@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

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-VYIO7T6J.js

@@ -0,0 +1,82 @@
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// plots/matrix/matrix.dom.js
+function setMatrixDom(opts) {
+  const holder = opts.controls ? opts.holder : opts.holder.append("div");
+  holder.style("position", "relative");
+  const controls = this.opts.controls || holder.append("div");
+  const errorDiv = holder.append("div");
+  const loadingDiv = holder.append("div").style("position", "relative").style("top", this.opts.controls ? 0 : "50px").style("left", "50px");
+  const errdiv = holder.append("div").attr("class", "sja_errorbar").style("display", "none");
+  const warningDiv = holder.append("div").attr("class", "sja_errorbar").style("display", "none");
+  const svg = holder.append("svg").attr("data-testid", "sjpp-matrix-svg").style("margin", "20px").style("overflow", "visible").on("mousemove.label", this.svgMousemove).on("mouseup.label", this.svgMouseup);
+  this.seriesClipId = `sjpp_clip_${this.id}`;
+  const mainG = svg.append("g").attr("class", "sjpp-matrix-maing").on("mouseover", this.showCellInfo).on("mousemove", this.showCellInfo).on("mouseout", this.mouseout);
+  const rectsG = mainG.append("g").attr("clip-path", `url(#${this.seriesClipId})`);
+  const sampleLabelsPG = mainG.append("g");
+  const termLabelsPG = mainG.append("g");
+  const tip = new Menu({ padding: "5px" });
+  this.dom = {
+    header: opts.header,
+    holder,
+    contentNode: opts.holder.node().closest(".sjpp-output-sandbox-content") || opts.holder.node().parentNode,
+    errdiv,
+    warningDiv,
+    controls,
+    errorDiv,
+    loadingDiv,
+    svg,
+    clipRect: svg.append("defs").append("clipPath").attr("id", this.seriesClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block"),
+    mainG,
+    cluster: rectsG.append("g").attr("class", "sjpp-matrix-cluster-g").on("mousedown", this.seriesesGMousedown).on("mousemove", this.seriesesGMousemove),
+    //.on('mouseup', this.seriesesGMouseup),
+    seriesesG: rectsG.append("g").attr("class", "sjpp-matrix-serieses-g").attr("data-testid", "sjpp_matrix_mainG_serieses").on("mousedown", this.seriesesGMousedown),
+    //.on('mousemove', this.seriesesGMousemove)
+    //.on('mouseup', this.seriesesGMouseup),
+    highlightBeamG: rectsG.append("g").attr("class", "sjpp-matrix-highlight-beam"),
+    sampleLabelsPG,
+    sampleGrpLabelG: sampleLabelsPG.append("g").attr("class", "sjpp-matrix-series-group-label-g").on("click", this.showSampleGroupMenu).on("mousedown.sjppMatrixLabelText", this.enableTextHighlight).on("mouseup.sjppMatrixLabelText", this.disableTextHighlight),
+    sampleLabelG: sampleLabelsPG.append("g").attr("class", "sjpp-matrix-series-label-g").on("click", (event) => this.mouseclick(event)),
+    /* // TODO: sample label drag to move
+    	.on('mouseover', this.sampleLabelMouseover)
+    	.on('mouseout', this.sampleLabelMouseout)
+    	.on('mousedown', this.sampleLabelMousedown)
+    	.on('mousemove', this.sampleLabelMousemove)
+    	.on('mouseup', this.sampleLabelMouseup)*/
+    termLabelsPG,
+    termGrpLabelG: termLabelsPG.append("g").attr("class", "sjpp-matrix-term-group-label-g").on("mouseover", this.termGrpLabelMouseover).on("mouseout", this.termGrpLabelMouseout).on("mousedown", this.termGrpLabelMousedown).on("mousemove", this.termGrpLabelMousemove).on("mouseup", this.termGrpLabelMouseup).on("mousedown.sjppMatrixLabelText", this.enableTextHighlight).on("mouseup.sjppMatrixLabelText", this.disableTextHighlight),
+    termLabelG: termLabelsPG.append("g").attr("class", "sjpp-matrix-term-label-g").on("mouseover", this.termLabelMouseover).on("mouseout", this.termLabelMouseout).on("mousedown", this.termLabelMousedown).on("mousemove", this.termLabelMousemove).on("mouseup", this.termLabelMouseup).on("mousedown.sjppMatrixLabelText", this.enableTextHighlight).on("mouseup.sjppMatrixLabelText", this.disableTextHighlight),
