@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-MGGAWPTR.js

@@ -0,0 +1,54 @@
+import {
+  getColors
+} from "./chunk-GEQUQ3GG.js";
+
+// termdb/handlers/junction.customTerm.ts
+var junctionCustomTermSource = "junction";
+function makeJunctionCustomTerm(junctions, eventlabel) {
+  if (!junctions.length) throw new Error("junctions[] is empty");
+  if (!eventlabel) {
+    const term = junctions[0];
+    return {
+      id: `junction:${term.id}`,
+      name: term.name,
+      source: junctionCustomTermSource,
+      tw: {
+        term,
+        q: { mode: "continuous" }
+      }
+    };
+  }
+  const termlst = [...new Map(junctions.map((term) => [term.id, term])).values()];
+  const colorScale = getColors(termlst.length);
+  const termIds = termlst.map((term) => term.id);
+  return {
+    id: `junction-event:${eventlabel}`,
+    name: eventlabel,
+    source: junctionCustomTermSource,
+    eventlabel,
+    tw: {
+      term: {
+        type: "termCollection",
+        isCustom: true,
+        memberType: "numeric",
+        name: eventlabel,
+        termIds,
+        termlst,
+        propsByTermId: Object.fromEntries(termlst.map((term) => [term.id, { color: colorScale(term.id) }])),
+        isleaf: true
+      },
+      q: {
+        mode: "continuous",
+        type: "values",
+        lst: termIds,
+        numerators: termIds
+      }
+    }
+  };
+}
+
+export {
+  junctionCustomTermSource,
+  makeJunctionCustomTerm
+};
+//# sourceMappingURL=chunk-MGGAWPTR.js.map

package/dist/chunk-MKPU5TWN.js

@@ -0,0 +1,194 @@
+import {
+  violinRenderer
+} from "./chunk-WPHUM5S5.js";
+import {
+  getValueConversionFactor
+} from "./chunk-75T7ESEO.js";
+import {
+  linear
+} from "./chunk-UJELJXJG.js";
+import {
+  drag_default
+} from "./chunk-5R63Q5KH.js";
+import {
+  pointer_default,
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// termsetting/handlers/NumericDensity.ts
+var NumericDensity = class {
+  constructor(opts) {
+    this.dom = {};
+    // WeakMap allows deletion of value when the object/DOM key is deleted,
+    // so better for avoiding memory leak
+    this.vrByDiv = /* @__PURE__ */ new WeakMap();
+    this.ranges = [];
+    this.no_density_data = false;
+    this.brushes = [];
+    this.plot_size = {
+      width: 500,
+      height: 100,
+      xpad: 10,
+      ypad: 20,
+      radius: 8
+    };
+    this.opts = opts;
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+  }
+  /* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in
+  	the term's user-facing unit; density_data is in the unit the values are stored in. only the two
+  	getters below cross that line, to put the plot's endpoints in the same unit as those values.
+  
+  	they multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown
+  	in an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown
+  	digit, and collapses the domain outright when the converted range is smaller than that (a stored
+  	range of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose
+  	axis this plot's lines overlay and which scales its own domain unrounded */
+  get scaleFactor() {
+    return getValueConversionFactor(this.tw.term);
+  }
+  get displayMin() {
+    return this.density_data.min * this.scaleFactor;
+  }
+  get displayMax() {
+    return this.density_data.max * this.scaleFactor;
+  }
+  async setData() {
+    const self = this.termsetting;
+    const d = await self.vocabApi.getViolinBox(
+      {
+        plotType: "violin",
+        tw: { type: self.tw.type, term: self.term, q: self.q },
+        svgw: this.plot_size.width,
+        radius: this.plot_size.radius,
+        filter: self.filter
+      },
+      self.opts.getBodyParams?.()
+    );
+    if (d.error) throw d;
+    this.density_data = d;
+    return this.density_data;
+  }
+  async showViolin(div, boundaryOpts) {
+    await this.setData();
+    if (!this.vrByDiv.has(div)) {
+      div.style("padding", "5px").selectAll("*").remove();
