@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

package/dist/chunk-W345H42C.js

@@ -0,0 +1,273 @@
+import {
+  TermTypes
+} from "./chunk-6ITDJ5UR.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/hierCluster.renderers.js
+var hierCluster_renderers_exports = {};
+__export(hierCluster_renderers_exports, {
+  maySetSandboxHeader: () => maySetSandboxHeader,
+  plotDendrogramHclust: () => plotDendrogramHclust,
+  renderImage: () => renderImage
+});
+function maySetSandboxHeader(appState) {
+  if (!this.dom.header) return;
+  switch (this.config.dataType) {
+    case TermTypes.GENE_EXPRESSION:
+      this.dom.header.text("Gene Expression Clustering");
+      break;
+    case TermTypes.METABOLITE_INTENSITY:
+      this.dom.header.text("Metabolite Intensity Clustering");
+      break;
+    case TermTypes.PROTEOME_ABUNDANCE:
+      this.dom.header.text(
+        this.config.assayCohortTitle ? `Protein Abundance Clustering (${this.config.assayCohortTitle})` : "Protein Abundance Clustering"
+      );
+      break;
+    default:
+      throw `dataType '${this.config.dataType}' not recognized`;
+  }
+}
+function plotDendrogramHclust(plotOnly) {
+  const d = this.dimensions;
+  const s = this.config.settings.matrix;
+  const xOffset = d.seriesXoffset;
+  const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
+  const obj = this.hierClusterData.clustering;
+  const row = obj.row;
+  const col = obj.col;
+  const rowHeight = this.settings.matrix.clusterRowh, { xDendrogramHeight, yDendrogramHeight } = this.settings.hierCluster, colWidth = this.dimensions.dx;
+  if (plotOnly !== "left") {
+    if (!this.settings.hierCluster.clusterSamples) {
+      this.dom.topDendrogram.selectAll("*").remove();
+    } else {
+      const height2px = getHclustHeightScalefactor(col.height, yDendrogramHeight);
+      const height = yDendrogramHeight + 1e-7;
+      const width = Math.min(colWidth * col.inputOrder.length, s.imgWMax);
+      if (width <= 0 || height <= 0) {
+        console.warn(
+          "Skipping top dendrogram render: invalid dimensions.",
+          "This may indicate a zoom feedback loop issue.",
+          {
+            width,
+            height,
+            colWidth,
+            sampleCount: col.inputOrder.length,
+            yDendrogramHeight
+          }
+        );
+        this.dom.topDendrogram.selectAll("*").remove();
+        return;
+      }
+      const canvas = new OffscreenCanvas(width * pxr, height * pxr);
+      const ctx = canvas.getContext("2d");
+      ctx.scale(pxr, pxr);
+      ctx.translate(-d.xMin, 0);
+      ctx.imageSmoothingEnabled = false;
+      ctx.imageSmoothingQuality = "high";
+      ctx.strokeStyle = "black";
+      const mergedClusters = /* @__PURE__ */ new Map();
+      for (const [clusterid0, pair] of col.merge.entries()) {
+        const clusterid = clusterid0 + 1;
+        const children = [];
+        const childrenClusters = [];
+        let x1, x2, y1, y2;
+        if (pair.n1 < 0) {
+          const [name, columnNumber] = getLeafNumber(pair.n1, col.inputOrder, col.order);
+          x1 = colWidth * (columnNumber + 0.5);
+          y1 = yDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n1);
+          x1 = c.x;
+          y1 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n1);
+        }
+        if (pair.n2 < 0) {
+          const [name, columnNumber] = getLeafNumber(pair.n2, col.inputOrder, col.order);
+          x2 = colWidth * (columnNumber + 0.5);
+          y2 = yDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n2);
+          x2 = c.x;
+          y2 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n2);
+        }
+        const clusterY = yDendrogramHeight - col.height[clusterid0].height * height2px;
+        const highlight = this.clickedClusterIds?.includes(clusterid);
+        ctx.strokeStyle = highlight ? "red" : "black";
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(x1, clusterY);
+        ctx.lineTo(x2, clusterY);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+        ctx.closePath();
+        mergedClusters.set(clusterid, {
+          x: (x1 + x2) / 2,
+          y: clusterY,
+          children,
+          childrenClusters,
+          clusterPosition: {
+            x1,
+            x2,
+            y1,
+            y2,
+            clusterY
+          }
+        });
+      }
+      this.renderImage(
+        this.api,
+        this.dom.topDendrogram,
+        canvas,
+        width,
