@sjcrh/proteinpaint-client 2.194.0 → 2.195.0

package/dist/block.init-3BF6L23D.js

@@ -0,0 +1,38 @@
+import {
+  block_init_default
+} from "./chunk-D3TU3RDU.js";
+import "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  block_init_default as default
+};
+//# sourceMappingURL=block.init-3BF6L23D.js.map

package/dist/block.mds.expressionrank-DSHATA2M.js

@@ -0,0 +1,359 @@
+import {
+  ase_color,
+  init_config,
+  measure,
+  showsingleitem_table
+} from "./chunk-RG222M4S.js";
+import {
+  axisstyle,
+  make_table_2col,
+  newpane,
+  ranksays
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import {
+  dofetch,
+  dofetch3
+} from "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import {
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import {
+  linear
+} from "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.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-RXQUOE3Y.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-DSHATA2M.js.map