@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/chunk-V6DLLX4N.js

@@ -0,0 +1,176 @@
+import {
+  __glob
+} from "./chunk-HFNDKYVF.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/DziViewer.js": () => import("./DziViewer-CF4WILTI.js"),
+  "../plots/alphaGenome.js": () => import("./alphaGenome-FSIGC5ZT.js"),
+  "../plots/barchart.data.js": () => import("./barchart.data-EXENRVMU.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-XRGND6I7.js"),
+  "../plots/barchart.js": () => import("./barchart-4Q6LVJY4.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-S7A7I6BQ.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-VSOOMITW.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-U6T6VRBD.js"),
+  "../plots/controls.config.js": () => import("./controls.config-TA4NNARU.js"),
+  "../plots/controls.js": () => import("./controls-324AGOZG.js"),
+  "../plots/cuminc.js": () => import("./cuminc-4DY2CSZF.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-3AE2N7KI.js"),
+  "../plots/dictionary.js": () => import("./dictionary-WHDZBW5M.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-DWXPOOQE.js"),
+  "../plots/facet.js": () => import("./facet-ZCSXKXIO.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-T6TQCJ3O.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-X2KXJPND.js"),
+  "../plots/geneORA.js": () => import("./geneORA-B5UK77KL.js"),
+  "../plots/geneset.js": () => import("./geneset-673KAZVX.js"),
+  "../plots/gsea.js": () => import("./gsea-25LD2LGP.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-M5VVWKQK.js"),
+  "../plots/imagePlot.js": () => import("./imagePlot-FPXZ2H5Z.js"),
+  "../plots/importPlot.js": () => import("./importPlot-VKWPSFEK.js"),
+  "../plots/matrix.js": () => import("./matrix-US3OXYRY.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-EDO3SH2P.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-FEFZDXML.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-7KU3K52V.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-A6MEGO2B.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-U7AQNEBP.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-43E3HCDL.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-Q57D7C3F.js"),
+  "../plots/matrix/matrix.controls.js": () => import("./matrix.controls-AWXDRSWP.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-EEIY6AO4.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-6QL3AJMW.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-CUB6UWC5.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-JW4AXAWO.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-73KRNXLM.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-I56KRVCO.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-42LQGAGX.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-IX3FCNBK.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-4B2WB526.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-BJACNR7G.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-W6XFYZY2.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-UOX7J2XD.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-PQH67KRM.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-3KKDKIPY.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-CMJ7EBIW.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-FEP7BR7L.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-U643YIK7.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-3BV6YEBC.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-GXB2GZO3.js"),
+  "../plots/proteomeAbundance.js": () => import("./proteomeAbundance-DE4NVBCN.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-2LU2XRGC.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-G57GL57T.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-JSEM3PXL.js"),
+  "../plots/regression.js": () => import("./regression-TTQTAEGD.js"),
+  "../plots/regression.results.js": () => import("./regression.results-3YNM6LLQ.js"),
+  "../plots/report.js": () => import("./report-YRAV4MY4.js"),
+  "../plots/sampleView.js": () => import("./sampleView-IUR3ZEN7.js"),
