@sjcrh/proteinpaint-client 2.224.2 → 2.225.0

package/dist/block.tk.junction.textmatrixui-FL5MZH7K.js

@@ -1,190 +0,0 @@
-import {
-  first_genetrack_tolist,
-  newpane3,
-  renderSandboxFormDiv,
-  tkt
-} from "./chunk-ZIMAIUZD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-AQSZLUDV.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-BOQYGAYA.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-ZUXXBQ7D.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-ZUG4EY4T.js";
-import "./chunk-5FD6NRGE.js";
-import "./chunk-R2H22S4J.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.tk.junction.textmatrixui.js
-function block_tk_junction_textmatrixui_default(genomes, hostURL, jwt, holder) {
-  let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
-  if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
-  else {
-    ;
-    [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
-    pane.header.text("Splice junctions by sample matrix visualization");
-  }
-  filediv.append("p").text("Enter junction-by-sample read count matrix data:");
-  const ul = filediv.append("ul").style("color", "#858585").style("font-size", ".8em");
-  ul.append("li").text("The matrix is tab-delimited, junctions on rows, samples on columns.");
-  ul.append("li").text("First row lists sample names");
-  ul.append("li").text("Each row is one junction, with read count in each sample");
-  ul.append("li").text("Junction position example: chr21:39739570:+,chr21:39817327:+[,type], the type is optional");
-  ul.append("li").text("Junction start and stop positions are 1-based and should be exonic bases but not intronic.");
-  const ta1 = filediv.append("div").append("textarea").attr("rows", 6).attr("cols", 50).attr("placeholder", "junction-by-sample matrix");
-  setTimeout(() => ta1.node().focus(), 1100);
-  const p = filediv.append("p");
-  p.append("button").text("Submit").on("click", () => {
-    saydiv.text("");
-    const gn = gselect.options[gselect.selectedIndex].innerHTML;
-    const genomeobj = genomes[gn];
-    if (!genomeobj) {
-      saydiv.text("invalid genome name: " + gn);
-      return;
-    }
-    const v = ta1.property("value");
-    if (v == "") {
-      return;
-    }
-    const [err, junctions, samples] = junction_parsematrix(v, genomeobj);
-    if (err) {
-      saydiv.text(err);
-      return;
-    }
-    const range = /* @__PURE__ */ new Map();
-    for (const j of junctions) {
-      if (!range.has(j.chr)) {
-        range.set(j.chr, {
-          chr: j.chr,
-          start: j.start,
-          stop: j.stop
-        });
-      }
-      range.get(j.chr).start = Math.min(j.start, range.get(j.chr).start);
-      range.get(j.chr).stop = Math.max(j.stop, range.get(j.chr).stop);
-    }
-    const arange = [...range][0][1];
-    const tracks = [
-      {
-        type: tkt.junction,
-        name: "Junction",
-        fixeddata: junctions,
-        tracks: [
-          {
-            samplecount: samples.length
-          }
-        ],
-        iscustom: true
-      }
-    ];
-    first_genetrack_tolist(genomeobj, tracks);
-    import("./block-DXRSU62C.js").then(
-      (b) => new b.Block({
-        hostURL,
-        jwt,
-        holder: holder !== void 0 ? holder : pane.body.append("div"),
-        genome: genomeobj,
-        chr: arange.chr,
-        start: arange.start,
-        stop: Math.min(arange.start + 1e5, arange.stop),
-        nobox: true,
-        tklst: tracks
-      })
-    );
-    inputdiv.remove();
-  });
-  p.append("button").text("Clear").on("click", () => {
-    ta1.property("value", "");
-  });
-  filediv.append("p").html("<a href=https://www.dropbox.com/s/xu52ke9cify24hw/junction.txt?dl=0 target=_blank>Example file</a>");
-}
-function junction_parsematrix(text, gn) {
-  const lines = text.trim().split("\n");
-  if (lines.length <= 1) {
-    return ["input should be at least 2 lines"];
-  }
-  const lst = lines[0].split("	");
-  const samples = [];
-  for (let i = 1; i < lst.length; i++) {
-    samples.push({
-      tkid: Math.random().toString(),
-      type: tkt.junction,
-      name: lst[i]
-    });
-  }
-  const junctions = [];
-  for (let i = 1; i < lines.length; i++) {
-    const jstr = lines[i].split("	")[0];
-    const [e, j] = junction_parsecoord(jstr, gn);
-    if (e) return ["Error parsing junction " + jstr + ": " + e];
-    j.data = [];
-    junctions.push(j);
-  }
-  if (junctions.length == 0) {
-    return ["No valid junctions"];
-  }
-  for (let i = 1; i < lines.length; i++) {
-    const lst2 = lines[i].split("	");
-    for (let j = 1; j < lst2.length; j++) {
-      if (lst2[j] == "") {
-        continue;
-      }
-      const readcount = Number.parseInt(lst2[j]);
-      if (Number.isNaN(readcount) || readcount < 0) {
-        return ["invalid read count " + lst2[j] + " at line " + (i + 1)];
-      }
-      if (readcount == 0) {
-        continue;
-      }
-      junctions[i - 1].data.push({
-        tkid: samples[j - 1].tkid,
-        sample: samples[j - 1].name,
-        v: readcount
-      });
-    }
-  }
-  return [null, junctions, samples];
-}
-function junction_parsecoord(s, g) {
-  const lst = s.split(",");
-  if (lst.length < 2) return ["expecting two fields separated by comma"];
-  const a = lst[0].split(":"), b = lst[1].split(":"), jtype = lst[2];
-  if (a.length != 3) return ["left position not 3 fields by :"];
-  if (b.length != 3) return ["right position not 3 fields by :"];
-  if (a[0] != b[0]) return ["disagreeing chromosomes"];
-  const pos1 = Number.parseInt(a[1]);
-  const pos2 = Number.parseInt(b[1]);
-  if (isNaN(pos1)) return ["invalid position 1"];
-  if (isNaN(pos2)) return ["invalid position 2"];
-  const start = Math.min(pos1, pos2) - 1;
-  const stop = Math.max(pos1, pos2) - 1;
-  let name = a[0].toLowerCase();
-  if (name.indexOf("chr") != 0) {
-    name = "chr" + name;
-  }
-  const chr = g.chrlookup[name.toUpperCase()];
-  if (!chr) return ["invalid chromosome"];
-  if (start <= 0 || start >= chr.len) return ["position 1 out of bound"];
-  if (stop <= 0 || stop >= chr.len) return ["position 2 out of bound"];
-  if (start >= stop) return ["start greater than stop"];
-  const j = { chr: chr.name, start, stop };
-  if (jtype) {
-    j.type = jtype;
-  }
-  return [null, j];
-}
-export {
-  block_tk_junction_textmatrixui_default as default
-};
-//# sourceMappingURL=block.tk.junction.textmatrixui-FL5MZH7K.js.map