+      const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
+      const densityDiv = div.append("div");
+      loadingDiv.remove();
+      const vr = new violinRenderer({
+        holder: densityDiv,
+        rd: this.density_data,
+        width: this.plot_size.width,
+        height: this.plot_size.height,
+        radius: this.plot_size.radius,
+        // axis ticks are labeled in the term's user-facing unit, e.g. years and not days
+        scaleFactor: this.scaleFactor
+      });
+      this.vrByDiv.set(div, vr);
+    }
+    this.vr = this.vrByDiv.get(div);
+    this.dom.svg = this.vr.svg;
+    this.vr.render();
+    if (boundaryOpts) await this.setBinLines(boundaryOpts);
+    return this.density_data;
+  }
+  async setBinLines(boundaryOpts) {
+    if (this.density_data.max == this.density_data.min) {
+      this.handleNoDensity();
+    } else {
+      if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
+      this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
+      const maxvalue = this.displayMax;
+      const minvalue = this.displayMin;
+      this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
+      this.ranges = [];
+      this.brushes = [];
+      this.renderBinLines(boundaryOpts);
+    }
+  }
+  handleNoDensity() {
+    this.no_density_data = true;
+    this.ranges = [];
+    this.brushes = [];
+  }
+  renderBinLines(boundaryOpts) {
+    const { plot_size, tw, xscale, scaleFactor } = this;
+    if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
+    const scaledMinX = Math.round(this.xscale(this.displayMin));
+    const scaledMaxX = Math.round(this.xscale(this.displayMax));
+    const lines = [];
+    for (const [index, v] of boundaryOpts.values.entries()) {
+      lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
+    }
+    const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
+    const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
+    const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
+    this.dom.binsize_g.selectAll("line").remove();
+    this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
+      if (d.isDraggable) select_default(this).style("stroke-width", 3);
+    }).on("mouseout", function() {
+      select_default(this).style("stroke-width", 1);
+    }).each(function(d) {
+      if (d.isDraggable) select_default(this).call(dragger);
+    });
+    const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
+    function toBoundaryValue(x) {
+      const inverted = xscale.invert(x);
+      return Number(
+        scaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3)
+      );
+    }
+    function toLineValue(line) {
+      return line.draggedX === void 0 ? line.x : toBoundaryValue(line.draggedX);
+    }
+    function getNeighbors(d) {
+      const x = d.draggedX ?? d.scaledX;
+      let lower, upper;
+      for (const line of lines) {
+        if (line.index === d.index || !line.isDraggable) continue;
+        const lineX = line.draggedX ?? line.scaledX;
+        if (lineX <= x) {
+          if (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line;
+        } else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line;
+      }
+      return [lower, upper];
+    }
+    function onDrag(event, _d) {
+      const d = _d;
+      const [lower, upper] = getNeighbors(d);
+      const lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX);
+      const upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX);
+      if (upperX - lowerX < 2) return;
+      const draggedX = Math.min(Math.max(pointer_default(event, this)[0], lowerX + 1), upperX - 1);
+      const value = toBoundaryValue(draggedX);
+      if (lower && value === toLineValue(lower)) return;
+      if (upper && value === toLineValue(upper)) return;
+      d.draggedX = draggedX;
+      select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
+      const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
