@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/chunk-42VFF74T.js

@@ -0,0 +1,397 @@
+import {
+  CNVkey2order
+} from "./chunk-SPFK5XZH.js";
+import {
+  TermTypes,
+  colorScaleMap,
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel,
+  dtsv
+} from "./chunk-57Z4VYLM.js";
+import {
+  convertUnits
+} from "./chunk-W5J3LTYS.js";
+
+// plots/matrix/matrix.cells.js
+function setNumericCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
+  const key = anno.key;
+  const values = tw.term.values || {};
+  cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
+  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color || self.data.refs.byTermId?.[tw.$id]?.bins?.find((b) => anno.key == b.name)?.color;
+  cell.order = t.ref.bins ? t.ref.bins.findIndex((bin) => bin.name == key) : 0;
+  if (tw.q?.mode == "continuous") {
+    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
+    const twSettings = twSpecificSettings[tw.$id];
+    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
+    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+    const specialValue = tw.term.values?.[cell.key];
+    if (specialValue?.uncomputable) {
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = height * i;
+      cell.height = twSettings.contBarH;
+      cell.fill = "transparent";
+      const group = tw.legend?.group || tw.$id;
+      return;
+    }
+    cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.contBarColor || "#555";
+    if (s.transpose) {
+      cell.height = t.scale(cell.key);
+      cell.x = twSettings.contBarGap;
+    } else {
+      const vc = cell.term.valueConversion;
+      let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
+      if (tw.q.convert2ZScore) {
+        renderV = (renderV - t.mean) / t.std;
+        cell.fill = renderV > 0 ? "#FF6666" : "#6666FF";
+        cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
+      }
+      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2);
+      cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
+      cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
+    }
+  } else {
+    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+    cell.y = height * i;
+    const group = tw.legend?.group || tw.$id;
+    return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
+  }
+}
+function setSurvivalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
+  const key = tw.q?.mode == "continuous" ? anno.value : anno.key;
+  cell.key = key;
+  cell.label = tw.q?.mode == "continuous" ? tw.term.unit ? `${key} ${tw.term.unit}` : key : tw.term.values?.[key].label ? tw.term.values?.[key].label : "Exit code: " + key;
+  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || (key == 1 ? "#a1a3a6" : "#a3c88b");
+  cell.order = 0;
+  if (tw.q?.mode == "continuous") {
+    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
+    const twSettings = twSpecificSettings[tw.$id];
+    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
+    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+    cell.exitCodeKey = tw.term.values?.[anno.key].label || "Exit code: " + anno.key;
+    cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[anno.key]?.color || (anno.key == 1 ? "#a1a3a6" : "#a3c88b");
+    if (s.transpose) {
+      cell.height = t.scale(cell.key);
+      cell.x = twSettings.contBarGap;
+    } else {
+      const vc = cell.term.valueConversion;
+      let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
+      if (tw.q.convert2ZScore) {
+        renderV = (renderV - t.mean) / t.std;
+        cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
+      }
+      cell.label = tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2);
+      cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
+      cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
+    }
+  } else {
