@sjcrh/proteinpaint-client 2.223.0 → 2.224.0

package/dist/block.init-MPTACJCT.js

@@ -1,29 +0,0 @@
-import {
-  block_init_default
-} from "./chunk-2CDIFQPW.js";
-import "./chunk-JP4IU7DO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-IRAB3OI7.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.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";
-export {
-  block_init_default as default
-};
-//# sourceMappingURL=block.init-MPTACJCT.js.map

package/dist/block.mds.expressionrank-EZBNMSDP.js

@@ -1,350 +0,0 @@
-import {
-  ase_color,
-  init_config,
-  measure,
-  showsingleitem_table
-} from "./chunk-SFLKPHIF.js";
-import {
-  axisstyle,
-  make_table_2col,
-  newpane,
-  ranksays
-} from "./chunk-JP4IU7DO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-IRAB3OI7.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch,
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import {
-  axisLeft
-} from "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.mds.expressionrank.js
-async function loadTk(tk, block) {
-  block.tkcloakon(tk);
-  block.block_setheight();
-  if (tk.uninitialized) {
-    makeTk(tk, block);
-    delete tk.uninitialized;
-  }
-  const regions = [];
-  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
-    });
-  }
-  if (block.subpanels.length == tk.subpanels.length) {
-    for (const [idx, r] of block.subpanels.entries()) {
-      regions.push({
-        chr: r.chr,
-        start: r.start,
-        stop: r.stop,
-        width: r.width,
-        exonsf: r.exonsf,
-        subpanelidx: idx
-      });
-    }
-  }
-  tk.regions = regions;
-  const tasks = [];
-  for (const r of regions) {
-    const arg = {
-      jwt: block.jwt,
-      genome: block.genome.name,
-      rglst: [{ chr: r.chr, start: r.start, stop: r.stop }],
-      sample: tk.sample
-    };
-    if (tk.iscustom) {
-      arg.iscustom = 1;
-      arg.file = tk.file;
-      arg.url = tk.url;
-      arg.indexURL = tk.indexURL;
-    } else {
-      arg.dslabel = tk.mds.label;
-      arg.querykey = tk.querykey;
-      arg.attributes = tk.attributes;
-    }
-    tasks.push(
-      dofetch("/mdsexpressionrank", arg).then((data) => {
-        if (data.error) throw { message: data.error };
-        if (data.result && data.result.length > 0) {
-          r.items = data.result;
-        }
-        tk.totalsamples = data.samplecount;
-        return;
-      })
-    );
-  }
-  Promise.all(tasks).then(() => {
-    if (!tk.regions.find((r) => r.items)) throw { message: "no data in view range" };
-  }).catch((err) => {
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    return err.message;
-  }).then((errmsg) => {
-    renderTk(tk, block);
-    block.tkcloakoff(tk, { error: errmsg });
-  });
-}
-function renderTk(tk, block) {
-  tk.glider.selectAll("*").remove();
-  for (const p of tk.subpanels) {
-    p.glider.attr("transform", "translate(0,0)").selectAll("*").remove();
-  }
-  let minv = null, maxv;
-  if (tk.showrank) {
-    minv = 0;
-    maxv = 100;
-  } else {
-    for (const r of tk.regions) {
-      if (!r.items) continue;
-      for (const i of r.items) {
-        if (minv == null) {
-          minv = maxv = i.thisvalue;
-        } else {
-          minv = Math.min(minv, i.thisvalue);
-          maxv = Math.max(maxv, i.thisvalue);
-        }
-      }
-    }
-    if (minv > 0) minv = 0;
-    else if (maxv < 0) maxv = 0;
-  }
-  const scale = bar_plot_y(minv, maxv, tk.barheight);
-  for (const r of tk.regions) {
-    if (!r.items) continue;
-    const g = r.subpanelidx != void 0 ? tk.subpanels[r.subpanelidx].glider : tk.glider;
-    for (const i of r.items) {
-      const startcoord = Math.max(r.start, i.start);
-      const stopcoord = Math.min(r.stop, i.stop);
-      let x1, x2;
