@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

package/dist/block.svg-7RCJLMAP.js

@@ -0,0 +1,159 @@
+import {
+  font,
+  getdomaintypes,
+  to_svg
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import {
+  mds3tkMclass,
+  morigin
+} from "./chunk-SB36AUG7.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./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.svg.js
+var ypad = 20;
+var xpad = 2;
+var rowh = 20;
+var rowpad = 3;
+var fontsize = 16;
+function block_svg_default(block) {
+  for (const tk of block.tklst) {
+    if (tk.config_handle) tk.config_handle.text("");
+    if (tk.label_close) tk.label_close.text("");
+  }
+  const oldheight = block.totalheight();
+  let newheight;
+  const [h1, g1] = proteindomain(block, oldheight + ypad);
+  const [h2, g2] = mclassorigin(block, oldheight + ypad);
+  newheight = oldheight + ypad + Math.max(h1, h2) + ypad;
+  block.svg.attr("height", newheight);
+  const lst = [];
+  if (block.usegm && block.usegm.name) lst.push(block.usegm.name);
+  if (block.usegm && block.usegm.isoform) lst.push(block.usegm.isoform);
+  to_svg(block.svg.node(), lst.length ? lst.join("_") : "screenshot");
+  for (const tk of block.tklst) {
+    if (tk.config_handle) tk.config_handle.text("CONFIG");
+    if (tk.label_close) tk.label_close.text("Close");
+  }
+  if (g1) g1.remove();
+  if (g2) g2.remove();
+  block.svg.attr("height", oldheight);
+}
+function proteindomain(block, height) {
+  const gm = block.usegm;
+  if (!gm) {
+    return [0, null];
+  }
+  const domains = getdomaintypes(gm);
+  if (domains.length == 0) {
+    return [0, null];
+  }
+  const showlst = [];
+  for (const domain of domains) {
+    if (!gm.domain_hidden[domain.name + domain.description]) {
+      showlst.push(domain);
+    }
+  }
+  if (showlst.length == 0) return [0, null];
+  const g = block.svg.append("g").attr("transform", "translate(" + (xpad + block.leftheadw) + "," + height + ")");
+  let h = 0;
+  for (const item of showlst) {
+    const row = g.append("g").attr("transform", "translate(0," + h + ")");
+    row.append("rect").attr("width", 15).attr("height", rowh).attr("stroke", item.stroke).attr("fill", item.fill).attr("shape-rendering", "crispEdges");
+    let w;
+    row.append("text").attr("x", 20).attr("y", rowh / 2).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("font-family", font).attr("fill", "black").text(item.name).each(function() {
+      w = this.getBBox().width;
+    });
+    if (item.description) {
+      row.append("text").attr("x", 30 + w).attr("y", rowh / 2).attr("dominant-baseline", "central").attr("font-size", 12).attr("font-family", font).attr("fill", "#858585").text(item.description.length > 80 ? item.description.substr(0, 70) + " ..." : item.description);
+    }
+    h += rowh + rowpad;
+  }
+  return [h, g];
+}
+function mclassorigin(block, height) {
+  if (!block.legend) {
+    return [0, null];
+  }
+  let totalitem = 0;
+  const mclass2show = getMclasses(block);
+  totalitem += mclass2show.length;
+  if (block.legend.morigins && block.legend.morigins.size > 0) {
+    for (const [cls, obj] of block.legend.morigins) {
+      if (!obj.hidden) {
+        totalitem++;
+      }
+    }
+  }
+  if (totalitem == 0) return [0, null];
+  let h = 0;
+  const g = block.svg.append("g").attr("transform", "translate(" + (xpad + block.leftheadw + block.lpad + block.width - 200) + "," + height + ")");
+  for (const [cls, count] of mclass2show) {
+    const { color, label } = mds3tkMclass(cls);
+    let label2 = label;
+    const tk = block.tklst.find((i) => i.type == "mds3");
+    if (tk) {