+    const vc = cell.term.valueConversion;
+    cell.timeToEventKey = vc ? convertUnits(anno.value, vc.fromUnit, vc.toUnit, vc.scaleFactor) : anno.value.toFixed(2);
+    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+    cell.y = height * i;
+    const group = tw.legend?.group || tw.$id;
+    return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
+  }
+}
+function setCategoricalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
+  const values = tw.term.values || {};
+  const key = anno.key;
+  cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
+  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color;
+  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+  cell.y = height * i;
+  const group = tw.legend?.group || tw.$id;
+  return { ref: t.ref, group, value: anno.key, entry: { key, label: cell.label, fill: cell.fill } };
+}
+function setMultivalueCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
+  const key = value?.key ?? anno.key;
+  const values = tw.term.values || {};
+  cell.key = key;
+  cell.label = values[key]?.label || key;
+  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || values[key]?.color;
+  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+  cell.y = height * i;
+  const group = tw.legend?.group || tw.$id;
+  return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
+}
+function setGeneVariantCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
+  if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
+    cell.label = value;
+    const groupset = tw.q.type == "custom-groupset" ? tw.q.customset : tw.term.groupsetting.lst[tw.q.predefined_groupset_idx];
+    if (!groupset) throw "groupset not found";
+    const group = groupset.groups.find((group2) => group2.name == value);
+    if (!group) throw "group not found";
+    cell.fill = group.color;
+    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+    cell.y = height * i;
+    return {
+      ref: t.ref,
+      group: tw.legend?.group || tw.$id,
+      value,
+      entry: { key: anno.key, label: cell.label, fill: cell.fill }
+    };
+  } else {
+    const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
+    const colorFromq = tw.q?.values && tw.q?.values[value.class]?.color;
+    cell.label = value.label || self.mclass[value.class].label;
+    cell.fill = self.getValueColor?.(value.value) || colorFromq || value.color || self.mclass[value.class]?.color;
+    cell.class = value.class;
+    cell.value = value;
+    const colw = self.dimensions.colw;
+    if (s.cellEncoding == "") {
+      cell.height = s.rowh / values.length;
+      cell.width = colw;
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = height * i;
+    } else if (value.dt == dtsnvindel || value.dt == dtfusionrna || value.dt == dtsv) {
+      if (s.cellEncoding == "single") {
+        cell.height = s.rowh;
+        cell.width = colw;
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = 0;
+      } else {
+        const divisor = 3;
+        cell.height = s.rowh / divisor;
+        cell.width = colw;
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = height * 0.33333;
+        if (s.oncoPrintSNVindelCellBorder) {
+          cell.border = true;
+        }
+      }
+    } else if (value.dt == dtcnv || value.dt == dtgeneexpression) {
+      cell.height = s.rowh;
+      cell.width = colw;
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = 0;
+    } else {
+      throw `cannot set cell props for dt='${value.dt}'`;
+    }
+    if (value.class == "Blank" || value.class == "WT") {
+      cell.label = `${self.dt2label[value.dt]} ${cell.label}`;
+    }
+    const byDt = self.state.termdbConfig.assayAvailability?.byDt;
+    const order = CNVkey2order(value.class);
+    if (value.dt == dtcnv) {
+      if (t.scales && value.class.startsWith("CNV_")) {
+        const {
+          /*maxLoss,*/
+          maxGain,