+        height,
+        xDendrogramHeight + 0.5 * colWidth + d.xMin,
+        s.margin.top + s.scrollHeight
+      );
+      col.mergedClusters = mergedClusters;
+    }
+  }
+  if (plotOnly !== "top") {
+    if (!this.settings.hierCluster.clusterRows) {
+      this.dom.leftDendrogram.selectAll("*").remove();
+    } else {
+      const height2px = getHclustHeightScalefactor(row.height, xDendrogramHeight);
+      const width = xDendrogramHeight + 1e-7;
+      const height = rowHeight * row.inputOrder.length;
+      const canvasWidthPx = Number.isFinite(width) && Number.isFinite(pxr) ? Math.max(0, Math.floor(width * pxr)) : 0;
+      const canvasHeightPx = Number.isFinite(height) && Number.isFinite(pxr) ? Math.max(0, Math.floor(height * pxr)) : 0;
+      if (!Number.isFinite(width) || !Number.isFinite(height) || !Number.isFinite(pxr) || width <= 0 || height <= 0 || pxr <= 0 || canvasWidthPx < 1 || canvasHeightPx < 1) {
+        console.warn(
+          "Skipping left dendrogram render: invalid dimensions.",
+          "This may indicate a zoom feedback loop issue.",
+          {
+            width,
+            height,
+            pxr,
+            canvasWidthPx,
+            canvasHeightPx,
+            rowHeight,
+            termCount: row.inputOrder.length,
+            xDendrogramHeight
+          }
+        );
+        this.dom.leftDendrogram.selectAll("*").remove();
+        return;
+      }
+      const canvas = new OffscreenCanvas(canvasWidthPx, canvasHeightPx);
+      const ctx = canvas.getContext("2d");
+      ctx.scale(pxr, pxr);
+      ctx.imageSmoothingEnabled = false;
+      ctx.imageSmoothingQuality = "high";
+      ctx.strokeStyle = "black";
+      const mergedClusters = /* @__PURE__ */ new Map();
+      for (const [clusterid0, pair] of row.merge.entries()) {
+        const clusterid = clusterid0 + 1;
+        const children = [];
+        const childrenClusters = [];
+        let x1, x2, y1, y2;
+        if (pair.n1 < 0) {
+          const [name, rowNumber] = getLeafNumber(pair.n1, row.inputOrder, row.order);
+          y1 = rowHeight * (rowNumber + 0.5);
+          x1 = xDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n1);
+          x1 = c.x;
+          y1 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n1);
+        }
+        if (pair.n2 < 0) {
+          const [name, rowNumber] = getLeafNumber(pair.n2, row.inputOrder, row.order);
+          y2 = rowHeight * (rowNumber + 0.5);
+          x2 = xDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n2);
+          x2 = c.x;
+          y2 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n2);
+        }
+        const clusterX = xDendrogramHeight - row.height[clusterid0].height * height2px;
+        const highlight = this.clickedLeftClusterIds?.includes(clusterid);
+        ctx.strokeStyle = highlight ? "red" : "black";
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(clusterX, y1);
+        ctx.lineTo(clusterX, y2);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+        ctx.closePath();
+        mergedClusters.set(clusterid, {
+          x: clusterX,
+          y: (y1 + y2) / 2,
+          children,
+          childrenClusters,
+          clusterPosition: {
+            x1,
+            x2,
+            y1,
+            y2,
+            clusterX
+          }
+        });
+      }
+      const t = this.termOrder.find((t2) => t2.grp.type == "hierCluster" || t2.grp.name == this.hcTermGroup.name);
+      const y = (
+        // t.labelOffset is commented out because it is already handled in adjustSvgDimensions
+        t.grpIndex * s.rowgspace + t.prevGrpTotalIndex * s.rowh + t.totalHtAdjustments + s.margin.top + s.scrollHeight + // left dendrogram image must be lower than the top dendrogram image height
+        yDendrogramHeight
+      );
+      this.renderImage(this.api, this.dom.leftDendrogram, canvas, width, height, 0, y);
+      row.mergedClusters = mergedClusters;
+    }
+  }
+}
+async function renderImage(componentApi, g, canvas, width, height, x, y) {
+  const sequenceId = componentApi.getSequenceId();
+  const reader = new FileReader();
+  reader.addEventListener(
+    "load",
+    () => {
+      if (componentApi.isStaleSequenceId(sequenceId)) return;
+      g.selectAll("*").remove();
+      g.append("image").attr("x", x + 0.033).attr("y", y + 0.033).attr("xlink:href", reader.result).attr("width", width).attr("height", height);
+    },
+    false
+  );
