@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/block.tk.ase-BPU25OLX.js

@@ -1,360 +0,0 @@
-import {
-  configPanel_rnabam,
-  rnabamtk_initparam
-} from "./chunk-AB6JQFIQ.js";
-import {
-  ase_color,
-  init_config,
-  measure,
-  showsingleitem_table
-} from "./chunk-Z4HW3FEE.js";
-import {
-  axisstyle,
-  keyupEnter,
-  make_table_2col
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch
-} from "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import {
-  bplen
-} from "./chunk-UYKJOBRO.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import {
-  axisLeft
-} from "./chunk-Z2ZITHT4.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.tk.ase.js
-async function loadTk(tk, block) {
-  block.tkcloakon(tk);
-  block.block_setheight();
-  if (tk.uninitialized) {
-    makeTk(tk, block);
-  }
-  const regions = [];
-  let xoff = 0;
-  for (let i = block.startidx; i <= block.stopidx; i++) {
-    const r = block.rglst[i];
-    regions.push({
-      chr: r.chr,
-      start: r.start,
-      stop: r.stop,
-      width: r.width,
-      x: xoff
-    });
-    xoff += r.width + block.regionspace;
-  }
-  if (block.subpanels.length == tk.subpanels.length) {
-    for (const [idx, r] of block.subpanels.entries()) {
-      xoff += r.leftpad;
-      regions.push({
-        chr: r.chr,
-        start: r.start,
-        stop: r.stop,
-        width: r.width,
-        exonsf: r.exonsf,
-        subpanelidx: idx,
-        x: xoff
-      });
-      xoff += r.width;
-    }
-  }
-  tk.regions = regions;
-  try {
-    tk.dna.coveragemax = 0;
-    if (tk.rna.coverageauto) tk.rna.coveragemax = 0;
-    for (const r of regions) {
-      await getdata_region(r, tk, block);
-    }
-    renderTk(tk, block);
-    block.tkcloakoff(tk, {});
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    tk.height_main = tk.height = 100;
-    block.tkcloakoff(tk, { error: e.message || e });
-  }
-  block.block_setheight();
-}
-function getdata_region(r, tk, block) {
-  const arg = {
-    genome: block.genome.name,
-    samplename: tk.samplename,
-    rnabamfile: tk.rnabamfile,
-    rnabamurl: tk.rnabamurl,
-    rnabamindexURL: tk.rnabamindexURL,
-    rnabamtotalreads: tk.rnabamtotalreads,
-    rnabamispairedend: tk.rnabamispairedend,
-    vcffile: tk.vcffile,
-    vcfurl: tk.vcfurl,
-    vcfindexURL: tk.vcfindexURL,
-    rnabarheight: tk.rna.coveragebarh,
-    dnabarheight: tk.dna.coveragebarh,
-    barypad: tk.barypad,
-    chr: r.chr,
-    start: r.start,
-    stop: r.stop,
-    width: r.width,
-    checkrnabam: tk.checkrnabam,
-    refcolor: tk.dna.refcolor,
-    altcolor: tk.dna.altcolor,
-    devicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1
-  };
-  if (!tk.rna.coverageauto) {
-    arg.rnamax = tk.rna.coveragemax;
-  }
-  return dofetch("ase", arg).then((data) => {
-    if (data.error) throw data.error;
-    r.genes = data.genes;
-    r.fpkmrangelimit = data.fpkmrangelimit;
-    if (data.covplotrangelimit) {
-      r.covplotrangelimit = data.covplotrangelimit;
-    } else {
-      r.coveragesrc = data.coveragesrc;
-      tk.dna.coveragemax = Math.max(tk.dna.coveragemax, data.dnamax);
-      if (tk.rna.coverageauto) {
-        tk.rna.coveragemax = Math.max(tk.rna.coveragemax, data.rnamax);
-      }
-    }
-  });
-}
-function renderTk(tk, block) {