+          minLoss,
+          /*minGain,*/
+          absMax
+        } = t.scales;
+        value.scaledValue = value.value < 0 ? value.value / -absMax : value.value / absMax;
+        cell.fill = value.value < 0 ? t.scales.loss(value.scaledValue) : t.scales.gain(value.scaledValue);
+        return {
+          ref: t.ref,
+          group: "CNV",
+          value: value.class,
+          order: -1,
+          entry: {
+            key: value.class,
+            label: cell.label,
+            scale: value.class == "CNV_loss" ? t.scales.loss : t.scales.gain,
+            domain: t.domain ? t.domain : value.class == "CNV_loss" ? [0, -minLoss] : [0, maxGain],
+            colors: t.range,
+            scales: value.dt == 4 && t.scales,
+            minLabel: 0,
+            maxLabel: value.class == "CNV_loss" ? minLoss : maxGain,
+            order,
+            dt: value.dt,
+            origin: value.origin
+          }
+        };
+      } else {
+        const group = "CNV";
+        return {
+          ref: t.ref,
+          group,
+          value: value.class,
+          order: -1,
+          entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
+        };
+      }
+    } else if (value.dt == dtfusionrna && byDt?.[dtfusionrna]) {
+      const group = "Fusion RNA";
+      return {
+        ref: t.ref,
+        group,
+        value: value.class,
+        order: -1,
+        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
+      };
+    } else if (value.dt == dtsv && byDt?.[dtsv]) {
+      const group = "Structural Variation";
+      return {
+        ref: t.ref,
+        group,
+        value: value.class,
+        order: -1,
+        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
+      };
+    } else if (value.dt == dtgeneexpression) {
+      return {
+        ref: t.ref,
+        group: self.config.settings.hierCluster?.termGroupName || "Gene Expression",
+        value: value.class,
+        order: -1,
+        entry: {
+          key: value.class,
+          label: "",
+          scale: self.geneExpValues.scale,
+          domain: [0, 0.5, 1],
+          minLabel: self.geneExpValues.min,
+          maxLabel: self.geneExpValues.max,
+          order,
+          dt: value.dt,
+          origin: value.origin
+        }
+      };
+    } else {
+      const controlLabels = self.settings.matrix.controlLabels;
+      const group = tw.legend?.group || (value.origin ? `${value.origin[0].toUpperCase() + value.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations);
+      return {
+        ref: t.ref,
+        group,
+        value: value.class,
+        order: -2,
+        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
+      };
+    }
+  }
+}
+function setHierClusterCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
+  const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
+  cell.label = value.value;
+  cell.fill = self.getValueColor?.(value.value);
+  cell.value = value;
+  const colw = self.dimensions.colw;
+  cell.height = s.clusterRowh;
+  cell.width = colw;
+  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+  cell.y = height * i;
+  const hierCluster = self.config.settings.hierCluster;
+  let groupName;
+  if (hierCluster?.termGroupName) {
+    groupName = hierCluster.termGroupName;
+  } else if (tw.term.type == "geneExpression") {
+    groupName = "Gene Expression";
+    const unit = self.app.vocabApi.termdbConfig.queries?.geneExpression?.unit;
+    if (hierCluster?.zScoreTransformation) groupName += " (Z-score)";
+    else if (unit) groupName += ` (${unit})`;
+  } else if (tw.term.type == "metaboliteIntensity") {
+    groupName = "Intensity";
+  } else if (tw.term.type == "proteomeAbundance") {
+    groupName = "Protein Abundance";
+  } else {
+    groupName = "Heatmap color scale";
+  }
+  return {
+    ref: t.ref,
+    group: groupName,