+  const blob = await canvas.convertToBlob({ quality: 1 });
+  reader.readAsDataURL(blob);
+}
+function getHclustHeightScalefactor(lst, ph) {
+  let max = lst[0].height;
+  for (const h of lst) max = Math.max(max, h.height);
+  return ph / max;
+}
+function getLeafNumber(minus, inputOrder, order) {
+  const name = inputOrder[-minus - 1];
+  if (!name) throw "minus not in inputOrder";
+  const i = order.findIndex((j) => j.name == name);
+  if (i == -1) throw "name not found in hc$order";
+  return [name, i];
+}
+
+export {
+  maySetSandboxHeader,
+  plotDendrogramHclust,
+  renderImage,
+  hierCluster_renderers_exports
+};
+//# sourceMappingURL=chunk-W345H42C.js.map

package/dist/chunk-W345H42C.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/hierCluster.renderers.js"],
+  "sourcesContent": ["import { TermTypes } from '#shared/terms.js'\n\nexport function maySetSandboxHeader(appState) {\n\t// run only once upon init, after state and dataType is given\n\tif (!this.dom.header) return // no header\n\tswitch (this.config.dataType) {\n\t\tcase TermTypes.GENE_EXPRESSION:\n\t\t\tthis.dom.header.text('Gene Expression Clustering')\n\t\t\tbreak\n\t\tcase TermTypes.METABOLITE_INTENSITY:\n\t\t\tthis.dom.header.text('Metabolite Intensity Clustering')\n\t\t\tbreak\n\t\tcase TermTypes.PROTEOME_ABUNDANCE:\n\t\t\tthis.dom.header.text(\n\t\t\t\tthis.config.assayCohortTitle\n\t\t\t\t\t? `Protein Abundance Clustering (${this.config.assayCohortTitle})`\n\t\t\t\t\t: 'Protein Abundance Clustering'\n\t\t\t)\n\t\t\tbreak\n\t\tdefault:\n\t\t\tthrow `dataType '${this.config.dataType}' not recognized`\n\t}\n}\n\nexport function plotDendrogramHclust(plotOnly) {\n\t/*\n\tbased on hclust() output\n\tplotOnly=top will only render column dendrograms\n\tplotOnly=left will only render row dendrograms\n\tif false will render both row and column\n\t*/\n\tconst d = this.dimensions\n\tconst s = this.config.settings.matrix\n\tconst xOffset = d.seriesXoffset // could be negative when zoomed\n\tconst pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio\n\n\tconst obj = this.hierClusterData.clustering\n\tconst row = obj.row\n\tconst col = obj.col\n\t/* both row{} and col{} are hclust() output structure:\n\t.merge[]       {n1,n2}\n\t.height[]      {height}\n\t.order[]       {name}\n\t.inputOrder[]  [str]\n\t*/\n\n\tconst rowHeight = this.settings.matrix.clusterRowh, //this.dimensions.dy,\n\t\t{ xDendrogramHeight, yDendrogramHeight } = this.settings.hierCluster,\n\t\tcolWidth = this.dimensions.dx\n\n\t// plot column dendrogram\n\tif (plotOnly !== 'left') {\n\t\tif (!this.settings.hierCluster.clusterSamples) {\n\t\t\tthis.dom.topDendrogram.selectAll('*').remove()\n\t\t} else {\n\t\t\tconst height2px = getHclustHeightScalefactor(col.height, yDendrogramHeight)\n\n\t\t\tconst height = yDendrogramHeight + 0.0000001\n\t\t\tconst width = Math.min(colWidth * col.inputOrder.length, s.imgWMax)\n\n\t\t\t// Safety check: prevent zero-sized canvas which causes convertToBlob error\n\t\t\tif (width <= 0 || height <= 0) {\n\t\t\t\tconsole.warn(\n\t\t\t\t\t'Skipping top dendrogram render: invalid dimensions.',\n\t\t\t\t\t'This may indicate a zoom feedback loop issue.',\n\t\t\t\t\t{\n\t\t\t\t\t\twidth,\n\t\t\t\t\t\theight,\n\t\t\t\t\t\tcolWidth,\n\t\t\t\t\t\tsampleCount: col.inputOrder.length,\n\t\t\t\t\t\tyDendrogramHeight\n\t\t\t\t\t}\n\t\t\t\t)\n\t\t\t\tthis.dom.topDendrogram.selectAll('*').remove()\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tconst canvas = new OffscreenCanvas(width * pxr, height * pxr)\n\t\t\tconst ctx = canvas.getContext('2d')\n\t\t\tctx.scale(pxr, pxr)\n\t\t\t// when the OffscreenCanvas width is too wide (>60k pixels as tested in Chrome and other browsers),\n\t\t\t// rendering outside of the usable width causes an IndexSizeError. The solution below is similar to\n\t\t\t// what's done in matrix.renderer: impose an upper limit of s.imgWMax for the canvas width and\n\t\t\t// translate the rendered x positions to the left, creating a viewport bounded by the max canvas\n\t\t\t// image width and where the segments/lines positioned outside of those bounds are clipped\n\t\t\t// by the canvas engine\n\t\t\tctx.translate(-d.xMin, 0) // d.xMin = 0 when imgWMax is not exceeded\n\t\t\t//ctx.translate(-d.xMin, 0)\n\t\t\tctx.imageSmoothingEnabled = false\n\t\t\tctx.imageSmoothingQuality = 'high'\n\t\t\tctx.strokeStyle = 'black'\n\n\t\t\tconst mergedClusters = new Map()\n\t\t\t/*\n\t\t\tas iterating through .merge[], collect merged clusters