+  "../plots/scatter/test/scatter.integration.spec.js": () => import("./scatter.integration.spec-6KRDNHHH.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-IWFEG44C.js"),
+  "../plots/stattable.js": () => import("./stattable-XXEIFPGM.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-C5YXOY77.js"),
+  "../plots/table.js": () => import("./table-PQB6KCEY.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-VQITP4YH.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-SFQPLMSF.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-DKOT6BJP.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-EDPX7V6K.js"),
+  "../plots/test/profile.spec.js": () => import("./profile.spec-JRW6KYUI.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-XJQJAIC3.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-S6WFCPSW.js"),
+  "../plots/test/sampleScatter.spec.js": () => import("./sampleScatter.spec-MBJ4XNTX.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-ULGRPICW.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-A4PNR4ES.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-TS4DYUE5.js"),
+  "../plots/violin.js": () => import("./violin-DPMJLHQG.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-53L4PXUT.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-E2LLE6HI.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-ZT3XKBBT.js");
+    case "barchart":
+      return await import("./barchart-4Q6LVJY4.js");
+    case "boxplot":
+      return await import("./BoxPlot-QGHLZ67V.js");
+    case "chat":
+      return await import("./chat-LW23PIG5.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-7SE4CTBW.js");
+    case "dictionary":
+      return await import("./dictionary-WHDZBW5M.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-L6BOEYVO.js");
+    case "Disco":
+      return await import("./Disco-6FDT6KRM.js");
+    case "dmr":
+      return await import("./DmrPlot-3R24PTXP.js");
+    case "genomeBrowser":
+      return await import("./GB-SZVYZASR.js");
+    case "grin2":
+      return await import("./grin2-OALS75LC.js");
+    case "gsea":
+      return await import("./gsea-25LD2LGP.js");
+    case "runChart2":
+    case "frequencyChart":
+      return await import("./RunChart2-ASGCKKER.js");
+    case "sampleScatter":
+      return await import("./scatter-SAHKZRFL.js");
+    case "sc":
+      return await import("./SC-H2YCKSBH.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-NWX4M6LZ.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-N5VTE2G6.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-5RHSG7L6.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-22YYXGS5.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-VV7CVAA7.js");
+    case "summaryInput":
+      return await import("./summaryInput-IH4EVNF5.js");
+    case "summary":
+      return await import("./summary-P3WIKJS7.js");
+    case "proteinView":
+      return await import("./proteinView-K3JFNORQ.js");
+    case "survival":
+      return await import("./survival-2ZE3N62A.js");
+    case "DEinput":
+      return await import("./DEinput-UZEQIU2V.js");
+    case "table":
+      return await import("./table-PQB6KCEY.js");
+    case "violin":
+      return await import("./violin-DPMJLHQG.js");
+    case "volcano":
+      return await import("./Volcano-QBYYJYVW.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-CXGWPCDL.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-NDHWFVAB.js");
+    case "profileRadar":
+      return await import("./profileRadar-ICEASI7W.js");
+    case "profileRadarFacility":
+      return await import("./profileRadarFacility-NFMRNJYX.js");
+    case "profileBarchart":
+      return await import("./profileBarchart-N7HJMYZ5.js");
+    case "profilePolar":
+      return await import("./polar-MZLIUXHO.js");
+    case "profilePolar2":
+      return await import("./polar2-IUVHNQM4.js");
+    case "profileForms":
+      return await import("./profileForms-Q5TPGPQP.js");
+    case "profilePlot":
+      return await import("./profilePlot-TXTUYDVE.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-V6DLLX4N.js.map

