEqual(
-    tw.term.genes[0],
-    { kind: "gene", id: "TP53", gene: "TP53", name: "TP53", type: "geneVariant" },
-    "term.genes[0] should have expected structure"
-  );
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Change mutation type", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
-  const mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type="radio"]');
-  const thirdRadio = mutationTypeRadios.nodes()[2];
-  thirdRadio.click();
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const geneSetDiv = inputTypeRadiosDiv.selectAll("div").filter((d) => d.value == "geneset");
-  test.equal(geneSetDiv.style("display"), "none", "Gene set option should be hidden for CNV");
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(tw.q.predefined_groupset_idx, 2, "q.predefined_groupset_idx should be 2 upon selecting third radio button");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene set input", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
-  const secondRadio = inputTypeRadios.nodes()[1];
-  secondRadio.click();
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  geneSearchInput.value = "KRAS";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
-  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
-  await sleep(100);
-  submitButton.click();
-  await sleep(100);
-  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
-  test.equal(tw.term.name, "TP53, KRAS", "term.name should concatenate gene names");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene set input - custom name", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
-  const secondRadio = inputTypeRadios.nodes()[1];
-  secondRadio.click();
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  geneSearchInput.value = "KRAS";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  const nameInput = holder.select('[data-testid="sja_genesetinput_name"]').node();
-  nameInput.value = "Test gene set";
-  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
-  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
-  await sleep(100);
-  submitButton.click();
-  await sleep(100);
-  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
-  test.equal(tw.term.name, "Test gene set", "term.name should be custom name");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-//# sourceMappingURL=geneVariant.integration.spec-Y2NPNTYX.js.map

package/dist/genefusion.ui-L3HIJM3N.js

@@ -1,309 +0,0 @@
-import {
-  makeBtn,
-  makeGenomeDropDown,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-5EBRF6Z7.js";
-import {
-  appear,
-  sayerror
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// src/genefusion/genefusion.ui.js
-function init_geneFusionUI(holder, genomes) {
-  const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
-    "font-family",
-    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
-  ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true);
-  const obj = {};
-  makeFusionInput(wrapper, obj);
-  const dropdown_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "10px");
-  genomeSelection(dropdown_div, genomes, obj);
-  makePositionDropDown(dropdown_div, obj);
-  const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "40px 0px 40px 130px");
-  makeSubmit(controlBtns_div, obj, holder, genomes);
-  makeResetBtn(controlBtns_div, obj, ".genefusion_input").style("margin", "0px 10px");
-  makeInfoSection(wrapper);
-  return obj;
-}
-function makeFusionInput(div, obj) {
-  const fusionInput = makeTextAreaInput({
-    div,
-    cols: 70,
-    // Increased to accommodate longer isoform format example
-    placeholder: "Example:\nPAX5,chr9,37002646,-::JAK2,chr9,5081726,+\nOr:\nPAX5,chr9,37002646,-,NM_016734::JAK2,chr9,5081726,+,NM_004972"