+      label2 = tk.mds?.termdbConfig?.mclass?.[cls]?.label || label;
+    }
+    const row = g.append("g").attr("transform", "translate(0," + h + ")");
+    row.append("circle").attr("cx", rowh / 2).attr("cy", rowh / 2).attr("r", rowh / 2).attr("fill", color);
+    row.append("text").text(`${label2}, n=${count}`).attr("x", rowh + 10).attr("y", rowh / 2).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("font-family", font).attr("fill", color);
+    h += rowh + rowpad;
+  }
+  if (block.legend.morigins && block.legend.morigins.size > 0) {
+    for (const [org, o] of block.legend.morigins) {
+      if (o.hidden) {
+        continue;
+      }
+      const row = g.append("g").attr("transform", "translate(0," + h + ")");
+      const circleg = row.append("g").attr("transform", "translate(5,0)");
+      circleg.html(morigin[org].legend);
+      row.append("text").text(morigin[org].label + ", n=" + o.count).attr("x", rowh + 10).attr("y", rowh / 2).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("font-family", font).attr("fill", "black");
+      h += rowh + rowpad;
+    }
+  }
+  return [h, g];
+}
+function getMclasses(block) {
+  const mclass2show = [];
+  if (block.legend.mclasses && block.legend.mclasses.size > 0) {
+    for (const [cls, o] of block.legend.mclasses) {
+      if (!o.hidden) mclass2show.push([cls, o.count]);
+    }
+  }
+  const tk = block.tklst.find((i) => i.type == "mds3");
+  if (tk && tk.legend?.mclass?.currentData) {
+    for (const m of tk.legend.mclass.currentData) {
+      if (!tk.legend.mclass.hiddenvalues.has(m[0])) {
+        mclass2show.push(m);
+      }
+    }
+  }
+  return mclass2show;
+}
+export {
+  block_svg_default as default
+};
+//# sourceMappingURL=block.svg-7RCJLMAP.js.map

package/dist/block.tk.aicheck-5N6EGZ6F.js

@@ -0,0 +1,278 @@
+import {
+  axisstyle,
+  font,
+  keyupEnter,
+  make_radios
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import {
+  dofetch3
+} from "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import "./chunk-SB36AUG7.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import {
+  axisLeft,
+  axisRight
+} 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.aicheck.js
+function makeTk(tk, block) {
+  tk.img = tk.glider.append("image");
+  if (!tk.dotsize) {
+    tk.dotsize = 1;
+  }
+  if (!tk.coveragemax) {
+    tk.coveragemax = 100;
+  }
+  if (!tk.vafheight) {
+    tk.vafheight = 50;
+  }
+  if (!tk.coverageheight) {
+    tk.coverageheight = 30;
+  }
+  if (!tk.rowspace) {
+    tk.rowspace = 5;
+  }
+  tk.tklabel.attr("y", 20);
+  tk.Tvafaxis = tk.gleft.append("g");
+  tk.Nvafaxis = tk.gleft.append("g");
+  tk.aiaxis = tk.gleft.append("g");
+  tk.label_tumor = tk.gleft.append("text").attr("font-family", font).attr("font-size", block.labelfontsize).attr("dominant-baseline", "central").attr("text-anchor", "end").attr("x", block.tkleftlabel_xshift).attr("fill-opacity", 0.6).text("Tumor");
+  tk.label_germline = tk.gleft.append("text").attr("font-family", font).attr("font-size", block.labelfontsize).attr("dominant-baseline", "central").attr("text-anchor", "end").attr("x", block.tkleftlabel_xshift).attr("fill-opacity", 0.6).text("Germline");
+  tk.label_ai = tk.gleft.append("text").attr("font-family", font).attr("font-size", block.labelfontsize).attr("dominant-baseline", "central").attr("text-anchor", "end").attr("x", block.tkleftlabel_xshift).attr("fill-opacity", 0.6).text("abs(T-G)");
+  tk.Tcovaxis = tk.gright.append("g");
+  tk.Ncovaxis = tk.gright.append("g");
+  tk.label_tumorcoverage = tk.gright.append("text").attr("font-family", font).attr("font-size", block.labelfontsize).attr("dominant-baseline", "central").attr("x", 10).attr("fill-opacity", 0.6).text("T coverage");