package/dist/chunk-V6DLLX4N.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/importPlot.js"],
+  "sourcesContent": ["export async function importPlot(chartType, notFoundMessage = '') {\n\t// TODO: move to dynamic import of exact plot names here, instead of string-pattern,\n\t// so that the bundler does not have to guess code file extension, directory names and letter casing\n\tswitch (chartType) {\n\t\tcase 'AIProjectAdmin':\n\t\t\treturn await import('./aiProjectAdmin/AIProjectAdmin.ts')\n\n\t\tcase 'barchart':\n\t\t\treturn await import(`./barchart.js`)\n\n\t\tcase 'boxplot':\n\t\t\treturn await import(`./boxplot/BoxPlot.ts`)\n\n\t\tcase 'chat':\n\t\t\treturn await import(`./chat/chat.ts`)\n\n\t\tcase 'correlationVolcano':\n\t\t\treturn await import(`./corrVolcano/CorrelationVolcano.ts`)\n\n\t\tcase 'dictionary':\n\t\t\treturn await import(`./dictionary.js`)\n\n\t\tcase 'differentialAnalysis':\n\t\t\treturn await import(`./diffAnalysis/DifferentialAnalysis.ts`)\n\n\t\tcase 'Disco':\n\t\t\treturn await import('./disco/Disco.ts')\n\n\t\tcase 'dmr':\n\t\t\treturn await import('./dmr/DmrPlot.ts')\n\n\t\tcase 'genomeBrowser':\n\t\t\treturn await import('./gb/GB.ts')\n\n\t\tcase 'grin2':\n\t\t\treturn await import('./grin2/grin2')\n\n\t\tcase 'gsea':\n\t\t\treturn await import(`./gsea.js`)\n\n\t\tcase 'runChart2':\n\t\tcase 'frequencyChart':\n\t\t\treturn await import(`./runChart2/RunChart2.ts`)\n\n\t\tcase 'sampleScatter':\n\t\t\treturn await import(`./scatter/scatter.js`)\n\n\t\tcase 'sc':\n\t\t\treturn await import('./sc/SC.ts')\n\n\t\tcase 'summarizeCnvGeneexp':\n\t\t\treturn await import(`./summarizeCnvGeneexp.ts`)\n\n\t\tcase 'summarizeGeneexpSurvival':\n\t\t\treturn await import(`./summarizeGeneexpSurvival.ts`)\n\n\t\tcase 'summarizeMutationDiagnosis':\n\t\t\treturn await import(`./summarizeMutationDiagnosis.ts`)\n\n\t\tcase 'summarizeMutationSurvival':\n\t\t\treturn await import(`./summarizeMutationSurvival.ts`)\n\n\t\tcase 'summarizeMutationCnv':\n\t\t\treturn await import(`./summarizeMutationCnv.ts`)\n\n\t\tcase 'summaryInput':\n\t\t\treturn await import(`./summaryInput.ts`)\n\n\t\tcase 'summary':\n\t\t\treturn await import(`./summary.ts`)\n\n\t\tcase 'proteinView':\n\t\t\treturn await import(`./proteinView.ts`)\n\t\tcase 'survival':\n\t\t\treturn await import(`./survival/survival.js`)\n\n\t\tcase 'DEinput':\n\t\t\treturn await import(`./DEinput.ts`)\n\n\t\tcase 'table':\n\t\t\treturn await import(`./table.js`)\n\n\t\tcase 'violin':\n\t\t\treturn await import(`./violin.js`)\n\n\t\tcase 'volcano':\n\t\t\treturn await import(`./volcano/Volcano.ts`)\n\n\t\tcase 'WSISamplesPlot':\n\t\t\treturn await import('./wsisamples/WsiSamplesPlot.ts')\n\n\t\tcase 'WSIViewer':\n\t\t\treturn await import('./wsiviewer/WSIViewer.ts')\n\n\t\tcase 'profileRadar':\n\t\t\treturn await import('./profile/profileRadar.ts')\n\n\t\tcase 'profileRadarFacility':\n\t\t\treturn await import('./profile/profileRadarFacility.ts')\n\n\t\tcase 'profileBarchart':\n\t\t\treturn await import('./profile/profileBarchart.ts')\n\n\t\tcase 'profilePolar':\n\t\t\treturn await import('./profile/polar.ts')\n\n\t\tcase 'profilePolar2':\n\t\t\treturn await import('./profile/polar2.ts')\n\n\t\tcase 'profileForms':\n\t\t\treturn await import('./profile/profileForms.ts')\n\n\t\tcase 'profilePlot':\n\t\t\treturn await import('./profile/profilePlot.ts')\n\n\t\tdefault:\n\t\t\t// temporary option to force an error, to bypass the default filename matching\n\t\t\tif (notFoundMessage) throw notFoundMessage\n\n\t\t\t// TODO: should always throw here once all chart types are handled separately as cases;\n\t\t\t// the pattern matching below is problematic because:\n\t\t\t// - it matches non-plot code file names\n\t\t\t// - it assumes a non-typescript, .js file extension\n\t\t\t// - it doesn't handle plot code that are organized under its own subdirectory\n\t\t\treturn await import(`../plots/${chartType}.js`)\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-VIPMLSZP.js

@@ -0,0 +1,217 @@
+import {
+  dofetch,
+  dofetch2
+} from "./chunk-7RN3L2BX.js";
+import {
+  contigNameNoChr2