package/dist/block.tk.ld-JKBXDOB5.js

@@ -1,90 +0,0 @@
-import {
-  showLDlegend
-} from "./chunk-N6AHRJAM.js";
-import {
-  legend_newrow
-} from "./chunk-RSCSTOUN.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-MUVXIOXM.js";
-import "./chunk-ZIMAIUZD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-AQSZLUDV.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-BOQYGAYA.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-ZUXXBQ7D.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-ZUG4EY4T.js";
-import "./chunk-5FD6NRGE.js";
-import "./chunk-R2H22S4J.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb_default
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.tk.ld.js
-async function loadTk(tk, block) {
-  if (tk.uninitiated) {
-    makeTk(tk, block);
-  }
-  block.tkcloakon(tk);
-  try {
-    const arg = {
-      genome: block.genome.name,
-      file: tk.file,
-      rglst: block.tkarg_rglst(tk),
-      width: block.width,
-      devicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1
-    };
-    const data = await dofetch3("tkld", { method: "POST", body: arg });
-    if (data.error) throw data.error;
-    tk.rglstG.selectAll("*").remove();
-    let tkheight = 0;
-    for (const r of data.rglst) {
-      const g = tk.rglstG.append("g");
-      if (r.rangetoobig) {
-        r.text_rangetoobig = g.append("text").text(r.rangetoobig).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("x", r.width / 2);
-        tkheight = Math.max(tkheight, 50);
-        continue;
-      }
-      if (r.img) {
-        g.append("image").attr("width", r.width).attr("height", r.img.height).attr("xlink:href", r.img.src);
-        tkheight = Math.max(tkheight, r.img.height);
-        continue;
-      }
-    }
-    tk.height_main = tk.toppad + tkheight + tk.bottompad;
-    block.tkcloakoff(tk, {});
-  } catch (e) {
-    tk.height_main = 50;
-    block.tkcloakoff(tk, { error: e.message || e });
-  }
-  block.block_setheight(tk);
-}
-function makeTk(tk, block) {
-  delete tk.uninitiated;
-  tk.rglstG = tk.glider.append("g");
-  const [tr, td] = legend_newrow(block, tk.name);
-  tk.tr_legend = tr;
-  tk.legend = {
-    div: td.append("div")
-  };
-  tk.legend.div.html("LD r<sup>2</sup>");
-  const scale = rgb_default("white", "red");
-  showLDlegend(tk.legend.div, scale);
-}
-export {
-  loadTk
-};
-//# sourceMappingURL=block.tk.ld-JKBXDOB5.js.map