-  }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("genefusion_input", true).on("keyup", async () => {
-    obj.data = fusionInput.property("value").trim();
-  });
-}
-async function genomeSelection(div, genomes, obj) {
-  const genome_div = div.append("div").style("margin-left", "40px");
-  const g = makeGenomeDropDown(genome_div, genomes).style("border", "1px solid rgb(138, 177, 212)");
-  obj.genome = g.node();
-}
-async function makePositionDropDown(div, obj) {
-  const dropdown_div = div.append("div");
-  const positionSelect = dropdown_div.append("select").style("border-radius", "5px").style("padding", "5px 10px").style("margin", "1px 10px 1px 10px");
-  positionSelect.append("option").text("Codon position").property("value", "codon");
-  positionSelect.append("option").text("RNA position").property("value", "rna");
-  positionSelect.append("option").text("Genomic position").property("value", "genomic").attr("selected", true);
-  obj.posType = positionSelect.node();
-}
-function makeSubmit(div, obj, holder) {
-  const submit = makeBtn({
-    div,
-    text: "Submit"
-  });
-  const errorMessage_div = div.append("div");
-  submit.style("display", "block").on("click", () => {
-    if (!obj.data || obj.data === void 0) {
-      const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
-      sayerror(sayerrorDiv, "Please provide data");
-      setTimeout(() => sayerrorDiv.remove(), 3e3);
-    } else {
-      select_default(".sjpp-app-ui").remove();
-      const runpp_arg = {
-        /** Do not use window.location.origin. See comment: line 180, renderContent(), client/appdrawer/adSandbox.js*/
-        host: sessionStorage.getItem("hostURL"),
-        nobox: true,
-        noheader: true,
-        parseurl: false,
-        genome: obj.genome.options[obj.genome.selectedIndex].text
-      };
-      makeSubmitResult(obj, holder, runpp_arg);
-    }
-  });
-}
-function makeInfoSection(div) {
-  div.append("div").style("margin", "10px").style("opacity", "0.65").html(`Limited to two-gene fusion products.<br>
-		One product per line.<br>
-		<br>
-		<strong>Format 1 (Basic):</strong> Each line has eight fields, four fields for each gene. For each gene join the following fields separated by a comma:
-		<ol><li>Gene symbol</li>
-		<li>Chromosome</li>
-		<li>Position, 1-based coordinate</li>
-		<li>Strand</li>
-		</ol>
-		<strong>Format 2 (With RefSeq isoforms):</strong> Each line has ten fields, five fields for each gene. For each gene join the following fields separated by a comma:
-		<ol><li>Gene symbol</li>
-		<li>Chromosome</li>
-		<li>Position, 1-based coordinate</li>
-		<li>Strand</li>
-		<li>RefSeq isoform (e.g., NM_001754)</li>
-		</ol>
-		Separate the two genes by a double colon (::). <br><br>
-		Examples: <br>
-		<p style="margin-left: 10px">
-		<strong>Format 1:</strong><br>
-		PAX5,chr9,37002646,-::JAK2,chr9,5081726,+<br>
-		ZCCHC7,chr9,37257786,-::PAX5,chr9,37024824,-<br>
-		BCR,chr22,23524427,+::ABL1,chr9,133729449,+<br><br>
-		<strong>Format 2:</strong><br>
-		RUNX1,chr21,36206706,-,NM_001754::MECOM,chr3,169099311,-,NM_004991<br>
-		PAX5,chr9,37002646,-,NM_016734::JAK2,chr9,5081726,+,NM_004972<p>`);
-}
-function validatePosition(position, geneName) {
-  if (!/^\d+$/.test(position)) {
-    throw new Error(`Invalid fusion format: position for ${geneName} must be a positive integer`);
-  }
-  const pos = Number(position);
-  if (pos <= 0) {
-    throw new Error(`Invalid fusion format: position for ${geneName} must be greater than 0 (1-based coordinates)`);
-  }
-}
-function parseFusionLine(line) {
