@sjcrh/proteinpaint-client 2.175.0 → 2.176.1-0

package/dist/{2dmaf-SPNVJWSC.js → 2dmaf-3XE3AV6H.js}

@@ -8,13 +8,13 @@ import {
   renderSandboxFormDiv,
   sayerror,
   to_svg
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-ZCZ5O42D.js";
+import "./chunk-FESR4FEX.js";
 import {
   Menu
 } from "./chunk-CXMZYVZT.js";
-import "./chunk-C66E6MW5.js";
+import "./chunk-GXJMO2WK.js";
 import "./chunk-3JH6BKPD.js";
 import {
   mclass,
@@ -23,12 +23,12 @@ import {
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
-import "./chunk-HLWTQJ7E.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
+import "./chunk-NPOWNTGW.js";
 import "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import {
   Symbol,
   circle_default,
@@ -1365,4 +1365,4 @@ export {
   d2mafparseinput,
   d2mafui
 };
-//# sourceMappingURL=2dmaf-SPNVJWSC.js.map
+//# sourceMappingURL=2dmaf-3XE3AV6H.js.map

package/dist/{AIProjectAdmin-ILQY2BGS.js → AIProjectAdmin-B45XJE6P.js}

@@ -7,14 +7,14 @@ import {
   getNormalRoot,
   renderTable,
   sayerror
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-ZCZ5O42D.js";
+import "./chunk-FESR4FEX.js";
 import "./chunk-CXMZYVZT.js";
 import {
   dofetch2,
   dofetch3
-} from "./chunk-C66E6MW5.js";
+} from "./chunk-GXJMO2WK.js";
 import "./chunk-3JH6BKPD.js";
 import {
   getColors
@@ -22,17 +22,17 @@ import {
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
 import {
   copyMerge,
   getCompInit
-} from "./chunk-HLWTQJ7E.js";
+} from "./chunk-NPOWNTGW.js";
 import {
   require_debounce
 } from "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import "./chunk-2MN5JLZB.js";
 import "./chunk-TOU7EVFQ.js";
 import "./chunk-LOZEKOES.js";
@@ -330,7 +330,7 @@ var AIProjectAdminInteractions = class {
       );
       images = response.images;
     }
-    const wsiViewer = await import("./plot.wsi-527GVPMI.js");
+    const wsiViewer = await import("./plot.wsi-YN556FXB.js");
     wsiViewer.default(this.dslabel, holder, { name: this.genome }, null, config.settings.project.id, images, true);
   }
   async appDispatchEdit(settings, config = {}) {
@@ -824,4 +824,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=AIProjectAdmin-ILQY2BGS.js.map
+//# sourceMappingURL=AIProjectAdmin-B45XJE6P.js.map