in here\n\t\t\tk: cluster id, positive integer, as in row.merge[]\n\t\t\tv: {\n\t\t\t\tx:\n\t\t\t\ty:\n\t\t\t\tchildren:[]\n\t\t\t}\n\t\t\t*/\n\t\t\tfor (const [clusterid0, pair] of col.merge.entries()) {\n\t\t\t\t// pair is {n1,n2}, n1 and n2 form a new cluster; id of which is clusterid\n\n\t\t\t\tconst clusterid = clusterid0 + 1 // id of this cluster formed by pair, as used in hclust$merge; positive integer\n\t\t\t\tconst children = [] // collect all children leaves for this cluster\n\t\t\t\tconst childrenClusters = [] // collect direct children cluster Ids for this cluster\n\n\t\t\t\tlet x1, x2, y1, y2\n\t\t\t\tif (pair.n1 < 0) {\n\t\t\t\t\t// n1 is leaf\n\t\t\t\t\tconst [name, columnNumber] = getLeafNumber(pair.n1, col.inputOrder, col.order)\n\t\t\t\t\tx1 = colWidth * (columnNumber + 0.5)\n\t\t\t\t\ty1 = yDendrogramHeight\n\t\t\t\t\tchildren.push({ name })\n\t\t\t\t} else {\n\t\t\t\t\t// n1 is cluster\n\t\t\t\t\tif (!mergedClusters.has(pair.n1)) throw 'pair.n1 is positive but not seen before'\n\t\t\t\t\tconst c = mergedClusters.get(pair.n1)\n\t\t\t\t\tx1 = c.x\n\t\t\t\t\ty1 = c.y\n\t\t\t\t\tchildren.push(...c.children)\n\t\t\t\t\tchildrenClusters.push(pair.n1)\n\t\t\t\t}\n\t\t\t\tif (pair.n2 < 0) {\n\t\t\t\t\t// n2 is leaf\n\t\t\t\t\tconst [name, columnNumber] = getLeafNumber(pair.n2, col.inputOrder, col.order)\n\t\t\t\t\tx2 = colWidth * (columnNumber + 0.5)\n\t\t\t\t\ty2 = yDendrogramHeight\n\t\t\t\t\tchildren.push({ name })\n\t\t\t\t} else {\n\t\t\t\t\tif (!mergedClusters.has(pair.n2)) throw 'pair.n1 is positive but not seen before'\n\t\t\t\t\tconst c = mergedClusters.get(pair.n2)\n\t\t\t\t\tx2 = c.x\n\t\t\t\t\ty2 = c.y\n\t\t\t\t\tchildren.push(...c.children)\n\t\t\t\t\tchildrenClusters.push(pair.n2)\n\t\t\t\t}\n\t\t\t\t// cluster y position\n\t\t\t\tconst clusterY = yDendrogramHeight - col.height[clusterid0].height * height2px\n\n\t\t\t\tconst highlight = this.clickedClusterIds?.includes(clusterid)\n\t\t\t\tctx.strokeStyle = highlight ? 'red' : 'black'\n\n\t\t\t\tctx.beginPath()\n\t\t\t\tctx.moveTo(x1, y1) // move to n1\n\t\t\t\tctx.lineTo(x1, clusterY) // vertical line up to cluster\n\t\t\t\tctx.lineTo(x2, clusterY) // h line to n2\n\t\t\t\tctx.lineTo(x2, y2) // v line down to n2\n\t\t\t\tctx.stroke()\n\t\t\t\tctx.closePath()\n\n\t\t\t\tmergedClusters.set(clusterid, {\n\t\t\t\t\tx: (x1 + x2) / 2,\n\t\t\t\t\ty: clusterY,\n\t\t\t\t\tchildren,\n\t\t\t\t\tchildrenClusters,\n\t\t\t\t\tclusterPosition: {\n\t\t\t\t\t\tx1,\n\t\t\t\t\t\tx2,\n\t\t\t\t\t\ty1,\n\t\t\t\t\t\ty2,\n\t\t\t\t\t\tclusterY\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tthis.renderImage(\n\t\t\t\tthis.api,\n\t\t\t\tthis.dom.topDendrogram,\n\t\t\t\tcanvas,\n\t\t\t\twidth,\n\t\t\t\theight,\n\t\t\t\txDendrogramHeight + 0.5 * colWidth + d.xMin,\n\t\t\t\ts.margin.top + s.scrollHeight\n\t\t\t)\n\n\t\t\tcol.mergedClusters = mergedClusters\n\t\t}\n\t}\n\n\t// plot row dendrogram\n\tif (plotOnly !== 'top') {\n\t\tif (!this.settings.hierCluster.clusterRows) {\n\t\t\tthis.dom.leftDendrogram.selectAll('*').remove()\n\t\t} else {\n\t\t\tconst height2px = getHclustHeightScalefactor(row.height, xDendrogramHeight)\n\t\t\tconst width = xDendrogramHeight + 0.0000001\n\t\t\tconst height = rowHeight * row.inputOrder.length\n\t\t\tconst canvasWidthPx = Number.isFinite(width) && Number.isFinite(pxr) ? Math.max(0, Math.floor(width * pxr)) : 0\n\t\t\tconst canvasHeightPx = Number.isFinite(height) && Number.isFinite(pxr) ? Math.max(0, Math.floor(height * pxr)) : 0\n\n\t\t\t// Safety check: prevent zero-sized canvas which causes OffscreenCanvas/convertToBlob errors\n\t\t\tif (\n\t\t\t\t!Number.isFinite(width) ||\n\t\t\t\t!Number.isFinite(height) ||\n\t\t\t\t!Number.isFinite(pxr) ||\n\t\t\t\twidth <= 0 ||\n\t\t\t\theight <= 0 ||\n\t\t\t\tpxr <= 0 ||\n\t\t\t\tcanvasWidthPx < 1 ||\n\t\t\t\tcanvasHeightPx < 1\n\t\t\t) {\n\t\t\t\tconsole.warn(\n\t\t\t\t\t'Skipping left dendrogram render: invalid dimensions.',\n\t\t\t\t\t'This may indicate a zoom feedback loop issue.',\n\t\t\t\t\t{\n\t\t\t\t\t\twidth,\n\t\t\t\t\t\theight,\n\t\t\t\t\t\tpxr,\n\t\t\t\t\t\tcanvasWidthPx,\n\t\t\t\t\t\tcanvasHeightPx,\n\t\t\t\t\t\trowHeight,\n\t\t\t\t\t\ttermCount: row.inputOrder.length,\n\t\t\t\t\t\txDendrogramHeight\n\t\t\t\t\t}\n\t\t\t\t)\n\t\t\t\tthis.dom.leftDendrogram.selectAll('*').remove()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst canvas = new OffscreenCanvas(canvasWidthPx, canvasHeightPx)\n\t\t\tconst ctx = canvas.getContext('2d')\n\t\t\tctx.scale(pxr, pxr)\n\t\t\tctx.imageSmoothingEnabled = false\n\t\t\tctx.imageSmoothingQuality = 'high'\n\t\t\tctx.strokeStyle = 'black'\n\n\t\t\tconst mergedClusters = new Map()\n\t\t\tfor (const [clusterid0, pair] of row.merge.entries()) {\n\t\t\t\t// pair is {n1,n2}, n1 and n2 form a new cluster; id of which is clusterid\n\n\t\t\t\tconst clusterid = clusterid0 + 1 // id of this cluster formed by pair, as used in hclust$merge; positive integer\n\t\t\t\tconst children = [] // collect all children leaves for this cluster\n\t\t\t\tconst childrenClusters = []\n\n\t\t\t\tlet x1, x2, y1, y2\n\t\t\t\tif (pair.n1 < 0) {\n\t\t\t\t\t// n1 is leaf\n\t\t\t\t\tconst [name, rowNumber] = getLeafNumber(pair.n1, row.inputOrder, row.order)\n\t\t\t\t\ty1 = rowHeight * (rowNumber + 0.5)\n\t\t\t\t\tx1 = xDendrogramHeight\n\t\t\t\t\tchildren.push({ name })\n\t\t\t\t} else {\n\t\t\t\t\t// n1 is cluster\n\t\t\t\t\tif (!mergedClusters.has(pair.n1)) throw 'pair.n1 is positive but not seen before'\n\t\t\t\t\tconst c = mergedClusters.get(pair.n1)\n\t\t\t\t\tx1 = c.x\n\t\t\t\t\ty1 = c.y\n\t\t\t\t\tchildren.push(...c.children)\n\t\t\t\t\tchildrenClusters.push(pair.n1)\n\t\t\t\t}\n\t\t\t\tif (pair.n2 < 0) {\n\t\t\t\t\t// n2 is leaf\n\t\t\t\t\tconst [name, rowNumber] = getLeafNumber(pair.n2, row.inputOrder, row.order)\n\t\t\t\t\ty2 = rowHeight * (rowNumber + 0.5)\n\t\t\t\t\tx2 = xDendrogramHeight\n\t\t\t\t\tchildren.push({ name })\n\t\t\t\t} else {\n\t\t\t\t\tif (!mergedClusters.has(pair.n2)) throw 'pair.n1 is positive but not seen before'\n\t\t\t\t\tconst c = mergedClusters.get(pair.n2)\n\t\t\t\t\tx2 = c.x\n\t\t\t\t\ty2 = c.y\n\t\t\t\t\tchildren.push(...c.children)\n\t\t\t\t\tchildrenClusters.push(pair.n2)\n\t\t\t\t}\n\t\t\t\t// cluster x position\n\t\t\t\tconst clusterX = xDendrogramHeight - row.height[clusterid0].height * height2px\n\n\t\t\t\tconst highlight = this.clickedLeftClusterIds?.includes(clusterid)\n\t\t\t\tctx.strokeStyle = highlight ? 'red' : 'black'\n\n\t\t\t\tctx.beginPath()\n\t\t\t\tctx.moveTo(x1, y1) // move to n1\n\t\t\t\tctx.lineTo(clusterX, y1) // h line right to cluster\n\t\t\t\tctx.lineTo(clusterX, y2) // v line down to n2\n\t\t\t\tctx.lineTo(x2, y2) // h line left to n2\n\t\t\t\tctx.stroke()\n\t\t\t\tctx.closePath()\n\n\t\t\t\tmergedClusters.set(clusterid, {\n\t\t\t\t\tx: clusterX,\n\t\t\t\t\ty: (y1 + y2) / 2,\n\t\t\t\t\tchildren,\n\t\t\t\t\tchildrenClusters,\n\t\t\t\t\tclusterPosition: {\n\t\t\t\t\t\tx1,\n\t\t\t\t\t\tx2,\n\t\t\t\t\t\ty1,\n\t\t\t\t\t\ty2,\n\t\t\t\t\t\tclusterX\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tconst t = this.termOrder.find(t => t.grp.type == 'hierCluster' || t.grp.name == this.hcTermGroup.name)\n\t\t\tconst y =\n\t\t\t\t// t.labelOffset is commented out because it is already handled in adjustSvgDimensions\n\t\t\t\tt.grpIndex * s.rowgspace +\n\t\t\t\tt.prevGrpTotalIndex * s.rowh /* + (t.labelOffset || 0) */ +\n\t\t\t\tt.totalHtAdjustments +\n\t\t\t\ts.margin.top +\n\t\t\t\ts.scrollHeight +\n\t\t\t\t// left dendrogram image must be lower than the top dendrogram image height\n\t\t\t\tyDendrogramHeight\n\t\t\tthis.renderImage(this.api, this.dom.leftDendrogram, canvas, width, height, 0, y)\n\n\t\t\trow.mergedClusters = mergedClusters\n\t\t}\n\t}\n}\n\nexport async function renderImage(componentApi, g, canvas, width, height, x, y) {\n\tconst sequenceId = componentApi.getSequenceId()\n\tconst reader = new FileReader()\n\treader.addEventListener(\n\t\t'load',\n\t\t() => {\n\t\t\tif (componentApi.isStaleSequenceId(sequenceId)) return\n\t\t\t// remove a previously rendered image, if applicable, right before replacing it\n\t\t\t// so that there will be no flicker on update\n\t\t\tg.selectAll('*').remove()\n\n\t\t\tg.append('image')\n\t\t\t\t.attr('x', x + 0.033)\n\t\t\t\t.attr('y', y + 0.033)\n\t\t\t\t.attr('xlink:href', reader.result)\n\t\t\t\t.attr('width', width)\n\t\t\t\t.attr('height', height)\n\t\t},\n\t\tfalse\n\t)\n\tconst blob = await canvas.convertToBlob({ quality: 1 })\n\treader.readAsDataURL(blob)\n\t// g.selectAll('*').remove()\n\t// const foCanvas = g.append('foreignObject').append('canvas').attr('width', width).attr('height', height).node()\n\t// const bitmap = canvas.transferToImageBitmap();\n\t// foCanvas.getContext(\"bitmaprenderer\").transferFromImageBitmap(bitmap);\n}\n\nfunction getHclustHeightScalefactor(lst, ph) {\n\t// scale hclust$height to on-screen max height (h) in number of pixels\n\tlet max = lst[0].height\n\tfor (const h of lst) max = Math.max(max, h.height)\n\treturn ph / max\n}\n\nfunction getLeafNumber(minus, inputOrder, order) {\n\tconst name = inputOrder[-minus - 1]\n\tif (!name) throw 'minus not in inputOrder'\n\tconst i = order.findIndex(j => j.name == name)\n\tif (i == -1) throw 'name not found in hc$order'\n\treturn [name, i]\n}\n"],