+} from "./chunk-XYFDBYOY.js";
+
+// tracks/hic/data/parseData.ts
+async function hicParseFile(hic, debugmode, errList = []) {
+  if (debugmode) window["hic"] = hic;
+  if (hic.tklst) {
+    const lst = [];
+    for (const t of hic.tklst) {
+      if (!t.type) {
+        errList.push("type missing from one of the tracks accompanying HiC");
+      } else {
+        t.iscustom = true;
+        lst.push(t);
+      }
+    }
+    if (lst.length) {
+      hic.tklst = lst;
+    } else {
+      delete hic.tklst;
+    }
+  }
+  if (hic.enzyme) {
+    if (hic.genome.hicenzymefragment) {
+      let frag = null;
+      for (const f of hic.genome.hicenzymefragment) {
+        if (f.enzyme == hic.enzyme) {
+          frag = f;
+          break;
+        }
+      }
+      if (frag) {
+        hic.enzymefile = frag.file;
+      } else {
+        errList.push("unknown enzyme: " + hic.enzyme);
+        delete hic.enzyme;
+      }
+    } else {
+      errList.push("no enzyme fragment information available for this genome");
+      delete hic.enzyme;
+    }
+  }
+  try {
+    if (hic.sv && hic.sv.file) {
+      const re = await dofetch(hic.hostURL + "/textfile", {
+        method: "POST",
+        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
+      });
+      const data2 = re.json();
+      const [err2, header, items] = parseSV(data2.text);
+      if (err2) throw { message: "Error parsing SV: " + err2 };
+      hic.sv.header = header;
+      hic.sv.items = items;
+    }
+    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
+    if (data.error) {
+      errList.push(data.error);
+      return;
+    }
+    const err = hicparsestat(hic, data.out);
+    if (err) throw { message: err };
+  } catch (err) {
+    errList.push(err.message || err);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+  }
+  return hic;
+}
+function parseSV(txt) {
+  const lines = txt.trim().split(/\r?\n/);
+  const [err, header] = parseSVheader(lines[0]);
+  if (err) return ["header error: " + err];
+  const items = [];
+  for (let i = 1; i < lines.length; i++) {
+    const line = lines[i];
+    if (line[0] == "#") continue;
+    const [e, m] = parseSVline(line, header);
+    if (e) return ["line " + (i + 1) + " error: " + e];
+    items.push(m);
+  }
+  return [null, header, items];
+}
+function parseSVheader(line) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_A missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_B missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("strand_a", "orta", "orienta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb", "orientb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("numreadsa");
+  if (i != -1) header[i] = "reads1";
+  i = htry("numreadsb");
+  if (i != -1) header[i] = "reads2";
+  return [null, header];
+}
+function parseSVline(line, header) {
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) return ["missing chr1"];
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) return ["missing chr2"];
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  if (!m.position1) return ["missing position1"];
+  let v = Number.parseInt(m.position1);
+  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
+  m.position1 = v;
+  if (!m.position2) return ["missing position2"];
+  v = Number.parseInt(m.position2);
+  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
+  m.position2 = v;
+  if (m.reads1) {
+    v = Number.parseInt(m.reads1);
+    if (Number.isNaN(v)) return ["reads1 invalid value"];
+    m.reads1 = v;
+  }
+  if (m.reads2) {
+    v = Number.parseInt(m.reads2);
+    if (Number.isNaN(v)) return ["reads2 invalid value"];
+    m.reads2 = v;
+  }
+  return [null, m];
+}
+function hicparsestat(hic, j) {
+  if (!j) return "cannot stat hic file";
+  hic.normalization = j.normalization;
+  hic.version = j.version;
+  if (!j.Chromosomes) return "Chromosomes not found in file stat";
+  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
+  if (j.chrorder.length == 0) return ".chrorder[] empty array";
+  hic.chrorder = j.chrorder;
+  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