-  const parts = line.trim().split("::");
-  if (parts.length !== 2) {
-    throw new Error('Invalid fusion format: must contain exactly two genes separated by "::"');
-  }
-  const gene1 = parts[0].split(",").map((s) => s.trim());
-  const gene2 = parts[1].split(",").map((s) => s.trim());
-  if (gene1.length !== 4 && gene1.length !== 5 || gene2.length !== 4 && gene2.length !== 5) {
-    throw new Error(
-      `Invalid fusion format: each gene must have 4 or 5 fields. Found gene1: ${gene1.length} fields, gene2: ${gene2.length} fields`
-    );
-  }
-  for (let i = 0; i < 4; i++) {
-    if (!gene1[i] || !gene2[i]) {
-      throw new Error("Invalid fusion format: gene symbol, chromosome, position, and strand are required");
-    }
-  }
-  validatePosition(gene1[2], gene1[0]);
-  validatePosition(gene2[2], gene2[0]);
-  if (!/^[+-]$/.test(gene1[3]) || !/^[+-]$/.test(gene2[3])) {
-    throw new Error('Invalid fusion format: strand must be "+" or "-"');
-  }
-  return [gene1, gene2];
-}
-function createFusionVariant(gene1, gene2) {
-  const variant = {
-    gene1: gene1[0],
-    chr1: gene1[1],
-    pos1: parseInt(gene1[2]) - 1,
-    strand1: gene1[3],
-    gene2: gene2[0],
-    chr2: gene2[1],
-    pos2: parseInt(gene2[2]) - 1,
-    strand2: gene2[3],
-    dt: 2,
-    class: "Fuserna"
-  };
-  const addIsoformIfPresent = (gene, fieldName) => {
-    if (gene.length > 4 && gene[4]?.trim()) {
-      variant[fieldName] = gene[4].trim();
-    }
-  };
-  addIsoformIfPresent(gene1, "isoform1");
-  addIsoformIfPresent(gene2, "isoform2");
-  return variant;
-}
-function makeSubmitResult(obj, div, runpp_arg) {
-  const lines = obj.data.split(/[\r\n]/).filter((line) => line.trim().length > 0);
-  if (lines.length === 1) {
-    try {
-      const [gene1, gene2] = parseFusionLine(lines[0]);
-      return makeFusionTabs(div, runpp_arg, gene1, gene2);
-    } catch (error) {
-      const errorDiv = div.append("div").style("color", "red").style("margin", "20px");
-      sayerror(errorDiv, `Error parsing fusion: ${error.message}`);
-      return;
-    }
-  }
-  const fusionSelect = div.append("div").append("select").style("border-radius", "5px").style("padding", "5px 10px").style("margin", "1px 10px 1px 10px");
-  fusionSelect.append("option").text(`Select Fusion (${lines.length})`);
-  const tabsDiv = div.append("div").style("margin", "20px");
-  const fusionsMap = /* @__PURE__ */ new Map();
-  for (const data of lines) {
-    try {
-      const [gene1, gene2] = parseFusionLine(data);
-      fusionsMap.set(`${gene1[0]}-${gene2[0]}`, [gene1, gene2]);
-    } catch (error) {
-      console.warn(`Skipping invalid fusion line: ${data}. Error: ${error.message}`);
-    }
-  }
-  if (fusionsMap.size === 0) {
-    const errorDiv = div.append("div").style("color", "red").style("margin", "20px");
-    sayerror(errorDiv, "No valid fusion lines found. Please check the format.");
-    return;
-  }
-  for (const fusion of fusionsMap) {
-    fusionSelect.append("option").property("value", fusion[0]).text(fusion[0]);
-  }
-  fusionSelect.on("change", () => {
-    tabsDiv.selectAll("*").remove();
-    const geneArrays = fusionsMap.get(fusionSelect.property("value"));
-    makeFusionTabs(tabsDiv, runpp_arg, geneArrays[0], geneArrays[1]);
-  });
-}
-function makeFusionTabs(div, runpp_arg, gene1, gene2) {
-  const tabs = [
-    // {
-    // ************ Keep for later, will introduce gene fusion view once data format settled *************
-    // 	label: 'Fusion',
-    // 	callback: async div => {
-    // 		if (!tabs[0].rendered) {
-    // 			appear(div)
-    // 			const text = `${gene1[0]}, ${gene1[1]},${gene1[2]},${gene2[0]},${gene2[1]},${gene2[2]}`