package/dist/{AppHeader-SCJLQQVV.js → AppHeader-BKTLVJTT.js}

@@ -1,20 +1,20 @@
 import {
   makeButton,
   openSandbox
-} from "./chunk-3C74JG25.js";
+} from "./chunk-HMEJBZ6Q.js";
 import {
   get_tklst
-} from "./chunk-QARJ3HW5.js";
-import "./chunk-VO6B2VPC.js";
-import "./chunk-ZM6RWRB2.js";
+} from "./chunk-ZZXZQR7R.js";
+import "./chunk-XIBVDFHH.js";
+import "./chunk-LK5I4ITQ.js";
 import {
   block_init_default
-} from "./chunk-ZISOUE3A.js";
+} from "./chunk-GFGNR4KV.js";
 import "./chunk-MKAF2BHB.js";
 import {
   urlmap_default
-} from "./chunk-AEH6KKVI.js";
-import "./chunk-J4AC2HR6.js";
+} from "./chunk-DONWY7TP.js";
+import "./chunk-IEAQH22G.js";
 import "./chunk-PRZWSBMA.js";
 import {
   InputSearch,
@@ -22,15 +22,15 @@ import {
   newSandboxDiv,
   sayerror,
   throwMsgWithFilePathAndFnName
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import {
   string2pos
 } from "./chunk-HJ6L54YS.js";
-import "./chunk-ZCZ5O42D.js";
+import "./chunk-FESR4FEX.js";
 import "./chunk-CXMZYVZT.js";
 import {
   dofetch3
-} from "./chunk-C66E6MW5.js";
+} from "./chunk-GXJMO2WK.js";
 import "./chunk-3JH6BKPD.js";
 import {
   defaultcolor
@@ -38,17 +38,17 @@ import {
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
 import {
   getAppInit,
   getCompInit,
   getInitFxn,
   getStoreInit
-} from "./chunk-HLWTQJ7E.js";
+} from "./chunk-NPOWNTGW.js";
 import "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import "./chunk-2MN5JLZB.js";
 import "./chunk-TOU7EVFQ.js";
 import "./chunk-LOZEKOES.js";
@@ -215,7 +215,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-7FP66UHL.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-NHRVQ5OR.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -801,7 +801,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-7FP66UHL.js").then((b) => new b.Block(par));
+      import("./block-NHRVQ5OR.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -814,4 +814,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-SCJLQQVV.js.map
+//# sourceMappingURL=AppHeader-BKTLVJTT.js.map

package/dist/{BoxPlot-WLFZJY3T.js → BoxPlot-ZM3SN3KE.js}

@@ -17,13 +17,13 @@ import {
   renderTable,
   renderTerm1Label,
   term0_term2_defaultQ
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-ZCZ5O42D.js";
+import "./chunk-FESR4FEX.js";
 import {
   Menu
 } from "./chunk-CXMZYVZT.js";
-import "./chunk-C66E6MW5.js";
+import "./chunk-GXJMO2WK.js";
 import {
   isNumericTerm
 } from "./chunk-3JH6BKPD.js";
@@ -31,15 +31,15 @@ import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
 import {
   copyMerge,
   getCompInit
-} from "./chunk-HLWTQJ7E.js";
+} from "./chunk-NPOWNTGW.js";
 import "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import "./chunk-2MN5JLZB.js";
 import "./chunk-TOU7EVFQ.js";
 import {
@@ -1175,4 +1175,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=BoxPlot-WLFZJY3T.js.map
+//# sourceMappingURL=BoxPlot-ZM3SN3KE.js.map

package/dist/{CorrelationVolcano-6WAVFCMZ.js → CorrelationVolcano-TLVOYBVU.js}

@@ -8,13 +8,13 @@ import {
   fillTwLst,
   table2col,
   to_svg
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-ZCZ5O42D.js";
+import "./chunk-FESR4FEX.js";
 import {
   Menu
 } from "./chunk-CXMZYVZT.js";
-import "./chunk-C66E6MW5.js";
+import "./chunk-GXJMO2WK.js";
 import {
   termType2label
 } from "./chunk-3JH6BKPD.js";
@@ -22,15 +22,15 @@ import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
 import {
   copyMerge,
   getCompInit
-} from "./chunk-HLWTQJ7E.js";
+} from "./chunk-NPOWNTGW.js";
 import "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import "./chunk-2MN5JLZB.js";
 import "./chunk-TOU7EVFQ.js";
 import {
@@ -611,4 +611,4 @@ export {
   getDefaultCorrVolcanoSettings,
   getPlotConfig
 };
-//# sourceMappingURL=CorrelationVolcano-6WAVFCMZ.js.map
+//# sourceMappingURL=CorrelationVolcano-TLVOYBVU.js.map

package/dist/{DifferentialAnalysis-BEL6F6JP.js → DifferentialAnalysis-ZESJ5GF2.js}