+    order: -1,
+    entry: {
+      label: "",
+      scale: self.hierClusterValues.scale,
+      domain: colorScaleMap[self.settings.hierCluster.colorScale].domain,
+      minLabel: self.hierClusterValues.min,
+      maxLabel: self.hierClusterValues.max,
+      order: 0,
+      dt: value.dt
+    }
+  };
+}
+function getEmptyCell(cellTemplate, s, d) {
+  const cell = Object.assign({}, cellTemplate);
+  cell.fill = s.cellbg;
+  cell.height = s.rowh;
+  cell.width = d.colw;
+  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
+  cell.y = 0;
+  return cell;
+}
+var setCellProps = {
+  // some of these have been replaced by addOns{setCellProps} in matrix.xtw.ts,
+  // but leaving here for now since non-classed tw's may still use these
+  categorical: setCategoricalCellProps,
+  condition: setCategoricalCellProps,
+  multivalue: setMultivalueCellProps,
+  integer: setNumericCellProps,
+  float: setNumericCellProps,
+  survival: setSurvivalCellProps,
+  geneVariant: setGeneVariantCellProps,
+  hierCluster: setHierClusterCellProps,
+  [TermTypes.GENE_EXPRESSION]: setNumericCellProps,
+  [TermTypes.METABOLITE_INTENSITY]: setNumericCellProps,
+  [TermTypes.PROTEOME_ABUNDANCE]: setNumericCellProps
+  //termCollection: setTermCollectionCellProps
+};
+var maySetEmptyCell = {
+  geneVariant: setVariantEmptyCell,
+  integer: setNumericEmptyCell,
+  float: setNumericEmptyCell,
+  categorical: setDefaultEmptyCell,
+  condition: setDefaultEmptyCell,
+  multivalue: setDefaultEmptyCell,
+  survival: setNumericEmptyCell,
+  [TermTypes.GENE_EXPRESSION]: setNumericEmptyCell,
+  [TermTypes.METABOLITE_INTENSITY]: setNumericEmptyCell,
+  [TermTypes.PROTEOME_ABUNDANCE]: setNumericEmptyCell
+};
+function setVariantEmptyCell(siblingCells, cellTemplate, s, d) {
+  if (siblingCells.find((c) => c.value.dt == dtcnv)) return;
+  const cell = Object.assign({}, cellTemplate);
+  cell.fill = s.cellbg;
+  cell.height = s.rowh;
+  cell.width = d.colw;
+  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
+  cell.y = 0;
+  return cell;
+}
+function setNumericEmptyCell(siblingCells, cellTemplate, s, d, self) {
+  const q = cellTemplate.tw.q;
+  if (q.mode != "continuous") {
+    if (siblingCells.length) return;
+    setDefaultEmptyCell(siblingCells, cellTemplate, s, d);
+  } else {
+    if (q?.mode != "continuous") return;
+    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+    const twSettings = twSpecificSettings[cellTemplate.$id];
+    const h = twSettings ? twSettings.contBarH + 2 * twSettings.contBarGap : s.rowh;
+    if (cellTemplate.height >= h) return;
+    const cell = Object.assign({}, cellTemplate);
+    cell.fill = s.cellbg;
+    cell.height = h || s.rowh;
+    cell.width = d.colw;
+    cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
+    cell.y = 0;
+    return cell;
+  }
+}
+function setDefaultEmptyCell(siblingCells, cellTemplate, s, d) {
+  if (siblingCells.length) return;
+  const cell = Object.assign({}, cellTemplate);
+  cell.fill = s.cellbg;
+  cell.height = s.rowh;
+  cell.width = d.colw;
+  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
+  cell.y = 0;
+  return cell;
+}
+
+export {
+  setGeneVariantCellProps,
+  setHierClusterCellProps,
+  getEmptyCell,
+  setCellProps,
+  maySetEmptyCell
+};
+//# sourceMappingURL=chunk-42VFF74T.js.map

package/dist/chunk-4ENIOXIT.js

@@ -0,0 +1,133 @@
+import {
+  formatRangeBounds
+} from "./chunk-6XKAOSQE.js";
+import {
+  roundValueAuto
+} from "./chunk-TLT4YIG3.js";
+import {
+  brushX
+} from "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// filter/tvs.density.js
+function addBrushes(self, new_brush_location) {
+  const brushes = self.num_obj.brushes;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  const rawDecile = (maxvalue - minvalue) / 10;
+  const decile = self.tvs.term.type == "integer" ? Math.floor(rawDecile) : rawDecile;