-    // 			const runpp_arg = {
-    // 				holder: div
-    // 					.append('div')
-    // 					.style('margin', '20px')
-    // 					.node(),
-    // 				host: window.location.origin,
-    // 				nobox: true,
-    // 				noheader: true,
-    // 				parseurl: false,
-    // 				genome,
-    // 				genefusion: {
-    // 					text,
-    // 					positionType: posType
-    // 					}
-    // 				}
-    // 			console.log(runpp_arg)
-    // 			runproteinpaint(Object.assign(runpp_arg))
-    // 			tabs[0].rendered = true
-    // 		}
-    // 	}
-    // },
-    {
-      label: gene1[0],
-      callback: async (event, tab) => {
-        appear(tab.contentHolder);
-        const variant = createFusionVariant(gene1, gene2);
-        const fusion_arg = {
-          holder: tab.contentHolder.append("div").style("margin", "20px").node(),
-          gene: gene1[0],
-          tracks: [
-            {
-              type: "mds3",
-              name: gene1[0],
-              custom_variants: [variant]
-            }
-          ]
-        };
-        runproteinpaint(Object.assign(runpp_arg, fusion_arg));
-        delete tab.callback;
-      }
-    },
-    {
-      label: gene2[0],
-      callback: async (event, tab) => {
-        appear(tab.contentHolder);
-        const variant = createFusionVariant(gene1, gene2);
-        const fusion_arg = {
-          holder: tab.contentHolder.append("div").style("margin", "20px").node(),
-          gene: gene2[0],
-          tracks: [
-            {
-              type: "mds3",
-              name: gene2[0],
-              custom_variants: [variant]
-            }
-          ]
-        };
-        runproteinpaint(Object.assign(runpp_arg, fusion_arg));
-        delete tab.callback;
-      }
-    }
-  ];
-  new Tabs({ holder: div, tabs }).main();
-}
-export {
-  init_geneFusionUI,
-  parseFusionLine
-};
-//# sourceMappingURL=genefusion.ui-L3HIJM3N.js.map

package/dist/genefusion.ui-L3HIJM3N.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/genefusion/genefusion.ui.js"],
-  "sourcesContent": ["import * as uiutils from '#dom/uiUtils'\nimport { select as d3select, selectAll as d3selectAll } from 'd3-selection'\nimport { sayerror } from '../client'\nimport { Tabs } from '../../dom/toggleButtons'\nimport { appear } from '#dom/animation'\n\n/*\n------ EXPORTED ------ \ninit_geneFusionUI()\n\tholder \n\tgenomes\nparseFusionLine()\n\tline\n\n------ Internal ------ \nmakeFusionInput\ngenomeSelection\nmakePositionDropDown\nmakeSubmit\nmakeInfoSection\nvalidatePosition\ncreateFusionVariant\nmakeSubmitResult\nmakeFusionTabs\n\n*/\n\nexport function init_geneFusionUI(holder, genomes) {\n\tconst wrapper = holder\n\t\t.append('div')\n\t\t.style('margin', '20px 20px 20px 40px')\n\t\t.style(\n\t\t\t'font-family',\n\t\t\t\"'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif\"\n\t\t)\n\t\t.style('place-items', 'center left')\n\t\t.style('overflow', 'hidden')\n\t\t.classed('sjpp-app-ui', true)\n\n\tconst obj = {}\n\n\tmakeFusionInput(wrapper, obj)\n\n\tconst dropdown_div = wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('margin', '10px')\n\tgenomeSelection(dropdown_div, genomes, obj)\n\tmakePositionDropDown(dropdown_div, obj)\n\n\tconst controlBtns_div = wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('margin', '40px 0px 40px 130px')\n\tmakeSubmit(controlBtns_div, obj, holder, genomes)\n\tuiutils.makeResetBtn(controlBtns_div, obj, '.genefusion_input').style('margin', '0px 10px')\n\n\tmakeInfoSection(wrapper)\n\n\treturn obj\n}\n\nfunction makeFusionInput(div, obj) {\n\tconst fusionInput = uiutils\n\t\t.makeTextAreaInput({\n\t\t\tdiv,\n\t\t\tcols: 70, // Increased to