@@ -1,21 +1,21 @@
 import {
   getDefaultGseaSettings
-} from "./chunk-CRTGS4HR.js";
-import "./chunk-GHWDFPUC.js";
+} from "./chunk-XMSXS7L6.js";
+import "./chunk-HEU7I3KP.js";
 import {
   PlotBase,
   Tabs,
   getDefaultVolcanoSettings,
   validateVolcanoSettings
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import "./chunk-HJ6L54YS.js";
 import {
   importPlot
-} from "./chunk-ZCZ5O42D.js";
+} from "./chunk-FESR4FEX.js";
 import {
   Menu
 } from "./chunk-CXMZYVZT.js";
-import "./chunk-C66E6MW5.js";
+import "./chunk-GXJMO2WK.js";
 import {
   TermTypes,
   termType2label
@@ -24,15 +24,15 @@ import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
 import {
   copyMerge,
   getCompInit
-} from "./chunk-HLWTQJ7E.js";
+} from "./chunk-NPOWNTGW.js";
 import "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import "./chunk-2MN5JLZB.js";
 import "./chunk-TOU7EVFQ.js";
 import "./chunk-LOZEKOES.js";
@@ -230,4 +230,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=DifferentialAnalysis-BEL6F6JP.js.map
+//# sourceMappingURL=DifferentialAnalysis-ZESJ5GF2.js.map

package/dist/{Disco-KNMRTGOV.js → Disco-BKJYN4PV.js}

@@ -1,19 +1,20 @@
 import {
   InvalidDataUI,
   configUiInit,
+  fillbar,
   getMaxLabelWidth,
   renderTable,
   svgLegend,
   table2col
-} from "./chunk-65QYUKDM.js";
+} from "./chunk-K5F35KN2.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-ZCZ5O42D.js";
+import "./chunk-FESR4FEX.js";
 import {
   Menu
 } from "./chunk-CXMZYVZT.js";
 import {
   dofetch3
-} from "./chunk-C66E6MW5.js";
+} from "./chunk-GXJMO2WK.js";
 import "./chunk-3JH6BKPD.js";
 import {
   bplen,
@@ -29,16 +30,16 @@ import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
 import {
   topBarInit
-} from "./chunk-VQ4BTEOI.js";
-import "./chunk-MRHUJWAH.js";
+} from "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
 import {
   copyMerge,
   getCompInit,
   multiInit
-} from "./chunk-HLWTQJ7E.js";
+} from "./chunk-NPOWNTGW.js";
 import "./chunk-TPK3G44P.js";
 import "./chunk-LD45BCVM.js";
-import "./chunk-XGIPMUHP.js";
+import "./chunk-BEWDIM6H.js";
 import {
   arc_default,
   line_default,
@@ -179,7 +180,7 @@ async function makeSvgraph(fusion, div, genome) {
   await getGm(svpair.a, genome.name, fusion.source.gene);
   await getGm(svpair.b, genome.name, fusion.target.gene);
   wait.remove();
-  const _ = await import("./svgraph-SZRXVFTC.js");
+  const _ = await import("./svgraph-LERWY3QM.js");
   _.default({
     pairlst: [svpair],
     genome,
@@ -278,7 +279,7 @@ var DiscoInteractions = class {
           }
         ]
       };
-      const _ = await import("./block.init-BK3QSZQR.js");
+      const _ = await import("./block.init-JRL2ODN3.js");
       await _.default(arg);
     };
     this.colorScaleNumericInputsCallback = async (obj) => {
@@ -385,6 +386,8 @@ var DataObjectMapper = class {
       chr: dObject.chr,
       ref: dObject.ref,
       alt: dObject.alt,
+      refCount: dObject.refCount,
+      altCount: dObject.altCount,
       position: dObject.pos ? dObject.pos : dObject.position,
       poschr: dObject.poschr,
       posbins: dObject.posbins,
@@ -1099,6 +1102,8 @@ var SnvArcsMapper = class {
             mname: data.mname,
             chr: data.chr,
             pos: data.position,
+            refCount: data.refCount,
+            altCount: data.altCount,
             sampleName: [data.sampleName]
           };
           snvArray.push(arc);
@@ -1485,7 +1490,9 @@ var LabelsMapper = class {
       color,
       dataClass,
       chr: data.chr,
-      position: data.position
+      position: data.position,
+      refCount: data.refCount,
+      altCount: data.altCount
     };
     if (!label) {
       this.labelMap.set(
@@ -1727,6 +1734,8 @@ var NonExonicSnvArcsMapper = class {
         mname: data.mname,
         chr: data.chr,
         pos: data.position,
+        refCount: data.refCount,
+        altCount: data.altCount,
         sampleName: [data.sampleName]
       };
       arcs.push(arc);
@@ -2475,6 +2484,31 @@ var ChromosomesRenderer = class {
   }
 };
 