+  for (const [i, r] of self.num_obj.ranges.entries()) {
+    const _b = brushes.find((b) => b.orig === r);
+    let brush;
+    if (!_b) {
+      brush = { orig: r, range: JSON.parse(JSON.stringify(r)) };
+      brushes.push(brush);
+    } else {
+      brush = _b;
+    }
+    if (r.start === "") {
+      if (new_brush_location == "center") brush.range.start = minvalue + decile * 4;
+      else brush.range.start = minvalue + decile * 8;
+    }
+    if (r.stop === "") {
+      if (new_brush_location == "center") brush.range.stop = minvalue + decile * 6;
+      else brush.range.stop = Math.floor(maxvalue);
+    }
+  }
+  const range_brushes = self.num_obj.brush_g.selectAll(".range_brush").data(brushes, (d) => brushes.indexOf(d));
+  range_brushes.exit().remove();
+  range_brushes.each(function(d, i) {
+    select_default(this).selectAll(".overlay").style("pointer-events", "all");
+  });
+  range_brushes.enter().append("g").attr("class", "range_brush").each(function(brush, i) {
+    applyBrush(self, this, brush, i);
+  });
+}
+function applyBrush(self, elem, brush) {
+  if (!brush.elem) brush.elem = select_default(elem);
+  const range = brush.range;
+  const plot_size = self.num_obj.plot_size;
+  const xscale = self.num_obj.xscale;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  brush.d3brush = brushX().extent([
+    [0, 0],
+    [plot_size.width, plot_size.height]
+  ]).on("brush", function(event, d) {
+    const s = event.selection;
+    if (!s) return;
+    const inputRange = brush.rangeInput.getRange();
+    if (inputRange?.value != void 0) {
+      brush.range = inputRange;
+      return;
+    }
+    updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, self.tvs.term.type);
+    const [start, stop] = setStartStopDisplays(range, inputRange, brush.rangeInput.scaleFactor);
+    brush.rangeInput.getInput().node().value = `${start} x ${stop}`;
+  }).on("end", function() {
+    brush.elem.selectAll(".overlay").style("pointer-events", "none");
+  });
+  const clamp = (v) => Math.min(Math.max(v, minvalue), maxvalue);
+  const brush_start = range.startunbounded ? minvalue : clamp(range.start);
+  const brush_stop = range.stopunbounded ? maxvalue : clamp(range.stop);
+  brush.init = () => {
+    if (range.value == void 0)
+      brush.elem.call(brush.d3brush).call(brush.d3brush.move, [brush_start, brush_stop].map(xscale));
+  };
+  if (range.startunbounded) delete range.start;
+  if (range.stopunbounded) delete range.stop;
+  brush.elem.selectAll(".selection").style(
+    "fill",
+    brush.orig.start === "" && brush.orig.stop === "" || JSON.stringify(range) != JSON.stringify(brush.orig) ? "#23cba7" : "#777777"
+  );
+}
+function updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, type) {
+  range.start = convertRangeValue(xscale, s[0]);
+  range.stop = convertRangeValue(xscale, s[1]);
+  const min = roundValueAuto(Number(minvalue));
+  const max = roundValueAuto(Number(maxvalue));
+  if (range.start < min) range.start = min;
+  if (range.stop > max) range.stop = max;
+  range.startunbounded = min == range.start && inputRange.startunbounded;
+  range.stopunbounded = max == range.stop && inputRange.stopunbounded;
+  const startAtEdge = !range.startunbounded && range.start == min, stopAtEdge = !range.stopunbounded && range.stop == max;
+  if (type == "integer") {
+    range.start = range.startunbounded ? "" : Math.round(range.start);
+    range.stop = range.stopunbounded ? "" : Math.round(range.stop);
+  }
+  if (startAtEdge && Number.isFinite(inputRange.start) && inputRange.start <= minvalue) range.start = inputRange.start;
+  if (stopAtEdge && Number.isFinite(inputRange.stop) && inputRange.stop >= maxvalue) range.stop = inputRange.stop;
+}
+function setStartStopDisplays(range, inputRange, scaleFactor = 1) {
+  return formatRangeBounds(
+    {
+      ...range,