accommodate longer isoform format example\n\t\t\tplaceholder:\n\t\t\t\t'Example:\\nPAX5,chr9,37002646,-::JAK2,chr9,5081726,+\\nOr:\\nPAX5,chr9,37002646,-,NM_016734::JAK2,chr9,5081726,+,NM_004972'\n\t\t})\n\t\t.style('border', '1px solid rgb(138, 177, 212)')\n\t\t.style('margin', '0px 0px 0px 20px')\n\t\t.classed('genefusion_input', true)\n\t\t.on('keyup', async () => {\n\t\t\tobj.data = fusionInput.property('value').trim()\n\t\t})\n}\n\nasync function genomeSelection(div, genomes, obj) {\n\tconst genome_div = div.append('div').style('margin-left', '40px')\n\tconst g = uiutils.makeGenomeDropDown(genome_div, genomes).style('border', '1px solid rgb(138, 177, 212)')\n\tobj.genome = g.node()\n}\n\nasync function makePositionDropDown(div, obj) {\n\tconst dropdown_div = div.append('div')\n\n\tconst positionSelect = dropdown_div\n\t\t.append('select')\n\t\t.style('border-radius', '5px')\n\t\t.style('padding', '5px 10px')\n\t\t.style('margin', '1px 10px 1px 10px')\n\tpositionSelect.append('option').text('Codon position').property('value', 'codon')\n\tpositionSelect.append('option').text('RNA position').property('value', 'rna')\n\tpositionSelect.append('option').text('Genomic position').property('value', 'genomic').attr('selected', true)\n\tobj.posType = positionSelect.node()\n}\n\nfunction makeSubmit(div, obj, holder) {\n\tconst submit = uiutils.makeBtn({\n\t\tdiv,\n\t\ttext: 'Submit'\n\t})\n\tconst errorMessage_div = div.append('div')\n\tsubmit.style('display', 'block').on('click', () => {\n\t\tif (!obj.data || obj.data === undefined) {\n\t\t\tconst sayerrorDiv = errorMessage_div.append('div').style('display', 'inline-block').style('max-width', '20vw')\n\t\t\tsayerror(sayerrorDiv, 'Please provide data')\n\t\t\tsetTimeout(() => sayerrorDiv.remove(), 3000)\n\t\t} else {\n\t\t\td3select('.sjpp-app-ui').remove()\n\t\t\tconst runpp_arg = {\n\t\t\t\t/** Do not use window.location.origin. See comment: line 180, renderContent(), client/appdrawer/adSandbox.js*/\n\t\t\t\thost: sessionStorage.getItem('hostURL'),\n\t\t\t\tnobox: true,\n\t\t\t\tnoheader: true,\n\t\t\t\tparseurl: false,\n\t\t\t\tgenome: obj.genome.options[obj.genome.selectedIndex].text\n\t\t\t}\n\t\t\tmakeSubmitResult(obj, holder, runpp_arg)\n\t\t}\n\t})\n}\n\nfunction makeInfoSection(div) {\n\tdiv.append('div').style('margin', '10px').style('opacity', '0.65').html(`Limited to two-gene fusion products.<br>\n\t\tOne product per line.<br>\n\t\t<br>\n\t\t<strong>Format 1 (Basic):</strong> Each line has eight fields, four fields for each gene. For each gene join the following fields separated by a comma:\n\t\t<ol><li>Gene symbol</li>\n\t\t<li>Chromosome</li>\n\t\t<li>Position, 1-based coordinate</li>\n\t\t<li>Strand</li>\n\t\t</ol>\n\t\t<strong>Format 2 (With RefSeq isoforms):</strong> Each line has ten fields, five fields for each gene. For each gene join the following fields separated by a comma:\n\t\t<ol><li>Gene symbol</li>\n\t\t<li>Chromosome</li>\n\t\t<li>Position, 1-based coordinate</li>\n\t\t<li>Strand</li>\n\t\t<li>RefSeq isoform (e.g., NM_001754)</li>\n\t\t</ol>\n\t\tSeparate the two genes by a double colon (::). <br><br>\n\t\tExamples: <br>\n\t\t<p style=\"margin-left: 10px\">\n\t\t<strong>Format 1:</strong><br>\n\t\tPAX5,chr9,37002646,-::JAK2,chr9,5081726,+<br>\n\t\tZCCHC7,chr9,37257786,-::PAX5,chr9,37024824,-<br>\n\t\tBCR,chr22,23524427,+::ABL1,chr9,133729449,+<br><br>\n\t\t<strong>Format 2:</strong><br>\n\t\tRUNX1,chr21,36206706,-,NM_001754::MECOM,chr3,169099311,-,NM_004991<br>\n\t\tPAX5,chr9,37002646,-,NM_016734::JAK2,chr9,5081726,+,NM_004972<p>`)\n}\n\n/**\n * Validates a position string\n * @param {string} position - The position string to validate\n * @param {string} geneName - Gene name for error messages\n * @throws {Error} If position is invalid\n */\nfunction validatePosition(position, geneName) {\n\tif (!