+  hic.bpresolution = j["Base pair-delimited resolutions"];
+  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
+  hic.fragresolution = j["Fragment-delimited resolutions"];
+  const chrlst = [];
+  for (const chr in j.Chromosomes) {
+    chrlst.push(chr);
+  }
+  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
+  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
+  if (nochrcount > 0) {
+    hic.nochr = true;
+    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
+  }
+  hic.chrlst = [];
+  for (const chr of hic.genome.majorchrorder) {
+    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
+    if (chrlst.indexOf(c2) != -1) {
+      hic.chrlst.push(chr);
+    }
+  }
+}
+function hicparsefragdata(items) {
+  const id2coord = /* @__PURE__ */ new Map();
+  let min = null, max;
+  for (const i of items) {
+    if (!i.rest || !i.rest[0]) {
+      return ["items[].rest data problem"];
+    }
+    const id = Number.parseInt(i.rest[0]);
+    if (Number.isNaN(id)) {
+      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
+    }
+    id2coord.set(id, [i.start, i.stop]);
+    if (min == null) {
+      min = id;
+      max = id;
+    } else {
+      min = Math.min(min, id);
+      max = Math.max(max, id);
+    }
+  }
+  return [null, id2coord, min, max];
+}
+
+export {
+  hicParseFile,
+  hicparsestat,
+  hicparsefragdata
+};
+//# sourceMappingURL=chunk-VIPMLSZP.js.map

package/dist/chunk-VQPS4SXU.js

@@ -0,0 +1,97 @@
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist,
+  getDNAMethUnit,
+  sayerror
+} from "./chunk-OXJ2TWDO.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  DNA_METHYLATION
+} from "./chunk-6ITDJ5UR.js";
+
+// termdb/handlers/dnaMethylation.ts
+var SearchHandler = class {
+  init(opts) {
+    this.opts = opts;
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("margin", "10px 0px");
+    this.dom = {};
+    this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
+    this.dom.geneSearchDiv = holder.append("div");
+    this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: this.dom.geneSearchDiv,
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          await this.handleGeneSearch(geneSearch);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e.message || e));
+          if (e.stack) console.log(e.stack);
+        }
+      }
+    });
+  }
+  async handleGeneSearch(geneSearch) {
+    if (geneSearch.geneSymbol) {
+      const { chr, start, stop } = geneSearch;
+      if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
+        throw new Error("unable to retrieve gene coordinate");
+      this.dom.blockDiv.selectAll("*").remove();
+      this.dom.blockDiv.style("display", "block");
+      this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
+      const arg = {
+        holder: this.dom.blockDiv,
+        genome: this.opts.genomeObj,
+        // genome obj
+        chr,
+        start,
+        stop,
+        tklst: [],
+        nobox: true,
+        width: 500,
+        hidegenelegend: true,
+        debugmode: this.opts.debug
+      };
+      first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
+      const _ = await import("./block-2MABX5QO.js");
+      this.blockInstance = new _.Block(arg);
+      this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
+        const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
+        const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
+        await this.callback(term);
+      });
+    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
+      const { chr, start, stop } = geneSearch;
+      const term = this.makeTerm({ chr, start, stop });
+      await this.callback(term);
+    } else {
+      throw new Error("invalid gene search input");
+    }
+  }
+  makeTerm(opts) {
+    const { chr, start, stop } = opts;
+    if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
+    const unit = getDNAMethUnit("region", this.app.vocabApi);
+    const term = {
+      chr,
+      start,
+      stop,
+      type: DNA_METHYLATION,
+      unit,
+      genomicFeatureType: "region"
+    };
+    return term;