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+  "names": ["t"]
+}

package/dist/chunk-WGL6FIUE.js

@@ -0,0 +1,330 @@
+import {
+  getColors
+} from "./chunk-XYFDBYOY.js";
+import {
+  convertUnits,
+  isNumeric,
+  isStrictNumeric
+} from "./chunk-TV74I3Y5.js";
+import {
+  format
+} from "./chunk-OAWQ6LOO.js";
+
+// ../shared/utils/src/termdb.bins.js
+function validate_bins(binconfig) {
+  const bc = binconfig;
+  if (!bc || typeof bc !== "object") throw "bin schema must be an object";
+  if (!("type" in bc)) bc.type = "regular-bin";
+  if (bc.type == "custom-bin") {
+    if (!Array.isArray(bc.lst)) throw "binconfig.lst must be an array";
+    if (!bc.lst.length) throw "binconfig.lst must have entries";
+    const first_bin = bc.lst[0];
+    const last_bin = bc.lst[bc.lst.length - 1];
+    for (const bin of bc.lst) {
+      if (!("startinclusive" in bin) && !("stopinclusive" in bin)) {
+        throw "custom bin.startinclusive and/or bin.stopinclusive must be defined";
+      }
+      if (bin == first_bin) {
+        if ("startunbounded" in bin && !bin.startunbounded) {
+          throw `a custom first bin must not set bin.startunbounded to false`;
+        }
+        bin.startunbounded = true;
+        if ("start" in bin) {
+          throw "a custom first bin must not set a bin.start value";
+        }
+        if ("start_percentile" in bin) {
+          throw "the first bin must not set a bin.start_percentile value";
+        }
+        if (!("stop" in bin)) {
+          throw `a custom first bin must define a bin.stop value`;
+        }
+        if (!isStrictNumeric(bin.stop)) {
+          throw `a custom first bin.stop value should be numeric`;
+        }
+      } else if (bin == last_bin) {
+        if (!("start" in bin)) {
+          throw `a custom last bin must define a bin.start value`;
+        }
+        if (!isStrictNumeric(bin.start)) {
+          throw `a custom last bin.start must be numeric`;
+        }
+        if ("stopunbounded" in bin && !bin.stopunbounded) {
+          throw "a custom last bin must not set bin.stopunbounded to false";
+        }
+        bin.stopunbounded = true;
+        if ("stop" in bin) {
+          throw "a custom last bin must not set a bin.stop value";
+        }
+      } else {
+        if (bin.startunbounded || bin.stopunbounded) {
+          throw "bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins";
+        }
+        if (!isStrictNumeric(bin.start))
+          throw "bin.start must be numeric for a non-first bin";
+        if (!isStrictNumeric(bin.stop))
+          throw "bin.stop must be numeric for a non-last bin";
+      }
+    }
+  } else if (bc.type == "regular-bin") {
+    if (!Number.isFinite(bc.bin_size)) throw "non-numeric bin_size";
+    if (bc.bin_size <= 0) throw "bin_size must be greater than 0";
+    if (!bc.startinclusive && !bc.stopinclusive) {
+      bc.startinclusive = 1;
+      bc.stopinclusive = 0;
+    }
+    if (!bc.first_bin) throw "first_bin{} missing";
+    if (typeof bc.first_bin != "object") throw "first_bin{} is not an object";
+    if (!Object.keys(bc.first_bin).length) throw "first_bin is an empty object";
+    {
+      const b = bc.first_bin;
+      b.startunbounded = true;
+      if (b.stop_percentile) {
+        if (!Number.isInteger(b.stop_percentile))
+          throw "first_bin.stop_percentile should be integer";
+        if (b.stop_percentile <= 0 || b.stop_percentile >= 100)
+          throw "first_bin.stop_percentile out of bound (0-100)";
+      } else if (!Number.isFinite(b.stop)) {
+        throw "first_bin.stop not a number when stop_percentile is not set";
+      }
+    }
+    if (bc.last_bin) {
+      const b = bc.last_bin;
+      if (b.start_percentile) {
+        if (!Number.isInteger(b.start_percentile))
+          throw "last_bin.start_percentile should be integer";
+        if (b.start_percentile <= 0 || b.start_percentile >= 100)
+          throw "last_bin.start_percentile out of bound (0-100)";
+      } else if (!Number.isFinite(b.start)) {
+        throw "last_bin.start not a number when start_percentile is not set";
+      }