+  tk.label_germlinecoverage = tk.gright.append("text").attr("font-family", font).attr("font-size", block.labelfontsize).attr("dominant-baseline", "central").attr("x", 10).attr("fill-opacity", 0.6).text("G coverage");
+  tk.config_handle = block.maketkconfighandle(tk).on("click", (event) => {
+    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+    configPanel(tk, block);
+  });
+}
+function tkarg(tk, block, width, rglst) {
+  const a = {
+    rglst: rglst || block.tkarg_rglst(),
+    genome: block.genome.name,
+    regionspace: block.regionspace,
+    width: width || block.width,
+    coveragemax: tk.coveragemax,
+    gtotalcutoff: tk.gtotalcutoff,
+    gmafrestrict: tk.gmafrestrict,
+    vafheight: tk.vafheight,
+    coverageheight: tk.coverageheight,
+    rowspace: tk.rowspace,
+    dotsize: tk.dotsize,
+    devicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1
+  };
+  if (tk.file) {
+    a.file = tk.file;
+  } else {
+    a.url = tk.url;
+    if (tk.indexURL) a.indexURL = tk.indexURL;
+  }
+  return a;
+}
+function loadTk(tk, block) {
+  if (tk.uninitialized) {
+    makeTk(tk, block);
+    delete tk.uninitialized;
+  }
+  block.tkcloakon(tk);
+  dofetch3("tkaicheck", { body: tkarg(tk, block) }).then((data) => {
+    if (data.error) throw { message: data.error };
+    const imgh = tk.vafheight * 3 + tk.rowspace * 4 + tk.coverageheight * 2;
+    tk.height_main = tk.toppad + imgh + tk.bottompad;
+    tk.img.attr("width", block.width).attr("height", imgh).attr("xlink:href", data.src);
+    if (data.coveragemax) {
+      tk.coveragemax = data.coveragemax;
+    }
+    if (!data.nodata) {
+      const scale = linear().domain([0, 1]).range([tk.vafheight, 0]);
+      let y = 0;
+      axisstyle({
+        axis: tk.Tvafaxis.attr("transform", "translate(0," + y + ")").call(
+          axisLeft().scale(scale).tickValues([0, 1])
+        ),
+        color: "black",
+        showline: true
+      });
+      tk.label_tumor.attr("y", y + tk.vafheight * 3 / 4);
+      y = tk.vafheight + tk.rowspace + tk.coverageheight + tk.rowspace;
+      axisstyle({
+        axis: tk.Nvafaxis.attr("transform", "translate(0," + y + ")").call(
+          axisLeft().scale(scale).tickValues([0, 1])
+        ),
+        color: "black",
+        showline: true
+      });
+      tk.label_germline.attr("y", y + tk.vafheight / 2);
+      y = 2 * (tk.vafheight + tk.rowspace + tk.coverageheight + tk.rowspace);
+      axisstyle({
+        axis: tk.aiaxis.attr("transform", "translate(0," + y + ")").call(axisLeft().scale(scale).tickValues([0, 1])),
+        color: "black",
+        showline: true
+      });
+      tk.label_ai.attr("y", y + tk.vafheight / 2);
+      const scale2 = linear().domain([0, tk.coveragemax]).range([tk.coverageheight, 0]);
+      y = tk.vafheight + tk.rowspace;
+      axisstyle({
+        axis: tk.Tcovaxis.attr("transform", "translate(0," + y + ")").call(
+          axisRight().scale(scale2).tickValues([0, tk.coveragemax])
+        ),
+        color: "black",
+        showline: true
+      });
+      tk.label_tumorcoverage.attr("y", y + tk.coverageheight / 2);
+      y = 2 * (tk.vafheight + tk.rowspace) + tk.coverageheight + tk.rowspace;
+      axisstyle({
+        axis: tk.Ncovaxis.attr("transform", "translate(0," + y + ")").call(
+          axisRight().scale(scale2).tickValues([0, tk.coveragemax])
+        ),
+        color: "black",
+        showline: true
+      });
+      tk.label_germlinecoverage.attr("y", y + tk.coverageheight / 2);
+    }
+    return null;