-      if (r.subpanelidx != void 0) {
-        x1 = (startcoord - r.start) * r.exonsf;
-        x2 = (stopcoord - r.start) * r.exonsf;
-      } else {
-        const a = block.seekcoord(r.chr, startcoord)[0];
-        const b = block.seekcoord(r.chr, stopcoord)[0];
-        if (!a || !b) continue;
-        x1 = Math.min(a.x, b.x);
-        x2 = Math.max(a.x, b.x);
-      }
-      const [y, h] = scale(tk.showrank ? i.rank : i.thisvalue);
-      measure(i, tk.gecfg);
-      const barcolor = ase_color(i, tk.gecfg);
-      const tt = rgb(barcolor);
-      const fillcolor = "rgba(" + tt.r + "," + tt.g + "," + tt.b + ",.2)";
-      const ig = g.append("g").attr("transform", "translate(" + x1 + ",0)");
-      ig.append("line").attr("x2", Math.max(2, x2 - x1)).attr("stroke", barcolor).attr("stroke-width", 1).attr("shape-rendering", "crispEdges").attr("y1", i.rank > 0 ? y : y + h).attr("y2", i.rank > 0 ? y : y + h);
-      ig.append("rect").attr("y", y).attr("width", Math.max(2, x2 - x1)).attr("height", h).attr("fill", fillcolor).attr("shape-rendering", "crispEdges").on("mouseover", (event) => {
-        event.target.setAttribute("stroke", barcolor);
-        tk.tktip.clear().show(event.clientX, event.clientY);
-        const lst = [
-          { k: "gene", v: i.gene },
-          { k: "rank", v: ranksays(i.rank) },
-          { k: tk.gecfg.datatype || "actual value", v: i.thisvalue }
-        ];
-        const table = make_table_2col(tk.tktip.d, lst).style("margin", "0px");
-        {
-          const tr = table.append("tr");
-          const td = tr.append("td").attr("colspan", 3);
-          td.text(i.chr + ":" + i.start + "-" + i.stop);
-        }
-        showsingleitem_table(i, tk.gecfg, table);
-      }).on("mouseout", (event) => {
-        tk.tktip.hide();
-        event.target.setAttribute("stroke", "");
-      }).on("click", (event) => {
-        const pane = newpane({ x: event.clientX, y: event.clientY });
-        pane.header.text(i.gene + " " + tk.gecfg.datatype);
-        const p = {
-          gene: i.gene,
-          chr: i.chr,
-          start: i.start,
-          stop: i.stop,
-          holder: pane.body,
-          genome: block.genome,
-          jwt: block.jwt,
-          hostURL: block.hostURL,
-          sample: { name: tk.sample, value: i.thisvalue }
-        };
-        if (tk.iscustom) {
-          p.file = tk.file;
-          p.url = tk.url;
-          p.indexURL = tk.indexURL;
-        } else {
-          p.dslabel = tk.mds.label;
-          p.querykey = tk.querykey;
-        }
-        import("./block.mds.geneboxplot-R6BS44BH.js").then((_) => {
-          _.init(p);
-        });
-      });
-    }
-  }
-  tk.rankaxis.label.text(tk.showrank ? "Rank" : tk.gecfg.datatype || "actual value");
-  axisstyle({
-    axis: tk.rankaxis.g.call(
-      axisLeft().scale(
-        linear().domain([minv, maxv]).range([tk.barheight, 0])
-      ).tickValues([minv, maxv])
-    ),
-    showline: true
-  });
-  set_height(tk, block);
-}
-function bar_plot_y(min, max, tkh) {
-  return (v) => {
-    if (min < 0) {
-      if (max <= 0) {
-        return [0, Math.max(1, tkh * v / min)];
-      }
-      const fs2 = tkh / (max - min);
-      if (v > 0) return [fs2 * (max - v), Math.max(1, fs2 * v)];
-      return [fs2 * max, Math.max(1, fs2 * -v)];
-    }
-    const fs = tkh / max;
-    return [fs * (max - v), Math.max(1, fs * v)];
-  };
-}
-function set_height(tk, block) {
-  tk.tklabel.attr("y", tk.barheight / 2 - block.labelfontsize / 2);
-  tk.rankaxis.label.attr("y", tk.barheight / 2 + block.labelfontsize / 2);
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  block.block_setheight();
-}
-async function makeTk(tk, block) {
-  if (!tk.sample) throw "sample name missing";