+      startinclusive: inputRange.startinclusive,
+      stopinclusive: inputRange.stopinclusive
+    },
+    scaleFactor
+  );
+}
+function convertRangeValue(xscale, sidx) {
+  const value = Number(xscale.invert(sidx));
+  return roundValueAuto(value);
+}
+function addNewBrush(self, new_brush_location = "end", callback) {
+  const new_range = { start: "", stop: "", index: self.tvs.ranges.length };
+  self.num_obj.ranges.push(new_range);
+  const brush = { orig: new_range, range: JSON.parse(JSON.stringify(new_range)) };
+  self.num_obj.brushes.push(brush);
+  addBrushes(self, new_brush_location);
+  if (callback) callback();
+  brush.init();
+}
+
+export {
+  addBrushes,
+  updateTempRanges,
+  setStartStopDisplays,
+  addNewBrush
+};
+//# sourceMappingURL=chunk-4ENIOXIT.js.map

package/dist/chunk-4ENIOXIT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../filter/tvs.density.js"],
+  "sourcesContent": ["import { select } from 'd3-selection'\nimport { brushX } from 'd3-brush'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { formatRangeBounds } from '#dom/numericRangeInput'\n\n/*\n********************** EXPORTED\naddBrushes()// add brushed to densityplot from self.num_obj.brushes and \n            // new brush at end or center of plot\naddNewBrush() // add new brush either at end (with existing ranges) or in center (no ranges)\n\n********************** INTERNAL\napplyBrush() // main function to define and init d3 brushes, \n             // it will handle events such as brush move, drag\n             // and will update input elements attached to brush, e.g. brush.rangeInput\n\n*/\n\nexport function addBrushes(self, new_brush_location) {\n\t// const ranges = self.num_obj.ranges\n\tconst brushes = self.num_obj.brushes\n\tconst maxvalue = self.num_obj.density_data.max\n\tconst minvalue = self.num_obj.density_data.min\n\tconst rawDecile = (maxvalue - minvalue) / 10\n\tconst decile = self.tvs.term.type == 'integer' ? Math.floor(rawDecile) : rawDecile\n\n\tfor (const [i, r] of self.num_obj.ranges.entries()) {\n\t\tconst _b = brushes.find(b => b.orig === r)\n\t\tlet brush\n\t\tif (!_b) {\n\t\t\tbrush = { orig: r, range: JSON.parse(JSON.stringify(r)) }\n\t\t\tbrushes.push(brush)\n\t\t} else {\n\t\t\tbrush = _b\n\t\t}\n\t\t// strict equality to not have false positive with start=0\n\t\tif (r.start === '') {\n\t\t\tif (new_brush_location == 'center') brush.range.start = minvalue + decile * 4\n\t\t\telse brush.range.start = minvalue + decile * 8\n\t\t}\n\t\tif (r.stop === '') {\n\t\t\tif (new_brush_location == 'center') brush.range.stop = minvalue + decile * 6\n\t\t\telse brush.range.stop = Math.floor(maxvalue)\n\t\t}\n\t}\n\n\tconst range_brushes = self.num_obj.brush_g.selectAll('.range_brush').data(brushes, d => brushes.indexOf(d))\n\n\trange_brushes.exit().remove()\n\n\t// add update to brush if required\n\trange_brushes.each(function (d, i) {\n\t\tselect(this).selectAll('.overlay').style('pointer-events', 'all')\n\t})\n\n\trange_brushes\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('class', 'range_brush')\n\t\t.each(function (brush, i) {\n\t\t\tapplyBrush(self, this, brush, i)\n\t\t})\n}\n\nfunction applyBrush(self, elem, brush) {\n\tif (!brush.elem) brush.elem = select(elem)\n\tconst range = brush.range\n\tconst plot_size = self.num_obj.plot_size\n\tconst xscale = self.num_obj.xscale\n\tconst maxvalue = self.num_obj.density_data.max\n\tconst minvalue = self.num_obj.density_data.min\n\n\tbrush.d3brush = brushX()\n\t\t.extent([\n\t\t\t[0, 0],\n\t\t\t[plot_size.width, plot_size.height]\n\t\t])\n\t\t.on('brush', function (event, d) {\n\t\t\tconst s = event.selection\n\t\t\tif (!s) return // not an event triggered by brush dragging\n\t\t\t// brush.rangeInput is created from NumericRangeInput() as called in tvs.numeric.js\n\t\t\t// when filling a menu with or without density