+      const xOffset = d.draggedX - d.scaledX;
+      if (xOffset) {
+        for (const elem of lineElems) {
+          const c = elem.__data__;
+          if (c.movesWithLineIndex !== d.index) continue;
+          c.draggedX = c.scaledX + xOffset;
+          select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
+        }
+        boundaryOpts.callback(d, value);
+      }
+    }
+  }
+  destroy() {
+    for (const [k, v] of Object.entries(this.dom)) {
+      delete this.dom[k];
+      if (typeof v.remove == "function") v.remove();
+    }
+  }
+};
+
+export {
+  NumericDensity
+};
+//# sourceMappingURL=chunk-MKPU5TWN.js.map

package/dist/chunk-MKPU5TWN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumericDensity.ts"],
+  "sourcesContent": ["import type { TermSetting } from '../TermSetting.ts'\nimport type { NumRegularBin, NumCustomBins, NumCont, NumSpline } from '#tw'\nimport type { NumericBin } from '#types'\nimport { violinRenderer } from '#dom'\nimport { select, pointer, type BaseType } from 'd3-selection'\nimport { scaleLinear, drag as d3drag } from 'd3'\nimport { getValueConversionFactor } from '#shared/helpers.js'\n//import { get_bin_label, get_bin_range_equation } from '#shared/termdb.bins.js'\n\nexport type BoundaryOpts = {\n\tvalues: BoundaryValue[]\n\tcallback: (d: DraggedLineData, value: number) => void\n}\n\nexport type BoundaryValue = {\n\tx: number\n\tisDraggable: boolean\n\tmovesWithLineIndex?: number\n\tisLastVisibleLine?: boolean\n}\n\nexport type LineData = BoundaryValue & {\n\tscaledX: number\n\tindex: number\n}\n\nexport type DraggedLineData = LineData & {\n\tdraggedX?: number\n\tstart?: number\n\tend?: number\n}\n\nexport class NumericDensity {\n\ttermsetting: TermSetting\n\topts: any // TODO\n\ttw: NumRegularBin | NumCustomBins | NumCont | NumSpline\n\n\tdom: {\n\t\t[name: string]: any\n\t} = {}\n\t// WeakMap allows deletion of value when the object/DOM key is deleted,\n\t// so better for avoiding memory leak\n\tvrByDiv: WeakMap<HTMLElement, any> = new WeakMap()\n\tvr!: violinRenderer\n\tdensity_data!: any\n\tranges: NumericBin[] = []\n\tno_density_data = false\n\tbrushes: any[] = []\n\txscale!: any\n\tplot_size: {\n\t\twidth: number\n\t\theight: number\n\t\txpad: number\n\t\typad: number\n\t\tradius: number\n\t} = {\n\t\twidth: 500,\n\t\theight: 100,\n\t\txpad: 10,\n\t\typad: 20,\n\t\tradius: 8\n\t}\n\n\tconstructor(opts) {\n\t\tthis.opts = opts\n\t\tthis.termsetting = opts.termsetting\n\t\tthis.tw = opts.termsetting.tw\n\t}\n\n\t/* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in\n\tthe term's user-facing unit; density_data is in the unit the values are stored in. only the two\n\tgetters below cross that line, to put the plot's endpoints in the same unit as those values.\n\n\tthey multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown\n\tin an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown\n\tdigit, and collapses the domain outright when the converted range is smaller than that (a stored\n\trange of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose\n\taxis this plot's lines overlay and which scales its own domain unrounded */\n\tget scaleFactor() {\n\t\treturn getValueConversionFactor(this.tw.term)\n\t}\n\n\tget displayMin() {\n\t\treturn this.density_data.min * this.scaleFactor\n\t}\n\n\tget displayMax() {\n\t\treturn this.density_data.max * this.scaleFactor\n\t}\n\n\tasync setData() {\n\t\t//if (this.density_data) return this.density_data\n\t\tconst self = this.termsetting\n\t\tconst d = await self.vocabApi.getViolinBox(\n\t\t\t{\n\t\t\t\tplotType: 'violin',\n\t\t\t\ttw: { type: self.tw.type, term: self.term, q: self.q },\n\t\t\t\tsvgw: this.plot_size.width,\n\t\t\t\tradius: this.plot_size.radius,\n\t\t\t\tfilter: self.filter\n\t\t\t},\n\t\t\tself.opts.getBodyParams?.