-  if (tk.dslabel) {
-    delete tk.iscustom;
-  }
-  if (tk.iscustom) {
-    if (!tk.file && !tk.url) throw "file or url missing for custom tk";
-    if (!tk.gecfg) tk.gecfg = {};
-  } else {
-    if (!tk.dslabel) throw "dslabel missing for native track";
-    if (!tk.querykey) throw "querykey missing for native track";
-    tk.mds = block.genome.datasets[tk.dslabel];
-    if (!tk.mds) throw "dataset not found: invalid value for dslabel";
-    if (tk.mds.mdsIsUninitiated) {
-      const d = await dofetch3(`getDataset?genome=${block.genome.name}&dsname=${tk.dslabel}`);
-      if (d.error) throw d.error;
-      if (!d.ds) throw "ds missing";
-      Object.assign(tk.mds, d.ds);
-      delete tk.mds.mdsIsUninitiated;
-    }
-    delete tk.dslabel;
-    tk.gecfg = tk.mds.queries[tk.querykey];
-    if (!tk.gecfg) throw "expression query not found: invalid value for querykey";
-  }
-  if (tk.datatype) {
-    tk.gecfg.datatype = tk.datatype;
-    delete tk.datatype;
-  }
-  if (!tk.barheight) tk.barheight = 60;
-  if (!("showrank" in tk)) tk.showrank = true;
-  if (!tk.gecfg.itemcolor) {
-    tk.gecfg.itemcolor = "green";
-  }
-  init_config(tk.gecfg);
-  tk.rankaxis = {
-    g: tk.gleft.append("g"),
-    label: block.maketklefthandle(tk).attr("class", null)
-  };
-  tk.config_handle = block.maketkconfighandle(tk).attr("y", 10 + block.labelfontsize).on("click", (event) => {
-    configPanel(tk, block);
-  });
-}
-function configPanel(tk, block) {
-  tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-  {
-    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "15px");
-    row.append("span").html("Height&nbsp;&nbsp;");
-    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
-      if (event.key != "Enter") return;
-      const s = event.target.value;
-      if (s == "") return;
-      const v = Number.parseInt(s);
-      if (Number.isNaN(v) || v <= 1) {
-        alert("track height must be positive integer");
-        return;
-      }
-      tk.barheight = v;
-      renderTk(tk, block);
-    });
-  }
-  {
-    const table = tk.tkconfigtip.d.append("table").style("margin-bottom", "15px").style("border-spacing", "5px");
-    const radioname = Math.random();
-    let rrank, rvalue;
-    {
-      const tr = table.append("tr");
-      tr.append("td").text("Show");
-      const td = tr.append("td");
-      rvalue = td.append("input").attr("type", "radio").attr("name", radioname).attr("id", radioname + 2).on("change", (event) => {
-        tk.showrank = false;
-        renderTk(tk, block);
-      });
-      td.append("label").html("&nbsp;" + (tk.gecfg.datatype || "actual value")).attr("for", radioname + 2).attr("class", "sja_clbtext");
-    }
-    {
-      const tr = table.append("tr");
-      tr.append("td");
-      const td = tr.append("td");
-      rrank = td.append("input").attr("type", "radio").attr("name", radioname).attr("id", radioname + 1).on("change", (event) => {
-        tk.showrank = true;
-        renderTk(tk, block);
-      });
-      td.append("label").html("&nbsp;Rank of a group of samples").attr("for", radioname + 1).attr("class", "sja_clbtext").style("margin-right", "10px");
-      const lst = [];
-      if (tk.attributes) {
-        for (const a of tk.attributes) {
-          lst.push({ k: a.label || a.k, v: a.fullvalue || a.kvalue });
-        }
-      }
-      if (tk.totalsamples) {
-        lst.push({ k: "Total number of samples", v: tk.totalsamples + 1 });
-      }
-      if (lst.length) {
-        make_table_2col(td, lst);
-      }
-    }
-    if (tk.showrank) {
-      rrank.property("checked", 1);
-    } else {
-      rvalue.property("checked", 1);
-    }
-  }
-  {
-  }
-}
-export {
-  loadTk
-};
-//# sourceMappingURL=block.mds.expressionrank-EZBNMSDP.js.map