+      b.stopunbounded = true;
+      if ("stop" in b) {
+        throw "a regular last bin must not set a bin.stop value";
+      }
+    }
+  } else {
+    throw `invalid binconfig.type="${bc.type}"`;
+  }
+}
+function compute_bins(binconfig, summaryfxn, valueConversion) {
+  const bc = binconfig;
+  validate_bins(bc);
+  if (bc.lst) {
+    const k2c2 = getColors(bc.lst.length);
+    for (const bin of bc.lst) bin.color = k2c2(bin.label);
+  }
+  if (bc.type == "custom-bin") return JSON.parse(JSON.stringify(bc.lst));
+  if (typeof summaryfxn != "function")
+    throw "summaryfxn required for modules/termdb.bins.js compute_bins()";
+  const percentiles = target_percentiles(bc);
+  const summary = summaryfxn(percentiles);
+  if (!summary || typeof summary !== "object")
+    throw "invalid returned value by summaryfxn";
+  bc.results = { summary };
+  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
+  const minFloor = Math.floor(summary.min * 100) / 100;
+  const maxCeil = Math.ceil(summary.max * 100) / 100;
+  const min = bc.first_bin.startunbounded ? minFloor : bc.first_bin.start_percentile ? summary["p" + bc.first_bin.start_percentile] : bc.first_bin.start;
+  let max = maxCeil, last_start, last_stop;
+  if (bc.last_bin) {
+    max = bc.last_bin.stopunbounded ? maxCeil : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max ? bc.last_bin.stop : maxCeil;
+    last_start = isStrictNumeric(bc.last_bin.start_percentile) ? summary["p" + bc.last_bin.start_percentile] : isStrictNumeric(bc.last_bin.start) ? bc.last_bin.start : void 0;
+    last_stop = bc.last_bin.stopunbounded ? null : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isStrictNumeric(bc.last_bin.stop) ? bc.last_bin.stop : null;
+  } else if (bc.lst) {
+    const last_bin = bc.lst[bc.lst.length - 1];
+    last_start = last_bin.start;
+    last_stop = "stop" in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil;
+    max = last_stop;
+  } else {
+    last_start = maxCeil;
+    last_stop = maxCeil;
+  }
+  const numericMax = isStrictNumeric(max);
+  const numericLastStart = isStrictNumeric(last_start);
+  const numericLastStop = isStrictNumeric(last_stop);
+  if (!numericMax && !numericLastStart) return [];
+  const bins = [];
+  let currBin = {
+    startunbounded: bc.first_bin.startunbounded,
+    start: bc.first_bin.startunbounded ? void 0 : min,
+    stop: isStrictNumeric(bc.first_bin.stop_percentile) ? +summary["p" + bc.first_bin.stop_percentile] : isStrictNumeric(bc.first_bin.stop) ? +bc.first_bin.stop : min + bc.bin_size,
+    startinclusive: bc.startinclusive,
+    stopinclusive: bc.stopinclusive
+  };
+  if (!isStrictNumeric(currBin.stop))
+    throw "the computed first_bin.stop is non-numeric" + currBin.stop;
+  const maxNumBins = 100;
+  while (numericMax && currBin.stop <= max || currBin.startunbounded && !bins.length || currBin.stopunbounded) {
+    bins.push(currBin);
+    if (currBin.stop >= max) {
+      currBin.stopunbounded = true;
+      if (bins.length > 1) {
+        delete currBin.stop;
+      }
+    }
+    currBin.label = get_bin_label(currBin, bc, valueConversion);
+    if (currBin.stopunbounded) break;
+    const upper = currBin.stop + bc.bin_size;
+    const previousStop = currBin.stop;
+    currBin = {
+      startinclusive: bc.startinclusive,
+      stopinclusive: bc.stopinclusive,
+      start: previousStop,
+      stop: numericLastStop && (previousStop == last_start || upper > last_stop) ? last_stop : numericLastStart && upper > last_start && previousStop != last_start ? last_start : upper
+    };
+    if (currBin.stop >= max) {
+      currBin.stop = max;
+      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
+      if (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1;
+    }
+    if (numericLastStart && currBin.start == last_start) {
+      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
+    }
+    if (currBin.start > currBin.stop) {
+      if (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)
+        currBin.stopunbounded = true;
+      else break;
+    }
+    if (bins.length + 1 >= maxNumBins) {
+      bc.error = "max_num_bins_reached";
+      break;
+    }
+  }
+  delete bc.binLabelFormatter;
+  if (bins.length > 1) {
+    delete bins[bins.length - 1].stop;
+  }
+  const k2c = getColors(bins.length);
+  for (const bin of bins) bin.color = k2c(bin.label);
+  return bins;
+}
+function getNumDecimalsFormatter(bc) {
+  return "rounding" in bc ? format(bc.rounding) : (d) => d;
