@sjcrh/proteinpaint-client 2.182.1 → 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-WGL6FIUE.js

@@ -1,330 +0,0 @@
-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

package/dist/chunk-WGL6FIUE.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/termdb.bins.js"],
-  "sourcesContent": ["import { format } from \"d3-format\"\nimport { getColors } from \"./common.js\"\nimport { isNumeric, isStrictNumeric, convertUnits } from \"./helpers.js\"\n\nexport default function validate_bins(binconfig) {\n\t// Number.isFinite('1') returns false, which is desired\n\n\tconst bc = binconfig\n\tif (!bc || typeof bc !== \"object\") throw \"bin schema must be an object\"\n\t// assign default type\n\tif (!(\"type\" in bc)) bc.type = \"regular-bin\"\n\n\tif (bc.type == \"custom-bin\") {\n\t\tif (!Array.isArray(bc.lst)) throw \"binconfig.lst must be an array\"\n\t\tif (!bc.lst.length) throw \"binconfig.lst must have entries\"\n\t\tconst first_bin = bc.lst[0]\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\n\t\tfor (const bin of bc.lst) {\n\t\t\tif (!(\"startinclusive\" in bin) && !(\"stopinclusive\" in bin)) {\n\t\t\t\tthrow \"custom bin.startinclusive and/or bin.stopinclusive must be defined\"\n\t\t\t}\n\n\t\t\tif (bin == first_bin) {\n\t\t\t\tif (\"startunbounded\" in bin && !bin.startunbounded) {\n\t\t\t\t\tthrow `a custom first bin must not set bin.startunbounded to false`\n\t\t\t\t}\n\t\t\t\tbin.startunbounded = true\n\t\t\t\tif (\"start\" in bin) {\n\t\t\t\t\tthrow \"a custom first bin must not set a bin.start value\"\n\t\t\t\t}\n\t\t\t\tif (\"start_percentile\" in bin) {\n\t\t\t\t\tthrow \"the first bin must not set a bin.start_percentile value\"\n\t\t\t\t}\n\t\t\t\tif (!(\"stop\" in bin)) {\n\t\t\t\t\tthrow `a custom first bin must define a bin.stop value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.stop)) {\n\t\t\t\t\tthrow `a custom first bin.stop value should be numeric`\n\t\t\t\t}\n\t\t\t} else if (bin == last_bin) {\n\t\t\t\tif (!(\"start\" in bin)) {\n\t\t\t\t\tthrow `a custom last bin must define a bin.start value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) {\n\t\t\t\t\tthrow `a custom last bin.start must be numeric`\n\t\t\t\t}\n\t\t\t\tif (\"stopunbounded\" in bin && !bin.stopunbounded) {\n\t\t\t\t\tthrow \"a custom last bin must not set bin.stopunbounded to false\"\n\t\t\t\t}\n\t\t\t\tbin.stopunbounded = true\n\t\t\t\tif (\"stop\" in bin) {\n\t\t\t\t\tthrow \"a custom last bin must not set a bin.stop value\"\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t\t\t\tthrow \"bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins\"\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start))\n\t\t\t\t\tthrow \"bin.start must be numeric for a non-first bin\"\n\t\t\t\tif (!isStrictNumeric(bin.stop))\n\t\t\t\t\tthrow \"bin.stop must be numeric for a non-last bin\"\n\t\t\t}\n\t\t}\n\t} else if (bc.type == \"regular-bin\") {\n\t\t// required custom_bin parameter\n\t\tif (!Number.isFinite(bc.bin_size)) throw \"non-numeric bin_size\"\n\t\tif (bc.bin_size <= 0) throw \"bin_size must be greater than 0\"\n\n\t\tif (!bc.startinclusive && !bc.stopinclusive) {\n\t\t\tbc.startinclusive = 1\n\t\t\tbc.stopinclusive = 0\n\t\t}\n\n\t\tif (!bc.first_bin) throw \"first_bin{} missing\"\n\t\tif (typeof bc.first_bin != \"object\") throw \"first_bin{} is not an object\"\n\t\tif (!Object.keys(bc.first_bin).length) throw \"first_bin is an empty object\"\n\n\t\t{\n\t\t\tconst b = bc.first_bin\n\t\t\tb.startunbounded = true\n\t\t\t// requires stop_percentile, or stop\n\t\t\tif (b.stop_percentile) {\n\t\t\t\tif (!Number.isInteger(b.stop_percentile))\n\t\t\t\t\tthrow \"first_bin.stop_percentile should be integer\"\n\t\t\t\tif (b.stop_percentile <= 0 || b.stop_percentile >= 100)\n\t\t\t\t\tthrow \"first_bin.stop_percentile out of bound (0-100)\"\n\t\t\t} else if (!Number.isFinite(b.stop)) {\n\t\t\t\tthrow \"first_bin.stop not a number when stop_percentile