+// plots/disco/snv/vafTooltip.ts
+function getIntegerCount(v) {
+  if (Number.isInteger(v)) return v;
+  if (typeof v == "string" && /^-?\d+$/.test(v)) {
+    const n = Number(v);
+    if (Number.isInteger(n)) return n;
+  }
+  return null;
+}
+function hasValidReadCounts(refCountValue, altCountValue) {
+  const refCount = getIntegerCount(refCountValue);
+  const altCount = getIntegerCount(altCountValue);
+  return refCount != null && altCount != null && refCount >= 0 && altCount >= 0 && refCount + altCount > 0;
+}
+function appendVafBar(td2, refCountValue, altCountValue) {
+  const refCount = getIntegerCount(refCountValue);
+  const altCount = getIntegerCount(altCountValue);
+  if (refCount == null || altCount == null) return;
+  const totalCount = refCount + altCount;
+  const fraction = altCount / totalCount;
+  const div = td2.append("div").style("margin-left", "5px").style("margin-top", "4px").style("display", "flex").style("align-items", "center").style("gap", "6px");
+  div.append("span").style("font-size", "0.8em").style("color", "#555").text("VAF");
+  fillbar(div, { f: fraction, v1: altCount, v2: totalCount });
+}
+
 // plots/disco/label/LabelsRenderer.ts
 var LabelsRenderer = class {
   constructor(animationDuration, fontSize, geneClickListener) {
@@ -2524,6 +2558,9 @@ var LabelsRenderer = class {
           const [td12, td22] = table.addRow();
           td12.text("Mutation");
           td22.append("span").style("margin-left", "5px").text(mutation.mname).append("span").style("margin-left", "5px").style("color", mutation.color).text(`${mutation.dataClass}`).append("span").style("margin-left", "5px").style("color", "black").style("font-size", "0.8em").text(` ${mutation.chr}:${mutation.position}`);
+          if (hasValidReadCounts(mutation.refCount, mutation.altCount)) {
+            appendVafBar(td22, mutation.refCount, mutation.altCount);
+          }
         }
       });
     }
@@ -2670,6 +2707,11 @@ var NonExonicSnvRenderer = class {
         td1.text("Occurrence");
         td2.text(snv.occurrence);
       }
+      if (hasValidReadCounts(arc.refCount, arc.altCount)) {
+        const [td1, td2] = table.addRow();
+        td1.text("Read count");
+        appendVafBar(td2, arc.refCount, arc.altCount);
+      }
       menu.show(mouseEvent.x, mouseEvent.y);
     }).on("mouseout", () => {
       menu.clear();
@@ -2722,6 +2764,11 @@ var SnvRenderer = class {
         td1.text("Occurrence");
         td2.text(snv.occurrence);
       }
+      if (hasValidReadCounts(arc.refCount, arc.altCount)) {
+        const [td1, td2] = table.addRow();
+        td1.text("Read count");
+        appendVafBar(td2, arc.refCount, arc.altCount);
+      }
       menu.show(mouseEvent.x, mouseEvent.y);
     }).on("mouseout", () => {
       menu.clear();
@@ -3124,4 +3171,4 @@ export {
   discoInit,
   getPlotConfig
 };
-//# sourceMappingURL=Disco-KNMRTGOV.js.map
+//# sourceMappingURL=Disco-BKJYN4PV.js.map