()\n\t\t)\n\t\tif (d.error) throw d\n\t\tthis.density_data = d\n\t\treturn this.density_data\n\t}\n\n\tasync showViolin(div, boundaryOpts?) {\n\t\tawait this.setData()\n\n\t\tif (!this.vrByDiv.has(div)) {\n\t\t\tdiv.style('padding', '5px').selectAll('*').remove()\n\t\t\tconst loadingDiv = div\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.html('Getting distribution data ...<br/>')\n\n\t\t\tconst densityDiv = div.append('div')\n\t\t\tloadingDiv.remove()\n\t\t\tconst vr = new violinRenderer({\n\t\t\t\tholder: densityDiv,\n\t\t\t\trd: this.density_data,\n\t\t\t\twidth: this.plot_size.width,\n\t\t\t\theight: this.plot_size.height,\n\t\t\t\tradius: this.plot_size.radius,\n\t\t\t\t// axis ticks are labeled in the term's user-facing unit, e.g. years and not days\n\t\t\t\tscaleFactor: this.scaleFactor\n\t\t\t})\n\t\t\tthis.vrByDiv.set(div, vr)\n\t\t}\n\n\t\tthis.vr = this.vrByDiv.get(div)\n\t\tthis.dom.svg = this.vr.svg\n\t\tthis.vr.render()\n\t\tif (boundaryOpts) await this.setBinLines(boundaryOpts)\n\n\t\treturn this.density_data\n\t}\n\n\tasync setBinLines(boundaryOpts) {\n\t\tif (this.density_data.max == this.density_data.min) {\n\t\t\tthis.handleNoDensity()\n\t\t} else {\n\t\t\t// svg for range plot\n\t\t\t// const div = self.q.mode == 'spline' ? self.dom.knots_div : self.dom.bins_div\n\t\t\t//this.vr.render()\n\n\t\t\t// add binsize_g for termsetting lines\n\t\t\tif (this.dom.binsize_g) this.dom.binsize_g.selectAll('*').remove()\n\t\t\tthis.dom.binsize_g = this.dom.svg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`)\n\t\t\t\t.attr('class', 'binsize_g')\n\n\t\t\t// boundary values come from the editors in the user-facing unit, so the domain is too\n\t\t\tconst maxvalue = this.displayMax\n\t\t\tconst minvalue = this.displayMin\n\n\t\t\tthis.xscale = scaleLinear()\n\t\t\t\t.domain([minvalue, maxvalue])\n\t\t\t\t.range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad])\n\n\t\t\tthis.ranges = []\n\t\t\tthis.brushes = []\n\t\t\tthis.renderBinLines(boundaryOpts)\n\t\t}\n\t}\n\n\thandleNoDensity() {\n\t\tthis.no_density_data = true\n\t\tthis.ranges = []\n\t\tthis.brushes = []\n\t}\n\n\trenderBinLines(boundaryOpts: BoundaryOpts) {\n\t\t//this.boundaryOpts = boundaryOpts\n\t\tconst { plot_size, tw, xscale, scaleFactor } = this\n\t\tif (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`\n\t\tconst scaledMinX = Math.round(this.xscale(this.displayMin))\n\t\tconst scaledMaxX = Math.round(this.xscale(this.displayMax))\n\t\tconst lines: DraggedLineData[] = []\n\t\tfor (const [index, v] of boundaryOpts.values.entries()) {\n\t\t\tlines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) })\n\t\t}\n\t\tconst lastVisibleLine = lines.find(l => l.isLastVisibleLine)\n\t\tconst lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX\n\t\tconst dragger = d3drag().on('drag', onDrag).on('end', onDrag)\n\n\t\tthis.dom.binsize_g.selectAll('line').remove()\n\t\tthis.dom.binsize_g\n\t\t\t.selectAll('line')\n\t\t\t.data(lines)\n\t\t\t.enter()\n\t\t\t.append('line')\n\t\t\t.style('stroke', (d: LineData) => (d.isDraggable ? '#cc0000' : '#555'))\n\t\t\t.style('stroke-width', 1)\n\t\t\t.attr('x1', (d: LineData) => d.scaledX)\n\t\t\t.attr('y1', 0)\n\t\t\t.attr('x2', (d: LineData) => d.scaledX)\n\t\t\t.attr('y2', plot_size.height)\n\t\t\t.style('cursor', (d: LineData) => (d.isDraggable ? 'ew-resize' : ''))\n\t\t\t.attr('display', (d: LineData) => (!d.isDraggable && d.scaledX > lastVisibleScaledX ? 'none' : ''))\n\t\t\t.on('mouseover', function (this: SVGLineElement, _, d: LineData) {\n\t\t\t\tif (d.isDraggable) select(this).style('stroke-width', 3)\n\t\t\t})\n\t\t\t.on('mouseout', function (this: BaseType) {\n\t\t\t\tselect(this).style('stroke-width', 1)\n\t\t\t})\n\t\t\t.each(function (this: Element, d: LineData) {\n\t\t\t\tif (d.isDraggable) select(this).call(dragger)\n\t\t\t})\n\n\t\tconst lineElems = this.dom.binsize_g.node().querySelectorAll('line')\n\n\t\t/* the boundary value that a line at this x reports. a converted value is on a much smaller\n\t\tscale than what it was converted from (e.g. 70 years vs 25868 days), so rounding an integer\n\t\tterm to