is not set\"\n\t\t\t}\n\t\t}\n\n\t\tif (bc.last_bin) {\n\t\t\tconst b = bc.last_bin\n\t\t\t// requires start_percentile or start\n\t\t\tif (b.start_percentile) {\n\t\t\t\tif (!Number.isInteger(b.start_percentile))\n\t\t\t\t\tthrow \"last_bin.start_percentile should be integer\"\n\t\t\t\tif (b.start_percentile <= 0 || b.start_percentile >= 100)\n\t\t\t\t\tthrow \"last_bin.start_percentile out of bound (0-100)\"\n\t\t\t} else if (!Number.isFinite(b.start)) {\n\t\t\t\tthrow \"last_bin.start not a number when start_percentile is not set\"\n\t\t\t}\n\n\t\t\tb.stopunbounded = true\n\t\t\tif (\"stop\" in b) {\n\t\t\t\tthrow \"a regular last bin must not set a bin.stop value\"\n\t\t\t}\n\t\t}\n\t} else {\n\t\tthrow `invalid binconfig.type=\"${bc.type}\"`\n\t}\n}\n\nexport function compute_bins(binconfig, summaryfxn, valueConversion) {\n\t/*\n  Bins generator\n  \nbinconfig   \n  configuration of bins per the Numerical Binning Scheme\n\nsummaryfxn (percentiles)=> return {min, max, pX, pY, ...}\n  - required function\n\n  - must accept an array of desired percentile values\n  and returns an object of computed properties\n  {\n    min: minimum value\n    max: maximum value\n    pX: percentile at X value, so p10 will be 10th percentile value\n    pY: .. corresponding to the desired percentile values \n  }\n*/\n\tconst bc = binconfig\n\n\tvalidate_bins(bc)\n\tif (bc.lst) {\n\t\tconst k2c = getColors(bc.lst.length) //to color bins\n\t\tfor (const bin of bc.lst) bin.color = k2c(bin.label)\n\t}\n\tif (bc.type == \"custom-bin\") return JSON.parse(JSON.stringify(bc.lst))\n\tif (typeof summaryfxn != \"function\")\n\t\tthrow \"summaryfxn required for modules/termdb.bins.js compute_bins()\"\n\tconst percentiles = target_percentiles(bc)\n\tconst summary = summaryfxn(percentiles)\n\tif (!summary || typeof summary !== \"object\")\n\t\tthrow \"invalid returned value by summaryfxn\"\n\tbc.results = { summary }\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\n\t// round the min and max values for use as bin start and stop\n\t// in the first and last bins, respectively\n\tconst minFloor = Math.floor(summary.min * 100) / 100\n\tconst maxCeil = Math.ceil(summary.max * 100) / 100\n\tconst min = bc.first_bin.startunbounded\n\t\t? minFloor\n\t\t: bc.first_bin.start_percentile\n\t\t? summary[\"p\" + bc.first_bin.start_percentile]\n\t\t: bc.first_bin.start\n\tlet max = maxCeil, // in order to include the max value in the last bin\n\t\tlast_start,\n\t\tlast_stop\n\n\tif (bc.last_bin) {\n\t\tmax = bc.last_bin.stopunbounded\n\t\t\t? maxCeil // in order to include the max value in the last bin\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary[\"p\" + bc.last_bin.stop_percentile]\n\t\t\t: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max // '0.0088' < 0.0088\n\t\t\t? bc.last_bin.stop\n\t\t\t: maxCeil // in order to include the max value in the last bin\n\t\tlast_start = isStrictNumeric(bc.last_bin.start_percentile)\n\t\t\t? summary[\"p\" + bc.last_bin.start_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.start)\n\t\t\t? bc.last_bin.start\n\t\t\t: undefined\n\t\tlast_stop = bc.last_bin.stopunbounded\n\t\t\t? null\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary[\"p\" + bc.last_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.stop)\n\t\t\t? bc.last_bin.stop\n\t\t\t: null\n\t} else if (bc.lst) {\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\t\tlast_start = last_bin.start\n\t\tlast_stop =\n\t\t\t\"stop\" in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil\n\t\tmax = last_stop\n\t} else {\n\t\tlast_start = maxCeil\n\t\tlast_stop = maxCeil\n\t}\n\n\tconst numericMax = isStrictNumeric(max)\n\tconst numericLastStart = isStrictNumeric(last_start)\n\tconst numericLastStop = isStrictNumeric(last_stop)\n\n\tif (!numericMax && !numericLastStart) return [] //throw 'unable to compute the last bin start or stop'\n\n\tconst bins = []\n\tlet currBin = {\n\t\tstartunbounded: bc.first_bin.startunbounded,\n\t\tstart: bc.first_bin.startunbounded ? undefined : min,\n\t\tstop: isStrictNumeric(bc.first_bin.stop_percentile)\n\t\t\t? +summary[\"p\" + bc.first_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.first_bin.stop)\n\t\t\t? +bc.first_bin.stop\n\t\t\t: min + bc.bin_size,\n\t\tstartinclusive: bc.startinclusive,\n\t\tstopinclusive: bc.stopinclusive,\n\t}\n\n\tif (!isStrictNumeric(currBin.stop))\n\t\tthrow \"the computed first_bin.stop is non-numeric\" + currBin.stop\n\tconst maxNumBins = 100 // harcoded limit for now to not stress sqlite\n\n\twhile (\n\t\t(numericMax && currBin.stop <= max) ||\n\t\t(currBin.startunbounded && !bins.length) ||\n\t\tcurrBin.stopunbounded\n\t) {\n\t\tbins.push(currBin)\n\t\t// force a computed last bin to have stopunbounded true\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stopunbounded = true\n\t\t\tif (bins.length > 1) {\n\t\t\t\tdelete currBin.stop\n\t\t\t}\n\t\t}\n\t\tcurrBin.label = get_bin_label(currBin, bc, valueConversion)\n\t\tif (currBin.stopunbounded) break\n\n\t\tconst upper = currBin.stop + bc.bin_size\n\t\tconst previousStop = currBin.stop\n\t\tcurrBin = {\n\t\t\tstartinclusive: bc.startinclusive,\n\t\t\tstopinclusive: bc.stopinclusive,\n\t\t\tstart: previousStop,\n\t\t\tstop:\n\t\t\t\tnumericLastStop && (previousStop == last_start || upper > last_stop)\n\t\t\t\t\t? last_stop\n\t\t\t\t\t: numericLastStart && upper > last_start && previousStop != last_start\n\t\t\t\t\t? last_start\n\t\t\t\t\t: upper,\n\t\t}\n\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stop = max\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t\tif (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1\n\t\t}\n\t\tif (numericLastStart && currBin.start == last_start) {\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t}\n\t\tif (currBin.start > currBin.stop) {\n\t\t\tif (\n\t\t\t\tnumericLastStart &&\n\t\t\t\tcurrBin.stop == last_start &&\n\t\t\t\tbc.last_bin &&\n\t\t\t\tbc.last_bin.stopunbounded\n\t\t\t)\n\t\t\t\tcurrBin.stopunbounded = true\n\t\t\telse break\n\t\t}\n\t\tif (bins.length + 1 >= maxNumBins) {\n\t\t\tbc.error = \"max_num_bins_reached\"\n\t\t\tbreak\n\t\t}\n\t}\n\tdelete bc.binLabelFormatter\n\tif (bins.length > 1) {\n\t\tdelete bins[bins.length - 1].stop\n\t}\n\tconst k2c = getColors(bins.length) //to color bins\n\tfor (const bin of bins) bin.color = k2c(bin.label)\n\treturn bins\n}\n\nfunction getNumDecimalsFormatter(bc) {\n\t//return format('rounding' in bc ? bc.rounding : '')\n\treturn \"rounding\" in bc ? format(bc.rounding) : (d) => d // default to labeling using the start/stop value as-is\n}\n\nexport function get_bin_label(bin, binconfig, valueConversion) {\n\t/*\n  Generate a numeric bin label given a bin configuration and an optional term valueConversion object\n*/\n\tif (!bin) return \"missing bin.label\"\n\tif (bin.label) return bin.label\n\n\tconst bc = binconfig\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\tif (\n\t\t!bin.startunbounded &&\n\t\t!bin.stopunbounded &&\n\t\t!(\"startinclusive\" in bin) &&\n\t\t!(\"stopinclusive\" in bin)\n\t) {\n\t\tif (bc.startinclusive) bin.startinclusive = true\n\t\telse if (bc.stopinclusive) bin.stopinclusive = true\n\t}\n\n\tconst start = bc.use_as == \"bins\" || bin.start\n\tconst stop = bc.use_as == \"bins\" || bin.stop\n\n\tlet label_offset = 0\n\tif (\"label_offset\" in bc) {\n\t\tbc.label_offset_ignored = \"bin_size\" in bc && bc.bin_size < bc.label_offset\n\t\tif (!bc.label_offset_ignored) label_offset = bc.label_offset\n\t} else if (bc.bin_size === 1 && bc.termtype == \"integer\") {\n\t\tlabel_offset = 1\n\t}\n\n\t// one side-unbounded bins\n\t// label will be \">v\" or \"<v\"\n\tif (bin.startunbounded) {\n\t\tconst oper = bin.stopinclusive ? \"\u2264\" : \"<\" // \\u2264\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstop,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: bc.binLabelFormatter(stop) //bin.startinclusive && label_offset ? stop - label_offset : stop)\n\t\treturn oper + v1\n\t}\n\t// a data value may coincide with the last bin's start\n\tif (bin.stopunbounded || start === stop) {\n\t\tconst oper = bin.startinclusive /*|| label_offset*/ ? \"\u2265\" : \">\" // \\u2265\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstart,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: bc.binLabelFormatter(start) //bin.startinclusive || start == min ? start : start + label_offset)\n\t\treturn oper + v0\n\t}\n\n\t// two-sided bins\n\tif (label_offset && bin.startinclusive && !bin.stopinclusive) {\n\t\tif (\n\t\t\tNumber.isInteger(bc.bin_size) &&\n\t\t\tMath.abs(start - stop) === label_offset\n\t\t) {\n\t\t\t// make a simpler label when the range simply spans the bin_size\n\t\t\treturn (\n\t\t\t\t\"\" +\n\t\t\t\t(valueConversion\n\t\t\t\t\t? convertUnits(\n\t\t\t\t\t\t\tstart,\n\t\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\t\ttrue\n\t\t\t\t\t  )\n\t\t\t\t\t: bc.binLabelFormatter(start))\n\t\t\t)\n\t\t} else {\n\t\t\tconst v0 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstart,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(start)\n\t\t\tconst v1 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstop - label_offset,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(stop - label_offset)\n\t\t\t// ensure that last two bin labels make sense (the last is stopunbounded)\n\t\t\treturn +v0 >= +v1 ? v0.toString() : v0 + \" to \" + v1\n\t\t}\n\t} else {\n\t\t// stop_inclusive || label_offset == 0\n\t\tconst oper0 = bin.startinclusive ? \"\" : \">\"\n\t\tconst oper1 = bin.stopinclusive ? \"\" : \"<\"\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstart,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: Number.isInteger(start)\n\t\t\t? start\n\t\t\t: bc.binLabelFormatter(start)\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstop,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: Number.isInteger(stop)\n\t\t\t? stop\n\t\t\t: bc.binLabelFormatter(stop)\n\t\t// after rounding the bin labels, the bin start may equal the last bin stop as derived from actual data\n\t\tif (+v0 >= +v1) {\n\t\t\tconst oper = bin.startinclusive ? \"\u2265\" : \">\" // \\u2265\n\t\t\treturn oper + v0\n\t\t} else {\n\t\t\treturn oper0 + v0 + \" to \" + oper1 + v1\n\t\t}\n\t}\n}\n\n// get bin range equation from bin label and bin properties\nexport function get_bin_range_equation(bin, binconfig) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;\">x</span>'\n\tlet range_eq\n\t// should always use computed (not user-customized) bin label to determine bin range text\n\tconst copy = structuredClone(bin)\n\tcopy.label = \"\" // mutate only the copy, and not the original bin argument\n\tconst bin_label = get_bin_label(copy, binconfig)\n\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t// first or last bins, e.g. x \u2264 14 and x > 16\n\t\trange_eq = x + \" \" + bin_label\n\t} else if (bin.startinclusive) {\n\t\t// bins with startinclusive, e.g. 14 \u2264 x < 16\n\t\trange_eq = bin_label.replace(\"to <\", \"\u2264 \" + x + \" <\")\n\t} else if (bin.stopinclusive) {\n\t\t// bins with stopinclusive, e.g. 14 < x \u2264 16\n\t\trange_eq = bin_label.replace(\">\", \"\").replace(\"to\", \"< \" + x + \" \u2264\")\n\t}\n\treturn range_eq\n}\n\nexport function target_percentiles(binconfig) {\n\tconst percentiles = []\n\tconst f = binconfig.first_bin\n\tif (f && isStrictNumeric(f.start_percentile))\n\t\tpercentiles.push(f.start_percentile)\n\tif (f && isStrictNumeric(f.stop_percentile))\n\t\tpercentiles.push(f.stop_percentile)\n\tconst l = binconfig.last_bin\n\tif (l && isStrictNumeric(l.start_percentile))\n\t\tpercentiles.push(l.start_percentile)\n\tif (l && isStrictNumeric(l.stop_percentile))\n\t\tpercentiles.push(l.stop_percentile)\n\treturn percentiles\n}\n"],
-  "mappings": 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