plot, should always be present\n\t\t\tconst inputRange = brush.rangeInput.getRange()\n\t\t\tif (inputRange?.value != undefined) {\n\t\t\t\tbrush.range = inputRange\n\t\t\t\treturn\n\t\t\t}\n\t\t\t//update temp_ranges\n\t\t\tupdateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, self.tvs.term.type)\n\n\t\t\t// the brush works in the unit the term's values are stored in, the <input> in the user-facing one\n\t\t\tconst [start, stop] = setStartStopDisplays(range, inputRange, brush.rangeInput.scaleFactor)\n\t\t\t// update inputs from brush move\n\t\t\tbrush.rangeInput.getInput().node().value = `${start} x ${stop}`\n\t\t})\n\t\t.on('end', function () {\n\t\t\t//diable pointer-event for multiple brushes\n\t\t\tbrush.elem.selectAll('.overlay').style('pointer-events', 'none')\n\t\t})\n\n\t// a saved bound may lie outside of the data, e.g. a typed bound kept by updateTempRanges(), or a range\n\t// saved under a filter that has since changed; clamp it so the brush stays on the plot\n\tconst clamp = v => Math.min(Math.max(v, minvalue), maxvalue)\n\tconst brush_start = range.startunbounded ? minvalue : clamp(range.start)\n\tconst brush_stop = range.stopunbounded ? maxvalue : clamp(range.stop)\n\tbrush.init = () => {\n\t\tif (range.value == undefined)\n\t\t\tbrush.elem.call(brush.d3brush).call(brush.d3brush.move, [brush_start, brush_stop].map(xscale))\n\t}\n\n\tif (range.startunbounded) delete range.start\n\tif (range.stopunbounded) delete range.stop\n\tbrush.elem\n\t\t.selectAll('.selection')\n\t\t.style(\n\t\t\t'fill',\n\t\t\t(brush.orig.start === '' && brush.orig.stop === '') || JSON.stringify(range) != JSON.stringify(brush.orig)\n\t\t\t\t? '#23cba7'\n\t\t\t\t: '#777777'\n\t\t)\n}\n\n/** Updates the number range returned from the brushing into\n * rounded values or integers.  Encapsulated and exported to verify\n * usage via testing and CI.\n *\n * xscale: d3 scale for x-axis\n * s: selection from brush, [start, stop]\n * range: range object to update\n * inputRange: input range object\n * minValue: min value of the density plot\n * maxValue: max value of the density plot\n * termType: term type\n *\n * A typed bound at or beyond the data, e.g. x>-1 for data starting at 0, is kept as typed while the\n * brush sits at that edge. Replacing it by the data min or max would change the selected samples:\n * the typed exclusivity would drop the samples at the min, e.g. 0<x, and the rounded min may lie\n * inside the data, e.g. 0.93 for a min of 0.925.\n */\nexport function updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, type) {\n\trange.start = convertRangeValue(xscale, s[0])\n\trange.stop = convertRangeValue(xscale, s[1])\n\tconst min = roundValueAuto(Number(minvalue))\n\tconst max = roundValueAuto(Number(maxvalue))\n\t//If the user inputs a value outside the brush, limit it to the brush\n\t//Otherwise the input displays a calculated position closest to the value.\n\tif (range.start < min) range.start = min\n\tif (range.stop > max) range.stop = max\n\t//Limit by the brush, not by the user\n\trange.startunbounded = min == range.start && inputRange.startunbounded\n\trange.stopunbounded = max == range.stop && inputRange.stopunbounded\n\tconst startAtEdge = !range.startunbounded && range.start == min,\n\t\tstopAtEdge = !range.stopunbounded && range.stop == max\n\t//Do not show decimals for integer types\n\tif (type == 'integer') {\n\t\trange.start = range.startunbounded ? '' : Math.round(range.start)\n\t\trange.stop = range.stopunbounded ? '' : Math.round(range.stop)\n\t}\n\t// not rounded for an integer term either, as rounding x>-0.5 to x>0 would also drop the samples at 0\n\tif (startAtEdge && Number.isFinite(inputRange.start) && inputRange.start <= minvalue) range.start = inputRange.start\n\tif (stopAtEdge && Number.isFinite(inputRange.stop) && inputRange.stop >= maxvalue) range.stop = inputRange.stop\n}\n\n/** Set the start and stop displayed to the user\n * Encapsulated and exported to verify usage via testing and CI.