@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-W345H42C.js

@@ -1,273 +0,0 @@
-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-WGHO2NCP.js

@@ -1,205 +0,0 @@
-import {
-  DownloadMenu,
-  ListSamples,
-  filterJoin,
-  getFilterItemByTag,
-  renderTable
-} from "./chunk-OXJ2TWDO.js";
-import {
-  niceNumLabels
-} from "./chunk-SEQLC4AD.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-6ITDJ5UR.js";
-
-// plots/violin.interactivity.js
-function setInteractivity(self) {
-  self.getChartImages = function() {
-    const charts = [];
-    for (const [key, chart] of Object.entries(self.data.charts)) {
-      const title = self.getChartTitle(chart.chartId);
-      const name = `${self.config.term.term.name}  ${title}`;
-      const chartDiv = chart.chartDiv;
-      charts.push({ name, svg: chartDiv.select("svg") });
-    }
-    return charts;
-  };
-  self.download = function(event) {
-    if (!self.state) return;
-    const name2svg = self.getChartImages();
-    const dm = new DownloadMenu(name2svg, self.config.term.term.name);
-    dm.show(event.clientX, event.clientY, event.target);
-  };
-  self.displayLabelClickMenu = function(t1, t2, plot, event) {
-    if (!t2) return;
-    if (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) return;
-    const label = t1.q.mode === "continuous" ? "term2" : "term";
-    const options = [];
-    if (this.app.getState().nav.header_mode !== "only_buttons")
-      options.push({
-        label: `Add filter: ${plot.label.split(",")[0]}`,
-        testid: "sjpp-violinLabOpt-addf",
-        callback: getAddFilterCallback(self, plot)
-      });
-    options.push({
-      label: `Hide: ${plot.label}`,
-      testid: "sjpp-violinLabOpt-hide",
-      callback: () => {
-        const term = self.config[label];
-        const isHidden = true;
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            [label]: {
-              isAtomic: true,
-              term: term.term,
-              q: getUpdatedQfromClick(plot, term, isHidden)
-            }
-          }
-        });
-      }
-    });
-    if (self.state.displaySampleIds && self.state.hasVerifiedToken) {
-      options.push({
-        label: `List samples`,
-        testid: "sjpp-violinLabOpt-list",
-        callback: async () => {
-          const [start, end] = [self.data.min, self.data.max];
-          await self.callListSamples(event, plot, start, end);
-        }
-      });
-    }
-    self.displayMenu(event, options);
-  };
-  self.displayBrushMenu = function(t1, t2, self2, plot, event, scale, isH) {
-    const selection = event.selection;
-    const [start, end] = isH ? [scale.invert(selection[0]), scale.invert(selection[1])] : [scale.invert(selection[1]), scale.invert(selection[0])];
-    const options = [];
-    if (this.app.getState().nav.header_mode === "with_tabs")
-      options.push({
-        label: `Add filter`,
-        testid: "sjpp-violinBrushOpt-addf",
-        callback: getAddFilterCallback(self2, plot, start, end)
-      });
-    if (self2.state.displaySampleIds && self2.state.hasVerifiedToken) {
-      options.push({
-        label: `List samples`,
-        testid: "sjpp-violinBrushOpt-list",
-        callback: async () => self2.callListSamples(event.sourceEvent, plot, start, end)
-      });
-    }
-    self2.displayMenu(event.sourceEvent, options, start, end);
-  };
-  self.displayMenu = function(event, options, start, end) {
-    const tip = self.dom.clicktip.clear().show(event.clientX, event.clientY);
-    const isBrush = start != null && end != null;
-    if (isBrush) {
-      const [niceStart, niceEnd] = self.config.term.term.type == "integer" ? [Math.round(start), Math.round(end)] : niceNumLabels([start, end]);
-      tip.d.append("div").style("margin", "10px").text(`From ${niceStart} to ${niceEnd}`);
-    }
-    tip.d.append("div").selectAll("div").data(options).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", (d) => d.testid).text((d) => d.label).on("click", async (event2, d) => {
-      if (event2.target._clicked) return;
-      event2.target._clicked = true;
-      event2.target.textContent = "Loading...";
-      await d.callback();
-      tip.hide();
-    });
-  };
-  self.getSampleList = function(plot, start, end) {
-    const { term, term2, term0 } = self.config;
-    const bins = self.data.bins;
-    const rangeStart = start !== void 0 ? start : null;
-    const rangeStop = end !== void 0 ? end : null;
-    const ls = new ListSamples({
-      app: self.app,
-      termfilter: self.state.termfilter,
-      term,
-      term2,
-      term0,
-      plot,
-      bins,
-      start: rangeStart,
-      end: rangeStop
-    });
-    return ls;
-  };
-  self.callListSamples = async function(event, plot, start, end) {
-    const ls = self.getSampleList(plot, start, end);
-    const data = await ls.getData();
-    const [rows, columns] = ls.setTableData(data);
-    const tip = self.dom.sampletabletip;
-    tip.clear().show(event.clientX, event.clientY, false);
-    renderTable({
-      rows,
-      columns,
-      div: tip.d,
-      showLines: true,
-      maxHeight: "40vh",
-      resize: true,
-      dataTestId: "sjpp-listsampletable"
-    });
-  };
-  self.labelHideLegendClicking = function(t2, plot) {
-    self.dom.legendDiv.selectAll(".sjpp-htmlLegend").on("click", (event) => {
-      event.stopPropagation();
-      const d = event.target.__data__;
-      const termNum = t2?.term.type === "condition" || t2?.term.type === "samplelst" || t2?.term.type === "categorical" || (t2?.term.type === "float" || t2?.term.type === "integer") && self.config.term?.q.mode === "continuous" ? "term2" : "term";
-      const term = self.config[termNum];
-      if (t2) {
-        for (const key of Object.keys(term?.q?.hiddenValues)) {
-          if (d.text === key) {
-            delete term.q.hiddenValues[key];
-          }
-        }
-        const isHidden = false;
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            [termNum]: {
-              isAtomic: true,
-              term: term.term,
-              q: getUpdatedQfromClick(plot, term, isHidden)
-            }
-          }
-        });
-      }
-    }).on("mouseover", (event) => {
-      const q = event.target.__data__;
-      if (q === void 0) return;
-      if (q.isHidden === true && q.isClickable === true) {
-        self.dom.hovertip.clear().show(event.clientX, event.clientY).d.append("span").text("Click to unhide plot");
-      }
-    }).on("mouseout", function() {
-      self.dom.hovertip.hide();
-    });
-  };
-}
-function getAddFilterCallback(self, plot, rangeStart, rangeStop) {
-  const ls = self.getSampleList(plot, rangeStart, rangeStop);
-  return () => {
-    const filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, "filterUiRoot");
-    const filter = filterJoin([filterUiRoot, ls.tvslst]);
-    filter.tag = "filterUiRoot";
-    self.app.dispatch({
-      type: "filter_replace",
-      filter
-    });
-  };
-}
-function getUpdatedQfromClick(plot, term, isHidden = false) {
-  const label = plot.label;
-  const valueId = term?.term?.values ? term?.term?.values?.[label]?.label : label;
-  const id = !valueId ? label : valueId;
-  const q = term.q;
-  if (!q.hiddenValues) q.hiddenValues = {};
-  if (isHidden) q.hiddenValues[id] = 1;
-  else delete q.hiddenValues[id];
-  return q;
-}
-
-export {
-  setInteractivity
-};
-//# sourceMappingURL=chunk-WGHO2NCP.js.map