+    scroll: mainG.append("g"),
+    //legendDiv: holder.append('div').style('margin', '5px 5px 15px 50px'),
+    legendG: mainG.append("g").attr("class", "sjpp-matrix-legend-g").on("mouseover", this.legendLabelMouseover).on("mouseout", this.legendLabelMouseout).on("mouseup", this.legendLabelMouseup),
+    // !!! Do NOT use self.dom.tip.clear(), since it will also get rid of menutop and menubody
+    tip,
+    menutop: tip.d.append("div"),
+    menubody: tip.d.append("div"),
+    clickMenu: new Menu({ padding: "0px" }),
+    brushMenu: new Menu({ padding: "0px" }),
+    dendroClickMenu: new Menu({ padding: "0px" }),
+    legendMenu: new Menu({ padding: "0px" }),
+    matrixCellHoverOver: new Menu({ padding: "0px" })
+  };
+  this.dom.colBeam = this.dom.highlightBeamG.append("rect").style("display", "none").style("stroke-width", "0.5px").style("fill", "transparent").style("pointer-events", "none");
+  this.dom.rowBeam = this.dom.highlightBeamG.append("rect").style("display", "none").style("stroke-width", "0.5px").style("fill", "transparent").style("pointer-events", "none");
+  this.dom.tip.onHide = () => {
+    this.lastActiveLabel = this.activeLabel;
+    delete this.activeLabel;
+  };
+  select_default("body").on(`mousedown.matrixZoom-${this.id}`, this.resetInteractions);
+  window.onscroll = this.delayedMouseoutHandler;
+  const contentDiv = this.dom.holder.node().closest(".sjpp-output-sandbox-content");
+  if (contentDiv) contentDiv.onscroll = this.delayedMouseoutHandler;
+}
+
+export {
+  setMatrixDom
+};
+//# sourceMappingURL=chunk-VYIO7T6J.js.map

package/dist/chunk-VYIO7T6J.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.dom.js"],
+  "sourcesContent": ["import { Menu } from '#dom/menu'\nimport { select } from 'd3-selection'\n\nexport function setMatrixDom(opts) {\n\tconst holder = opts.controls ? opts.holder : opts.holder.append('div')\n\tholder.style('position', 'relative')\n\tconst controls = this.opts.controls || holder.append('div')\n\tconst errorDiv = holder.append('div')\n\tconst loadingDiv = holder\n\t\t.append('div')\n\t\t.style('position', 'relative')\n\t\t.style('top', this.opts.controls ? 0 : '50px')\n\t\t.style('left', '50px')\n\tconst errdiv = holder.append('div').attr('class', 'sja_errorbar').style('display', 'none')\n\tconst warningDiv = holder.append('div').attr('class', 'sja_errorbar').style('display', 'none')\n\tconst svg = holder\n\t\t.append('svg')\n\t\t.attr('data-testid', 'sjpp-matrix-svg')\n\t\t.style('margin', '20px')\n\t\t.style('overflow', 'visible')\n\t\t.on('mousemove.label', this.svgMousemove)\n\t\t.on('mouseup.label', this.svgMouseup)\n\n\tthis.seriesClipId = `sjpp_clip_${this.id}`\n\n\tconst mainG = svg\n\t\t.append('g')\n\t\t.attr('class', 'sjpp-matrix-maing')\n\t\t//.style('overflow', 'hidden')\n\t\t.on('mouseover', this.showCellInfo)\n\t\t.on('mousemove', this.showCellInfo)\n\t\t.on('mouseout', this.mouseout)\n\n\tconst rectsG = mainG.append('g').attr('clip-path', `url(#${this.seriesClipId})`)\n\t// parent g for sample, term labels g\n\tconst sampleLabelsPG = mainG.append('g')\n\tconst termLabelsPG = mainG.append('g')\n\tconst tip = new Menu({ padding: '5px' })\n\n\tthis.dom = {\n\t\theader: opts.header,\n\t\tholder,\n\t\tcontentNode: opts.holder.node().closest('.sjpp-output-sandbox-content') || opts.holder.node().parentNode,\n\t\terrdiv,\n\t\twarningDiv,\n\t\tcontrols,\n\t\terrorDiv,\n\t\tloadingDiv,\n\t\tsvg,\n\t\tclipRect: svg\n\t\t\t.append('defs')\n\t\t\t.append('clipPath')\n\t\t\t.attr('id', this.seriesClipId)\n\t\t\t//.attr('clipPathUnits', 'objectBoundingBox')\n\t\t\t.attr('clipPathUnits', 'userSpaceOnUse')\n\t\t\t.append('rect')\n\t\t\t.attr('display', 'block'),\n\t\tmainG,\n\t\tcluster: rectsG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-cluster-g')\n\t\t\t.on('mousedown', this.seriesesGMousedown)\n\t\t\t.on('mousemove', this.seriesesGMousemove),\n\t\t//.on('mouseup', this.seriesesGMouseup),\n\t\tseriesesG: rectsG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-serieses-g')\n\t\t\t.attr('data-testid', 'sjpp_matrix_mainG_serieses')\n\t\t\t.on('mousedown', this.seriesesGMousedown),\n\t\t//.on('mousemove', this.seriesesGMousemove)\n\t\t//.on('mouseup', this.seriesesGMouseup),\n\n\t\thighlightBeamG: rectsG.append('g').attr('class', 'sjpp-matrix-highlight-beam'),\n\n\t\tsampleLabelsPG,\n\t\tsampleGrpLabelG: sampleLabelsPG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-series-group-label-g')\n\t\t\t.on('click', this.showSampleGroupMenu)\n\t\t\t.on('mousedown.sjppMatrixLabelText', this.enableTextHighlight)\n\t\t\t.on('mouseup.sjppMatrixLabelText', this.disableTextHighlight),\n\t\tsampleLabelG: sampleLabelsPG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-series-label-g')\n\t\t\t// .on('mousedown.sjppMatrixLabelText', this.enableTextHighlight)\n\t\t\t// .on('mouseup.sjppMatrixLabelText', this.disableTextHighlight)\n\t\t\t.on('click', event => this.mouseclick(event)),\n\t\t/* // TODO: sample label drag to move\n\t\t\t.on('mouseover', this.sampleLabelMouseover)\n\t\t\t.on('mouseout', this.sampleLabelMouseout)\n\t\t\t.on('mousedown', this.sampleLabelMousedown)\n\t\t\t.on('mousemove', this.sampleLabelMousemove)\n\t\t\t.on('mouseup', this.sampleLabelMouseup)*/\n\t\ttermLabelsPG,\n\t\ttermGrpLabelG: termLabelsPG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-term-group-label-g')\n\t\t\t.on('mouseover', this.termGrpLabelMouseover)\n\t\t\t.on('mouseout', this.termGrpLabelMouseout)\n\t\t\t.on('mousedown', this.termGrpLabelMousedown)\n\t\t\t.on('mousemove', this.termGrpLabelMousemove)\n\t\t\t.on('mouseup', this.termGrpLabelMouseup)\n\t\t\t.on('mousedown.sjppMatrixLabelText', this.enableTextHighlight)\n\t\t\t.on('mouseup.sjppMatrixLabelText', this.disableTextHighlight),\n\t\ttermLabelG: termLabelsPG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-term-label-g')\n\t\t\t.on('mouseover', this.termLabelMouseover)\n\t\t\t.on('mouseout', this.termLabelMouseout)\n\t\t\t.on('mousedown', this.termLabelMousedown)\n\t\t\t.on('mousemove', this.termLabelMousemove)\n\t\t\t.on('mouseup', this.termLabelMouseup)\n\t\t\t.on('mousedown.sjppMatrixLabelText', this.enableTextHighlight)\n\t\t\t.on('mouseup.sjppMatrixLabelText', this.disableTextHighlight),\n\t\tscroll: mainG.append('g'),\n\t\t//legendDiv: holder.append('div').style('margin', '5px 5px 15px 50px'),\n\t\tlegendG: mainG\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-legend-g')\n\t\t\t.on('mouseover', this.legendLabelMouseover)\n\t\t\t.on('mouseout', this.legendLabelMouseout)\n\t\t\t.on('mouseup', this.legendLabelMouseup),\n\t\t// !!! Do NOT use self.dom.tip.clear(), since it will also get rid of menutop and menubody\n\t\ttip,\n\t\tmenutop: tip.d.append('div'),\n\t\tmenubody: tip.d.append('div'),\n\t\tclickMenu: new Menu({ padding: '0px' }),\n\t\tbrushMenu: new Menu({ padding: '0px' }),\n\t\tdendroClickMenu: new Menu({ padding: '0px' }),\n\t\tlegendMenu: new Menu({ padding: '0px' }),\n\t\tmatrixCellHoverOver: new Menu({ padding: '0px' })\n\t}\n\n\tthis.dom.colBeam = this.dom.highlightBeamG\n\t\t.append('rect')\n\t\t.style('display', 'none')\n\t\t.style('stroke-width', '0.5px')\n\t\t.style('fill', 'transparent')\n\t\t.style('pointer-events', 'none')\n\n\tthis.dom.rowBeam = this.dom.highlightBeamG\n\t\t.append('rect')\n\t\t.style('display', 'none')\n\t\t.style('stroke-width', '0.5px')\n\t\t.style('fill', 'transparent')\n\t\t.style('pointer-events', 'none')\n\n\tthis.dom.tip.onHide = () => {\n\t\tthis.lastActiveLabel = this.activeLabel\n\t\tdelete this.activeLabel\n\t}\n\n\t// remove the matrix brush zoom area when clicking on body\n\tselect('body').on(`mousedown.matrixZoom-${this.id}`, this.resetInteractions)\n\n\twindow.onscroll = this.delayedMouseoutHandler\n\tconst contentDiv = this.dom.holder.node().closest('.sjpp-output-sandbox-content')\n\tif (contentDiv) contentDiv.onscroll = this.delayedMouseoutHandler\n}\n"],
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+}