\n *\n * range: range object to update. Note this is already altered by updateTempRanges\n * inputRange: input range object\n */\n\nexport function setStartStopDisplays(range, inputRange, scaleFactor = 1) {\n\t// the brushed range supplies the values, the input's range supplies the inclusivity\n\treturn formatRangeBounds(\n\t\t{\n\t\t\t...range,\n\t\t\tstartinclusive: inputRange.startinclusive,\n\t\t\tstopinclusive: inputRange.stopinclusive\n\t\t},\n\t\tscaleFactor\n\t)\n}\n\nfunction convertRangeValue(xscale, sidx) {\n\tconst value = Number(xscale.invert(sidx))\n\treturn roundValueAuto(value)\n}\n\n//Add new blank range temporary, save after entering values\nexport function addNewBrush(self, new_brush_location = 'end', callback) {\n\tconst new_range = { start: '', stop: '', index: self.tvs.ranges.length }\n\tself.num_obj.ranges.push(new_range)\n\tconst brush = { orig: new_range, range: JSON.parse(JSON.stringify(new_range)) }\n\tself.num_obj.brushes.push(brush)\n\taddBrushes(self, new_brush_location)\n\tif (callback) callback()\n\tbrush.init()\n}\n"],
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+  "names": []
+}

package/dist/chunk-4HTRCXLS.js

@@ -0,0 +1,98 @@
+import {
+  keyupEnter
+} from "./chunk-K7HFOAR7.js";
+import {
+  require_debounce
+} from "./chunk-KV4W2ACA.js";
+import {
+  Menu
+} from "./chunk-7XZA2XR2.js";
+import {
+  dofetch,
+  dofetch3
+} from "./chunk-GP4VLNMZ.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// src/gene.js
+var import_debounce = __toESM(require_debounce(), 1);
+var tip;
+function gene_searchbox(p) {
+  if (!tip) {
+    tip = new Menu({ padding: "" });
+    tip.d.style("z-index", 1e3);
+  }
+  const input = p.div.append("input").attr("placeholder", "Search gene").style("width", p.width || "100px");
+  const printdiv = p.resultdiv || (p.tip ? p.tip.d : tip.d);
+  function fold() {
+    if (p.resultdiv) {
+      p.resultdiv.selectAll("*").remove();
+    } else if (p.tip) {
+      p.tip.hide();
+    } else {
+      tip.hide();
+    }
+  }
+  input.on("keyup", (event) => {
+    const str = event.target.value;
+    if (str.length <= 1) {
+      fold();
+      return;
+    }
+    if (keyupEnter(event)) {
+      const hitgene = printdiv.select(".sja_menuoption");
+      if (hitgene.size() > 0) {
+        p.callback(hitgene.text());
+        fold();
+      }
+      return;
+    }
+    debouncer();
+  });
+  input.node().focus();
+  function genesearch() {
+    dofetch("genelookup", { genome: p.genome, input: input.property("value") }).then((data) => {
+      if (data.error) throw data.error;
+      if (!data.hits) throw ".hits[] missing";
+      if (p.resultdiv) {
+        p.resultdiv.selectAll("*").remove();
+      } else if (p.tip) {
+        p.tip.clear().showunder(input.node());
+      } else {
+        tip.clear().showunder(input.node());
+      }
+      for (const name of data.hits) {
+        printdiv.append("div").attr("class", "sja_menuoption").text(name).on("click", () => {
+          p.callback(name);
+          fold();
+        });
+      }
+    }).catch((err) => {
+      printdiv.append("div").text(err.message || err);
+      if (err.stack) console.log(err.stack);
+    });
+  }
+  const debouncer = (0, import_debounce.debounce)(genesearch, 300);
+}
+function findgenemodel_bysymbol(genome, str) {
+  return dofetch3("genelookup", {
+    body: {
+      deep: 1,
+      input: str,
+      genome
+    }
+  }).then((data) => {
+    if (data.error) throw data.error;
+    if (!data.gmlst || data.gmlst.length == 0) return null;
+    return data.gmlst;
+  }).catch((e) => {
+    throw e;
+  });
+}
+
+export {
+  gene_searchbox,
+  findgenemodel_bysymbol
+};
+//# sourceMappingURL=chunk-4HTRCXLS.js.map