a whole number would make the line jump by a year at a time. round to 2 decimals in\n\t\tthat case instead */\n\t\tfunction toBoundaryValue(x: number): number {\n\t\t\tconst inverted = xscale.invert(x)\n\t\t\treturn Number(\n\t\t\t\tscaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == 'integer' ? Math.round(inverted) : inverted.toFixed(3)\n\t\t\t)\n\t\t}\n\n\t\t// the boundary a line currently stands for, which is its dragged position once it has been moved\n\t\tfunction toLineValue(line: DraggedLineData): number {\n\t\t\treturn line.draggedX === undefined ? line.x : toBoundaryValue(line.draggedX)\n\t\t}\n\n\t\t/* the nearest draggable line on either side, if there is one. a boundary may not be dragged\n\t\tonto or past one of them: an editor addresses a boundary by the index its line had when the\n\t\tlines were rendered, so two boundaries that swap order make the next drag event overwrite the\n\t\twrong one, and two boundaries of the same value are merged into a single one, leaving the\n\t\teditor with fewer boundaries than the plot has lines */\n\t\tfunction getNeighbors(d: DraggedLineData): [DraggedLineData | undefined, DraggedLineData | undefined] {\n\t\t\tconst x = d.draggedX ?? d.scaledX\n\t\t\tlet lower, upper\n\t\t\tfor (const line of lines) {\n\t\t\t\tif (line.index === d.index || !line.isDraggable) continue\n\t\t\t\tconst lineX = line.draggedX ?? line.scaledX\n\t\t\t\tif (lineX <= x) {\n\t\t\t\t\tif (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line\n\t\t\t\t} else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line\n\t\t\t}\n\t\t\treturn [lower, upper]\n\t\t}\n\n\t\tfunction onDrag(this: any, event: PointerEvent, _d: any) {\n\t\t\tconst d = _d as DraggedLineData\n\t\t\tconst [lower, upper] = getNeighbors(d)\n\t\t\t/* a line follows the pointer but stops at the edge of the plot and at its neighboring\n\t\t\tlines. clamping rather than ignoring an out of bounds drag keeps a line draggable when it\n\t\t\tstarts outside those limits, as a boundary kept from a wider cohort does: its line is\n\t\t\tdrawn past the edge of the plot, where every pointer position is out of bounds */\n\t\t\tconst lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX)\n\t\t\tconst upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX)\n\t\t\tif (upperX - lowerX < 2) return // no room to drag between the limits\n\t\t\tconst draggedX = Math.min(Math.max(pointer(event, this)[0], lowerX + 1), upperX - 1)\n\t\t\tconst value = toBoundaryValue(draggedX)\n\t\t\t/* the rounded value may still land on a neighboring boundary a pixel or two away. the\n\t\t\tedges of the plot are not boundaries, so only a neighboring line is compared */\n\t\t\tif (lower && value === toLineValue(lower)) return\n\t\t\tif (upper && value === toLineValue(upper)) return\n\n\t\t\td.draggedX = draggedX\n\t\t\tselect(this).attr('x1', d.draggedX).attr('y1', 0).attr('x2', d.draggedX).attr('y2', plot_size.height)\n\n\t\t\tconst lastVisibleScaledX = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX\n\n\t\t\tconst xOffset = d.draggedX - d.scaledX\n\t\t\tif (xOffset) {\n\t\t\t\tfor (const elem of lineElems) {\n\t\t\t\t\tconst c = elem.__data__\n\t\t\t\t\tif (c.movesWithLineIndex !== d.index) continue\n\t\t\t\t\tc.draggedX = c.scaledX + xOffset\n\t\t\t\t\tselect(elem)\n\t\t\t\t\t\t.attr('x1', c.draggedX)\n\t\t\t\t\t\t.attr('x2', c.draggedX)\n\t\t\t\t\t\t.style('display', c.draggedX >= lastVisibleScaledX ? 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+  "names": ["lastVisibleScaledX"]
+}

package/dist/chunk-MUJMZ6W6.js

@@ -0,0 +1,129 @@
+import {
+  keyupEnter
+} from "./chunk-K6OVOHIZ.js";
+
+// src/block.mds.svcnv.share.js
+function rnabamtk_initparam(c) {
+  if (!c.dna_mintotalreads) c.dna_mintotalreads = 8;
+  if (!c.rna_mintotalreads) c.rna_mintotalreads = 8;
+  if (!c.hetsnp_minbaf) c.hetsnp_minbaf = 0.3;
+  if (!c.hetsnp_maxbaf) c.hetsnp_maxbaf = 0.7;
+  if (c.rnapileup_q == void 0) c.rnapileup_q = 0;