+}
+function get_bin_label(bin, binconfig, valueConversion) {
+  if (!bin) return "missing bin.label";
+  if (bin.label) return bin.label;
+  const bc = binconfig;
+  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
+  if (!bin.startunbounded && !bin.stopunbounded && !("startinclusive" in bin) && !("stopinclusive" in bin)) {
+    if (bc.startinclusive) bin.startinclusive = true;
+    else if (bc.stopinclusive) bin.stopinclusive = true;
+  }
+  const start = bc.use_as == "bins" || bin.start;
+  const stop = bc.use_as == "bins" || bin.stop;
+  let label_offset = 0;
+  if ("label_offset" in bc) {
+    bc.label_offset_ignored = "bin_size" in bc && bc.bin_size < bc.label_offset;
+    if (!bc.label_offset_ignored) label_offset = bc.label_offset;
+  } else if (bc.bin_size === 1 && bc.termtype == "integer") {
+    label_offset = 1;
+  }
+  if (bin.startunbounded) {
+    const oper = bin.stopinclusive ? "\u2264" : "<";
+    const v1 = valueConversion ? convertUnits(
+      stop,
+      valueConversion.fromUnit,
+      valueConversion.toUnit,
+      valueConversion.scaleFactor,
+      true
+    ) : bc.binLabelFormatter(stop);
+    return oper + v1;
+  }
+  if (bin.stopunbounded || start === stop) {
+    const oper = bin.startinclusive ? "\u2265" : ">";
+    const v0 = valueConversion ? convertUnits(
+      start,
+      valueConversion.fromUnit,
+      valueConversion.toUnit,
+      valueConversion.scaleFactor,
+      true
+    ) : bc.binLabelFormatter(start);
+    return oper + v0;
+  }
+  if (label_offset && bin.startinclusive && !bin.stopinclusive) {
+    if (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {
+      return "" + (valueConversion ? convertUnits(
+        start,
+        valueConversion.fromUnit,
+        valueConversion.toUnit,
+        valueConversion.scaleFactor,
+        true
+      ) : bc.binLabelFormatter(start));
+    } else {
+      const v0 = valueConversion ? convertUnits(
+        start,
+        valueConversion.fromUnit,
+        valueConversion.toUnit,
+        valueConversion.scaleFactor,
+        true
+      ) : bc.binLabelFormatter(start);
+      const v1 = valueConversion ? convertUnits(
+        stop - label_offset,
+        valueConversion.fromUnit,
+        valueConversion.toUnit,
+        valueConversion.scaleFactor,
+        true
+      ) : bc.binLabelFormatter(stop - label_offset);
+      return +v0 >= +v1 ? v0.toString() : v0 + " to " + v1;
+    }
+  } else {
+    const oper0 = bin.startinclusive ? "" : ">";
+    const oper1 = bin.stopinclusive ? "" : "<";
+    const v0 = valueConversion ? convertUnits(
+      start,
+      valueConversion.fromUnit,
+      valueConversion.toUnit,
+      valueConversion.scaleFactor,
+      true
+    ) : Number.isInteger(start) ? start : bc.binLabelFormatter(start);
+    const v1 = valueConversion ? convertUnits(
+      stop,
+      valueConversion.fromUnit,
+      valueConversion.toUnit,
+      valueConversion.scaleFactor,
+      true
+    ) : Number.isInteger(stop) ? stop : bc.binLabelFormatter(stop);
+    if (+v0 >= +v1) {
+      const oper = bin.startinclusive ? "\u2265" : ">";
+      return oper + v0;
+    } else {
+      return oper0 + v0 + " to " + oper1 + v1;
+    }
+  }
+}
+function get_bin_range_equation(bin, binconfig) {
+  const x = '<span style="font-family:Times;font-style:italic;">x</span>';
+  let range_eq;
+  const copy = structuredClone(bin);
+  copy.label = "";
+  const bin_label = get_bin_label(copy, binconfig);
+  if (bin.startunbounded || bin.stopunbounded) {
+    range_eq = x + " " + bin_label;
+  } else if (bin.startinclusive) {
+    range_eq = bin_label.replace("to <", "\u2264 " + x + " <");
+  } else if (bin.stopinclusive) {
+    range_eq = bin_label.replace(">", "").replace("to", "< " + x + " \u2264");
+  }
+  return range_eq;
+}
+function target_percentiles(binconfig) {
+  const percentiles = [];
+  const f = binconfig.first_bin;
+  if (f && isStrictNumeric(f.start_percentile))
+    percentiles.push(f.start_percentile);
+  if (f && isStrictNumeric(f.stop_percentile))
+    percentiles.push(f.stop_percentile);
+  const l = binconfig.last_bin;
+  if (l && isStrictNumeric(l.start_percentile))
+    percentiles.push(l.start_percentile);
+  if (l && isStrictNumeric(l.stop_percentile))
+    percentiles.push(l.stop_percentile);
+  return percentiles;
+}
+
+export {
+  compute_bins,
+  get_bin_label,
+  get_bin_range_equation
+};
+//# sourceMappingURL=chunk-WGL6FIUE.js.map