/^\\d+$/.test(position)) {\n\t\tthrow new Error(`Invalid fusion format: position for ${geneName} must be a positive integer`)\n\t}\n\tconst pos = Number(position)\n\tif (pos <= 0) {\n\t\tthrow new Error(`Invalid fusion format: position for ${geneName} must be greater than 0 (1-based coordinates)`)\n\t}\n}\n\n/**\n * Parses a fusion line into two gene arrays\n * Supports both formats:\n * - Format 1 (4 fields per gene): gene,chr,pos,strand\n * - Format 2 (5 fields per gene): gene,chr,pos,strand,isoform\n * @param {string} line - The fusion line to parse\n * @returns {Array} [gene1Array, gene2Array] where each array contains [gene, chr, pos, strand] and optionally [isoform]\n * @throws {Error} If the line format is invalid\n */\nexport function parseFusionLine(line) {\n\tconst parts = line.trim().split('::')\n\tif (parts.length !== 2) {\n\t\tthrow new Error('Invalid fusion format: must contain exactly two genes separated by \"::\"')\n\t}\n\n\tconst gene1 = parts[0].split(',').map(s => s.trim())\n\tconst gene2 = parts[1].split(',').map(s => s.trim())\n\n\t// Validate that each gene has either 4 fields (basic format) or 5 fields (with isoform)\n\tif ((gene1.length !== 4 && gene1.length !== 5) || (gene2.length !== 4 && gene2.length !== 5)) {\n\t\tthrow new Error(\n\t\t\t`Invalid fusion format: each gene must have 4 or 5 fields. Found gene1: ${gene1.length} fields, gene2: ${gene2.length} fields`\n\t\t)\n\t}\n\n\t// Validate required fields are not empty\n\tfor (let i = 0; i < 4; i++) {\n\t\tif (!gene1[i] || !gene2[i]) {\n\t\t\tthrow new Error('Invalid fusion format: gene symbol, chromosome, position, and strand are required')\n\t\t}\n\t}\n\n\t// Validate positions\n\tvalidatePosition(gene1[2], gene1[0])\n\tvalidatePosition(gene2[2], gene2[0])\n\n\t// Validate strand is + or -\n\tif (!/^[+-]$/.test(gene1[3]) || !/^[+-]$/.test(gene2[3])) {\n\t\tthrow new Error('Invalid fusion format: strand must be \"+\" or \"-\"')\n\t}\n\n\treturn [gene1, gene2]\n}\n\n/**\n * Creates a fusion variant object from gene arrays\n * @param {Array} gene1 - First gene array [gene, chr, pos, strand, (isoform)]\n * @param {Array} gene2 - Second gene array [gene, chr, pos, strand, (isoform)]\n * @returns {Object} Variant object for proteinpaint\n */\nfunction createFusionVariant(gene1, gene2) {\n\tconst variant = {\n\t\tgene1: gene1[0],\n\t\tchr1: gene1[1],\n\t\tpos1: parseInt(gene1[2]) - 1,\n\t\tstrand1: gene1[3],\n\t\tgene2: gene2[0],\n\t\tchr2: gene2[1],\n\t\tpos2: parseInt(gene2[2]) - 1,\n\t\tstrand2: gene2[3],\n\t\tdt: 2,\n\t\tclass: 'Fuserna'\n\t}\n\t// Add isoform information if available (check for non-empty strings)\n\tconst addIsoformIfPresent = (gene, fieldName) => {\n\t\tif (gene.length > 4 && gene[4]?.trim()) {\n\t\t\tvariant[fieldName] = gene[4].trim()\n\t\t}\n\t}\n\taddIsoformIfPresent(gene1, 'isoform1')\n\taddIsoformIfPresent(gene2, 'isoform2')\n\treturn variant\n}\n\nfunction makeSubmitResult(obj, div, runpp_arg) {\n\t// Filter out empty lines\n\tconst lines = obj.data.split(/[\\r\\n]/).filter(line => line.trim().length > 0)\n\n\tif (lines.length === 1) {\n\t\t//Only one line entered, no dropdown\n\t\ttry {\n\t\t\tconst [gene1, gene2] = parseFusionLine(lines[0])\n\t\t\treturn makeFusionTabs(div, runpp_arg, gene1, gene2)\n\t\t} catch (error) {\n\t\t\tconst errorDiv = div.append('div').style('color', 'red').style('margin', '20px')\n\t\t\tsayerror(errorDiv, `Error parsing fusion: ${error.message}`)\n\t\t\treturn\n\t\t}\n\t}\n\t//Make