+  if (!c.rnapileup_Q) c.rnapileup_Q = 13;
+  if (!c.binompvaluecutoff) c.binompvaluecutoff = 0.05;
+  if (!c.clientcolor_snpinuse) c.clientcolor_snpinuse = "blue";
+  if (!c.clientcolor_markernotinuse) c.clientcolor_markernotinuse = "#bbb";
+}
+function configPanel_rnabam(tk, block, loadTk) {
+  const c = tk.checkrnabam;
+  if (!c) return;
+  tk.tkconfigtip.d.append("hr");
+  const d = tk.tkconfigtip.d.append("div").style("margin", "15px 0px");
+  d.append("div").style("opacity", 0.5).style("font-size", ".9em").text("Finding heterozygous SNPs in DNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("DNA minimum total read count ");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.dna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.dna_mintotalreads == v) {
+        return;
+      }
+      c.dna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.");
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_minbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_minbaf == v) {
+        return;
+      }
+      c.hetsnp_minbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("span").style("opacity", ".5").style("font-size", ".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_maxbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_maxbaf == v) {
+        return;
+      }
+      c.hetsnp_maxbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.");
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Counting alleles in RNA-seq BAM file");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip alignments with mapQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v < 0) return;
+      if (c.rnapileup_q == v) {
+        return;
+      }
+      c.rnapileup_q = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_Q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rnapileup_Q == v) {
+        return;
+      }
+      c.rnapileup_Q = v;
+      loadTk(tk, block);
+    });
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("P-value cutoff&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.binompvaluecutoff).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0 || v >= 1) return;
+      if (c.binompvaluecutoff == v) {
+        return;
+      }
+      c.binompvaluecutoff = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("RNA minimum total read count&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rna_mintotalreads == v) {
+        return;
+      }
+      c.rna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.");
+  }
+}
+
+export {
+  rnabamtk_initparam,
+  configPanel_rnabam
+};
+//# sourceMappingURL=chunk-MUJMZ6W6.js.map

package/dist/chunk-NRP55BOF.js

@@ -0,0 +1,50 @@
+import {
+  addGeneSearchbox,
+  getSCGEunit
+} from "./chunk-K6OVOHIZ.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-GEQUQ3GG.js";
+
+// termdb/handlers/singleCellGeneExpression.ts
+var SearchHandler = class {
+  init(opts) {
+    this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => this.selectGene(geneSearch.geneSymbol, opts.usecase?.specialCase?.config?.sample)
+    });
+  }
+  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
+   * with sample info not included.*/
+  async selectGene(gene, sample) {
+    if (!gene) throw new Error("No gene selected");
+    const unit = getSCGEunit(this.app.vocabApi);
+    const name = `${gene} ${unit}`;
+    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
+  }
+  validateOpts(opts) {
+    if (opts.callback == null) throw new Error("callback is required");
+    if (opts.app == null) throw new Error("app is required");
+    if (opts.holder == null) throw new Error("holder is required");
+    if (opts.genomeObj == null) throw new Error("genomeObj is required");
+    if (opts.usecase == null) throw new Error("usecase is required");
+    if (!opts.usecase?.specialCase?.config?.sample) {
+      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
+    }
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-NRP55BOF.js.map