-  tk.glider.selectAll("*").remove();
-  for (const p of tk.subpanels) {
-    p.glider.attr("transform", "translate(0,0)").selectAll("*").remove();
-  }
-  renderTk_covplot(tk, block);
-  renderTk_fpkm(tk, block);
-  block.setllabel();
-  tk.height_main += tk.toppad + tk.bottompad;
-}
-function renderTk_covplot(tk, block) {
-  const noploth = 30;
-  const anyregionwithcovplot = tk.regions.find((r) => r.coveragesrc);
-  if (anyregionwithcovplot) {
-    axisstyle({
-      axis: tk.rna.coverageaxisg.attr("transform", "scale(1) translate(0,0)").call(
-        axisLeft().scale(linear().domain([0, tk.rna.coveragemax]).range([tk.rna.coveragebarh, 0])).tickValues([0, tk.rna.coveragemax])
-      ),
-      showline: true
-    });
-    tk.tklabel.attr("y", tk.rna.coveragebarh / 2 - 7);
-    tk.rna.coveragelabel.attr("y", tk.rna.coveragebarh / 2 + 2).attr("transform", "scale(1)");
-    axisstyle({
-      axis: tk.dna.coverageaxisg.attr("transform", "scale(1) translate(0," + (tk.rna.coveragebarh + tk.barypad) + ")").call(
-        axisLeft().scale(linear().domain([0, tk.dna.coveragemax]).range([0, tk.dna.coveragebarh])).tickValues([0, tk.dna.coveragemax])
-      ),
-      showline: true
-    });
-    tk.dna.coveragelabel.attr("transform", "scale(1)").attr("y", tk.rna.coveragebarh + tk.barypad + tk.dna.coveragebarh / 2).each(function() {
-      tk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width);
-    });
-    tk.height_main = tk.rna.coveragebarh + tk.barypad + tk.dna.coveragebarh;
-  } else {
-    tk.dna.coverageaxisg.attr("transform", "scale(0)");
-    tk.rna.coverageaxisg.attr("transform", "scale(0)");
-    tk.dna.coveragelabel.attr("transform", "scale(0)");
-    tk.rna.coveragelabel.attr("transform", "scale(0)");
-    tk.height_main = noploth;
-  }
-  for (const r of tk.regions) {
-    if (r.covplotrangelimit) {
-      tk.glider.append("text").text("Zoom in under " + bplen(r.covplotrangelimit) + " to show coverage plot").attr("font-size", block.laelfontsize).attr("text-anchor", "middle").attr("x", r.x + r.width / 2).attr("y", noploth / 2);
-      continue;
-    }
-    tk.glider.append("image").attr("x", r.x).attr("width", r.width).attr("height", tk.rna.coveragebarh + tk.barypad + tk.dna.coveragebarh).attr("xlink:href", r.coveragesrc);
-  }
-}
-function renderTk_fpkm(tk, block) {
-  const noploth = 30;
-  const anyregionwithfpkm = tk.regions.find((r) => !r.fpkmrangelimit);
-  let maxfpkm = 0;
-  for (const r of tk.regions) {
-    if (r.fpkmrangelimit) continue;
-    if (r.genes) {
-      for (const g of r.genes) {
-        if (Number.isFinite(g.fpkm)) maxfpkm = Math.max(maxfpkm, g.fpkm);
-        measure(g, tk.gecfg);
-      }
-    }
-  }
-  const y = tk.height_main + tk.yspace1;
-  if (anyregionwithfpkm && maxfpkm > 0) {
-    axisstyle({
-      axis: tk.fpkm.axisg.attr("transform", "scale(1) translate(0," + y + ")").call(
-        axisLeft().scale(linear().domain([0, maxfpkm]).range([tk.fpkm.barh, 0])).tickValues([0, maxfpkm])
-      ),
-      showline: true
-    });
-    tk.fpkm.label.attr("y", y + tk.fpkm.barh / 2).attr("transform", "scale(1)");
-    tk.height_main += tk.yspace1 + tk.fpkm.barh;
-  } else {
-    tk.fpkm.axisg.attr("transform", "scale(0)");
-    tk.fpkm.label.attr("transform", "scale(0)");
-    tk.height_main += noploth;
-  }