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-VQPS4SXU.js.map

package/dist/chunk-VQPS4SXU.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/dnaMethylation.ts"],
+  "sourcesContent": ["import { Menu, addGeneSearchbox, sayerror } from '#dom'\nimport { DNA_METHYLATION } from '#shared/terms.js'\nimport { getDNAMethUnit } from '#tw/dnaMethylation'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\n\n// TODO: currently, when inputting a single position (e.g. chr17:7661778 or chr17:7661778-7661778), the output is a region 400bp long. Need to support single position input.\n// TODO: verify whether coordiante is 0-based or 1-based (need to do the same for other search handlers e.g. geneVariant.ts, snp.ts, etc.)\n\nexport class SearchHandler {\n\topts: any\n\tcallback: any\n\tapp: any\n\tdom: any\n\tblockInstance: any\n\tinit(opts) {\n\t\tthis.opts = opts\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tconst holder = opts.holder.append('div').style('margin', '10px 0px')\n\t\tthis.dom = {}\n\t\tthis.dom.errDiv = holder.append('div').style('margin', '5px 0px').style('display', 'none')\n\t\tthis.dom.geneSearchDiv = holder.append('div')\n\t\tthis.dom.blockDiv = holder.append('div').style('display', 'none').style('margin', '15px 4px')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: opts.genomeObj,\n\t\t\trow: this.dom.geneSearchDiv,\n\t\t\tcallback: async () => {\n\t\t\t\ttry {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'none')\n\t\t\t\t\tawait this.handleGeneSearch(geneSearch)\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'block')\n\t\t\t\t\tsayerror(this.dom.errDiv, 'Error: ' + (e.message || e))\n\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tasync handleGeneSearch(geneSearch) {\n\t\tif (geneSearch.geneSymbol) {\n\t\t\t// gene input\n\t\t\t// embed block of gene locus to allow navigation to region of interest\n\t\t\tconst { chr, start, stop } = geneSearch\n\t\t\tif (!chr || !Number.isInteger(start) || !Number.isInteger(stop))\n\t\t\t\tthrow new Error('unable to retrieve gene coordinate')\n\n\t\t\tthis.dom.blockDiv.selectAll('*').remove()\n\t\t\tthis.dom.blockDiv.style('display', 'block')\n\t\t\tthis.dom.blockDiv.append('div').style('opacity', 0.6).text('Navigate genome browser to desired region')\n\n\t\t\tconst arg: any = {\n\t\t\t\tholder: this.dom.blockDiv,\n\t\t\t\tgenome: this.opts.genomeObj, // genome obj\n\t\t\t\tchr,\n\t\t\t\tstart,\n\t\t\t\tstop,\n\t\t\t\ttklst: [],\n\t\t\t\tnobox: true,\n\t\t\t\twidth: 500,\n\t\t\t\thidegenelegend: true,\n\t\t\t\tdebugmode: this.opts.debug\n\t\t\t}\n\t\t\tfirst_genetrack_tolist(this.opts.genomeObj, arg.tklst)\n\t\t\tconst _ = await import('#src/block')\n\t\t\tthis.blockInstance = new _.Block(arg)\n\n\t\t\tthis.dom.submitBtn = this.dom.blockDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-dnaMethylation-submitDiv')\n\t\t\t\t.style('margin', '10px 0px')\n\t\t\t\t.append('button')\n\t\t\t\t.style('border', 'none')\n\t\t\t\t.style('border-radius', '20px')\n\t\t\t\t.style('padding', '10px 15px')\n\t\t\t\t.text('Submit Region')\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tconst { chr, start, stop } = this.blockInstance.rglst[0]\n\t\t\t\t\tconst term = this.makeTerm({ chr, start, stop })\n\t\t\t\t\tawait this.callback(term)\n\t\t\t\t})\n\t\t} else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {\n\t\t\t// coordinate input\n\t\t\t// directly use coordinate to make term\n\t\t\tconst { chr, start, stop } = geneSearch\n\t\t\tconst term = this.makeTerm({ chr, start, stop })\n\t\t\tawait this.callback(term)\n\t\t} else {\n\t\t\tthrow new Error('invalid gene search input')\n\t\t}\n\t}\n\n\tmakeTerm(opts) {\n\t\tconst { chr, start, stop } = opts\n\t\tif (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error('invalid coordinate')\n\t\tconst unit = getDNAMethUnit('region', this.app.vocabApi)\n\n\t\tconst term = {\n\t\t\tchr,\n\t\t\tstart,\n\t\t\tstop,\n\t\t\ttype: DNA_METHYLATION,\n\t\t\tunit,\n\t\t\tgenomicFeatureType: 'region'\n\t\t}\n\t\treturn term\n\t}\n}\n"],
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+}