+  }).catch((obj) => {
+    tk.img.attr("width", 1).attr("height", 1);
+    if (obj.stack) {
+      console.log(obj.stack);
+    }
+    return obj.message;
+  }).then((errtext) => {
+    block.tkcloakoff(tk, { error: errtext });
+    block.block_setheight();
+    for (const panel of tk.subpanels) {
+      loadTksubpanel(tk, block, panel);
+    }
+  });
+}
+function loadTksubpanel(tk, block, panel) {
+  block.tkcloakon_subpanel(panel);
+  const par = tkarg(tk, block, panel.width, [
+    {
+      chr: panel.chr,
+      start: panel.start,
+      stop: panel.stop,
+      width: panel.width
+    }
+  ]);
+  dofetch3("tkaicheck", { body: par }).then((data) => {
+    if (data.error) throw { message: data.error };
+    panel.img.attr("width", panel.width).attr("height", tk.vafheight * 3 + tk.rowspace * 4 + tk.coverageheight * 2).attr("xlink:href", data.src);
+    return null;
+  }).catch((obj) => {
+    panel.img.attr("width", 1).attr("height", 1);
+    if (obj.stack) {
+      console.log(obj.stack);
+    }
+    return obj.message;
+  }).then((errtext) => {
+    block.tkcloakoff_subpanel(panel, { error: errtext });
+  });
+}
+function configPanel(tk, block) {
+  tk.tkconfigtip.clear();
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Coverage max: ");
+    row.append("input").attr("type", "number").style("width", "60px").property("value", tk.coveragemax).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseInt(s);
+      if (Number.isNaN(v) || v <= 1) {
+        alert("coverage max must be positive integer");
+        return;
+      }
+      tk.coveragemax = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Marker dot size:&nbsp;");
+    make_radios({
+      holder: row,
+      options: [
+        { label: "1 pixel", value: 1, checked: tk.dotsize == 1 },
+        { label: "2 pixels", value: 2, checked: tk.dotsize == 2 },
+        { label: "3 pixels", value: 3, checked: tk.dotsize == 3 }
+      ],
+      callback: (v) => {
+        tk.dotsize = v;
+        loadTk(tk, block);
+      },
+      styles: {
+        "margin-right": "5px"
+      }
+    });
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Filter markers by minimum total germline coverage:&nbsp;");
+    row.append("input").attr("type", "number").style("width", "60px").property("value", tk.gtotalcutoff || 0).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseInt(s);
+      if (Number.isNaN(v) || v < 0) {
+        alert("coverage max must be non-negative integer");
+        return;
+      }
+      if (v == tk.gtotalcutoff) return;
+      tk.gtotalcutoff = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("font-size", ".7em").style("opacity", 0.5).text("Set to 0 to use all markers");
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Filter markers by narrowing range of germline B-allele fraction:&nbsp;");
+    row.append("input").attr("type", "number").style("width", "60px").property("value", tk.gmafrestrict || 0).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseFloat(s);
+      if (Number.isNaN(v) || v < 0 || v > 0.5) {
+        alert("Must enter a value between 0 and 0.5");
+        return;
+      }
+      if (tk.gmafrestrict == v) return;
+      tk.gmafrestrict = v;
+      loadTk(tk, block);
+      configPanel(tk, block);
+    });
+    row.append("div").style("font-size", ".7em").style("opacity", 0.5).text(
+      (tk.gmafrestrict ? "Keeping markers with BAF range " + tk.gmafrestrict + " to " + (1 - tk.gmafrestrict) + ". " : "") + "Set to 0 to use all markers"
+    );
+  }
+}
+export {
+  loadTk,
+  loadTksubpanel
+};
+//# sourceMappingURL=block.tk.aicheck-5N6EGZ6F.js.map