-  for (const r of tk.regions) {
-    if (r.fpkmrangelimit) {
-      tk.glider.append("text").text("Zoom in under " + bplen(r.fpkmrangelimit) + " to show gene " + tk.gecfg.datatype + " values").attr("font-size", block.laelfontsize).attr("text-anchor", "middle").attr("x", r.x + r.width / 2).attr("y", y + noploth / 2);
-      continue;
-    }
-    if (!r.genes) continue;
-    if (maxfpkm == 0) {
-      continue;
-    }
-    const rsf = r.width / (r.stop - r.start);
-    for (const gene of r.genes) {
-      if (!Number.isFinite(gene.fpkm)) continue;
-      const color = ase_color(gene, tk.gecfg);
-      const boxh = tk.fpkm.barh * gene.fpkm / maxfpkm;
-      let x1, x2;
-      if (r.reverse) {
-        x1 = r.x + rsf * (r.stop - Math.min(r.stop, gene.stop));
-        x2 = r.x + rsf * (r.stop - Math.max(r.start, gene.start));
-      } else {
-        x1 = r.x + rsf * (Math.max(r.start, gene.start) - r.start);
-        x2 = r.x + rsf * (Math.min(r.stop, gene.stop) - r.start);
-      }
-      const line = tk.glider.append("line").attr("x1", x1).attr("x2", x2).attr("y1", y + tk.fpkm.barh - boxh).attr("y2", y + tk.fpkm.barh - boxh).attr("stroke", color).attr("stroke-width", 2).attr("stroke-opacity", 0.4);
-      const box = tk.glider.append("rect").attr("x", x1).attr("y", y + tk.fpkm.barh - boxh).attr("width", x2 - x1).attr("height", boxh).attr("fill", color).attr("fill-opacity", 0.2);
-      tk.glider.append("rect").attr("x", x1).attr("y", y + tk.fpkm.barh - boxh - 2).attr("width", x2 - x1).attr("height", boxh + 2).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event2) => {
-        line.attr("stroke-opacity", 0.5);
-        box.attr("fill-opacity", 0.3);
-        tooltip_genefpkm(gene, tk);
-      }).on("mouseout", (event2) => {
-        line.attr("stroke-opacity", 0.4);
-        box.attr("fill-opacity", 0.2);
-        tk.tktip.hide();
-      });
-    }
-  }
-}
-function tooltip_genefpkm(gene, tk) {
-  tk.tktip.clear().show(event.clientX, event.clientY);
-  const lst = [
-    {
-      k: gene.gene + " " + tk.gecfg.datatype,
-      v: gene.fpkm
-    }
-  ];
-  const table = make_table_2col(tk.tktip.d, lst);
-  showsingleitem_table(gene, tk.gecfg, table);
-}
-function makeTk(tk, block) {
-  delete tk.uninitialized;
-  if (!tk.barypad) tk.barypad = 0;
-  if (!tk.rna) tk.rna = {};
-  tk.rna.coverageaxisg = tk.gleft.append("g");
-  tk.rna.coveragelabel = block.maketklefthandle(tk).attr("class", null).attr("dominant-baseline", "hanging").text("RNA coverage");
-  tk.rna.coverageauto = true;
-  if (!tk.rna.coveragebarh) tk.rna.coveragebarh = 50;
-  if (!tk.dna) tk.dna = {};
-  tk.dna.coverageaxisg = tk.gleft.append("g");
-  tk.dna.coveragelabel = block.maketklefthandle(tk).attr("class", null).text("DNA coverage");
-  tk.dna.coveragemax = 0;
-  if (!tk.dna.coveragebarh) tk.dna.coveragebarh = 50;
-  if (!tk.dna.refcolor) tk.dna.refcolor = "#188FF5";
-  if (!tk.dna.altcolor) tk.dna.altcolor = "#F51818";
-  if (!tk.yspace1) tk.yspace1 = 15;
-  tk.gecfg = { datatype: "FPKM" };
-  init_config(tk.gecfg);
-  if (!tk.fpkm) tk.fpkm = {};
-  tk.fpkm.axisg = tk.gleft.append("g");
-  tk.fpkm.label = block.maketklefthandle(tk).attr("class", null).text("Gene " + tk.gecfg.datatype);
-  if (!tk.fpkm.barh) tk.fpkm.barh = 50;