dropdown to select fusions\n\t//On select, toggle tabs for each gene appears underneath with the track for each gene\n\tconst fusionSelect = div\n\t\t.append('div')\n\t\t.append('select')\n\t\t.style('border-radius', '5px')\n\t\t.style('padding', '5px 10px')\n\t\t.style('margin', '1px 10px 1px 10px')\n\n\tfusionSelect.append('option').text(`Select Fusion (${lines.length})`)\n\n\tconst tabsDiv = div.append('div').style('margin', '20px')\n\n\tconst fusionsMap = new Map()\n\n\tfor (const data of lines) {\n\t\ttry {\n\t\t\tconst [gene1, gene2] = parseFusionLine(data)\n\t\t\tfusionsMap.set(`${gene1[0]}-${gene2[0]}`, [gene1, gene2])\n\t\t} catch (error) {\n\t\t\tconsole.warn(`Skipping invalid fusion line: ${data}. Error: ${error.message}`)\n\t\t}\n\t}\n\n\tif (fusionsMap.size === 0) {\n\t\tconst errorDiv = div.append('div').style('color', 'red').style('margin', '20px')\n\t\tsayerror(errorDiv, 'No valid fusion lines found. Please check the format.')\n\t\treturn\n\t}\n\n\tfor (const fusion of fusionsMap) {\n\t\tfusionSelect.append('option').property('value', fusion[0]).text(fusion[0])\n\t}\n\tfusionSelect.on('change', () => {\n\t\ttabsDiv.selectAll('*').remove()\n\t\tconst geneArrays = fusionsMap.get(fusionSelect.property('value'))\n\t\tmakeFusionTabs(tabsDiv, runpp_arg, geneArrays[0], geneArrays[1])\n\t})\n}\n\nfunction makeFusionTabs(div, runpp_arg, gene1, gene2) {\n\tconst tabs = [\n\t\t// {\n\t\t// ************ Keep for later, will introduce gene fusion view once data format settled *************\n\t\t// \tlabel: 'Fusion',\n\t\t// \tcallback: async div => {\n\t\t// \t\tif (!tabs[0].rendered) {\n\t\t// \t\t\tappear(div)\n\t\t// \t\t\tconst text = `${gene1[0]}, ${gene1[1]},${gene1[2]},${gene2[0]},${gene2[1]},${gene2[2]}`\n\t\t// \t\t\tconst runpp_arg = {\n\t\t// \t\t\t\tholder: div\n\t\t// \t\t\t\t\t.append('div')\n\t\t// \t\t\t\t\t.style('margin', '20px')\n\t\t// \t\t\t\t\t.node(),\n\t\t// \t\t\t\thost: window.location.origin,\n\t\t// \t\t\t\tnobox: true,\n\t\t// \t\t\t\tnoheader: true,\n\t\t// \t\t\t\tparseurl: false,\n\t\t// \t\t\t\tgenome,\n\t\t// \t\t\t\tgenefusion: {\n\t\t// \t\t\t\t\ttext,\n\t\t// \t\t\t\t\tpositionType: posType\n\t\t// \t\t\t\t\t}\n\t\t// \t\t\t\t}\n\t\t// \t\t\tconsole.log(runpp_arg)\n\t\t// \t\t\trunproteinpaint(Object.assign(runpp_arg))\n\t\t// \t\t\ttabs[0].rendered = true\n\t\t// \t\t}\n\t\t// \t}\n\t\t// },\n\t\t{\n\t\t\tlabel: gene1[0],\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\tappear(tab.contentHolder)\n\t\t\t\tconst variant = createFusionVariant(gene1, gene2)\n\t\t\t\tconst fusion_arg = {\n\t\t\t\t\tholder: tab.contentHolder.append('div').style('margin', '20px').node(),\n\t\t\t\t\tgene: gene1[0],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\t\tname: gene1[0],\n\t\t\t\t\t\t\tcustom_variants: [variant]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t\trunproteinpaint(Object.assign(runpp_arg, fusion_arg))\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: gene2[0],\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\tappear(tab.contentHolder)\n\t\t\t\tconst variant = createFusionVariant(gene1, gene2)\n\t\t\t\tconst fusion_arg = {\n\t\t\t\t\tholder: tab.contentHolder.append('div').style('margin', '20px').node(),\n\t\t\t\t\tgene: gene2[0],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\t\tname: gene2[0],\n\t\t\t\t\t\t\tcustom_variants: [variant]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t\trunproteinpaint(Object.assign(runpp_arg, fusion_arg))\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t}\n\t]\n\n\tnew Tabs({ holder: div, tabs }).main()\n}\n"],
-  "mappings": 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