@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-JTX4Z2DL.js

@@ -1,274 +0,0 @@
-import {
-  TermTypes
-} from "./chunk-SOED2SLH.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:
-      const headerText = this.config?.headerText ? `${this.config.headerText} ` : "";
-      this.dom.header.text(`${headerText}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-JTX4Z2DL.js.map

package/dist/chunk-JTX4Z2DL.js.map

@@ -1,7 +0,0 @@
-{
-  "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\tconst headerText = this.config?.headerText ? `${this.config.headerText} ` : ''\n\t\t\tthis.dom.header.text(`${headerText}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) ? 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