-  tk.config_handle = block.maketkconfighandle(tk).attr("y", 10 + block.labelfontsize).on("click", (event2) => {
-    configPanel(tk, block);
-  });
-  if (!tk.checkrnabam) tk.checkrnabam = {};
-  rnabamtk_initparam(tk.checkrnabam);
-}
-function configPanel(tk, block) {
-  tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-  const d = tk.tkconfigtip.d.append("div");
-  d.append("div").text("RNA-seq coverage is shown at all covered bases.").style("font-size", ".8em").style("opacity", 0.5);
-  {
-    const row = d.append("div").style("margin", "5px 0px");
-    row.append("span").html("Bar height&nbsp;");
-    row.append("input").attr("type", "numeric").property("value", tk.rna.coveragebarh).style("width", "80px").on("keyup", (event2) => {
-      if (!keyupEnter(event2)) return;
-      const v = Number.parseInt(event2.target.value);
-      if (v <= 20) return;
-      if (v == tk.rna.coveragebarh) return;
-      tk.rna.coveragebarh = v;
-      loadTk(tk, block);
-    });
-  }
-  {
-    const row = d.append("div").style("margin", "5px 0px");
-    const id = Math.random();
-    row.append("input").attr("type", "checkbox").attr("id", id).property("checked", tk.rna.coverageauto).on("change", (event2) => {
-      tk.rna.coverageauto = event2.target.checked;
-      fixed.style("display", tk.rna.coverageauto ? "none" : "inline");
-      loadTk(tk, block);
-    });
-    row.append("label").html("&nbsp;automatic scale").attr("for", id);
-    const fixed = row.append("div").style("display", tk.rna.coverageauto ? "none" : "inline").style("margin-left", "20px");
-    fixed.append("span").html("Fixed max&nbsp");
-    fixed.append("input").attr("value", "numeric").property("value", tk.rna.coveragemax).style("width", "50px").on("keyup", (event2) => {
-      if (!keyupEnter(event2)) return;
-      const v = Number.parseInt(event2.target.value);
-      if (v <= 0) return;
-      if (v == tk.rna.coveragemax) return;
-      tk.rna.coveragemax = v;
-      loadTk(tk, block);
-    });
-  }
-  d.append("div").text("SNPs are only shown for those heterozygous in DNA.").style("font-size", ".8em").style("opacity", 0.5).style("margin-top", "25px");
-  {
-    const row = d.append("div").style("margin", "5px 0px");
-    row.append("span").html("Bar height&nbsp;");
-    row.append("input").attr("type", "numeric").property("value", tk.dna.coveragebarh).style("width", "80px").on("keyup", (event2) => {
-      if (!keyupEnter(event2)) return;
-      const v = Number.parseInt(event2.target.value);
-      if (v <= 20) return;
-      if (v == tk.dna.coveragebarh) return;
-      tk.dna.coveragebarh = v;
-      loadTk(tk, block);
-    });
-  }
-  {
-    const row = d.append("div").style("margin", "5px 0px 25px 0px");
-    row.append("span").html("Allele color&nbsp;&nbsp;Ref:&nbsp;");
-    row.append("input").attr("type", "color").property("value", tk.dna.refcolor).on("change", (event2) => {
-      tk.dna.refcolor = event2.target.value;
-      loadTk(tk, block);
-    });
-    row.append("span").html("&nbsp;Alt:&nbsp;");
-    row.append("input").attr("type", "color").property("value", tk.dna.altcolor).on("change", (event2) => {
-      tk.dna.altcolor = event2.target.value;
-      loadTk(tk, block);
-    });
-  }
-  configPanel_rnabam(tk, block, loadTk);
-}
-export {
-  loadTk
-};
-//# sourceMappingURL=block.tk.ase-BPU25OLX.js.map