@sjcrh/proteinpaint-client 2.191.0 → 2.191.2

package/dist/chunk-MW3PIRGF.js

@@ -1,229 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-6FF5VLGO.js";
-import {
-  get_bin_label,
-  get_bin_range_equation
-} from "./chunk-B4VRYXOQ.js";
-
-// termsetting/handlers/NumCustomBinEditor.ts
-var NumCustomBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  async render(div) {
-    if (this.q?.type != "custom-bin") this.q = this.getDefaultQ();
-    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (this.dom.inputsDiv) {
-      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return;
-      else {
-        this.dom.inputsDiv.remove();
-        delete this.dom.inputsDiv;
-      }
-    }
-    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
-    this.renderCustomBinInputs();
-  }
-  getBoundaryOpts() {
-    return {
-      values: this.q.lst.slice(1).map((bin) => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),
-      callback: (d, value) => {
-        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? d2.start : "");
-        boundaryValues[d.index] = value;
-        this.dom.customBinBoundaryInput.text(boundaryValues.join(",\n"));
-        this.handleInputChange("drag");
-        return 0;
-      }
-    };
-  }
-  getDefaultQ() {
-    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
-      const copy = JSON.parse(JSON.stringify(this.tw.q));
-      copy.lst.forEach((bin) => {
-        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
-        bin.range = get_bin_range_equation(bin, this.tw.q);
-      });
-      return copy;
-    }
-    const { min, max } = this.editHandler.handler.density_data;
-    const defaultCustomBoundary = (
-      /* when no sample is annotated by this term,
-      minvalue and maxvalue are both null
-      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
-      but remains to be evaluated if is really okay to use 0
-      */
-      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
-        // minvalue and maxvalue is valid number
-        max != min ? min + (max - min) / 2 : max
-      )
-    );
-    const firstBin = {
-      startunbounded: true,
-      startinclusive: false,
-      stopinclusive: false,
-      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    const lastBin = {
-      stopunbounded: true,
-      startinclusive: true,
-      stopinclusive: false,
-      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst: [
-        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
-        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
-        {
-          ...firstBin,
-          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(firstBin, this.tw.q)
-        },
-        {
-          ...lastBin,
-          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(lastBin, this.tw.q)
-        }
-        //satisfies StopUnboundedBin
-      ]
-    };
-  }
-  /******************* Functions for Numerical Custom size bins *******************/
-  renderCustomBinInputs() {
-    const q = this.q;
-    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
-    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
-    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
-    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
-      q.lst.slice(1).map((d) => "start" in d ? d.start : "").join("\n")
-    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
-      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
-      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
-      this.handleInputChange();
-    });
-    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-    this.renderBoundaryInputDivs();
-  }
-  renderBoundaryInputDivs() {
-    const data = this.q.lst;
-    const holder = this.dom.rangeAndLabelDiv;
-    holder.selectAll("*").remove();
-    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
-    for (const d of data) {
-      grid.append("div").attr("name", "range").html(d.range);
-      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
-        d.label = this.value;
-      });
-    }
-    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
-    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
-  }
-  handleInputChange(eventType = "") {
-    const self = this.tw;
-    const inputs = this.dom.inputsDiv.selectAll("input");
-    inputs.property("value", "");
-    const data = this.processCustomBinInputs();
-    if (data == void 0) {
-      return;
-    }
-    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
-    if (this.binsChanged(data, this.q.lst)) {
-      this.q.lst = data;
-    }
-    this.renderBoundaryInputDivs();
-    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  binsChanged(data, qlst) {
-    if (data.length != qlst.length) return true;
-    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
-    for (const [i, bin] of qlst.entries()) {
-      for (const k of Object.keys(bin)) {
-        if (bin[k] && bin[k] !== data[i][k]) {
-          return true;
-        }
-      }
-    }
-    return false;
-  }
-  processCustomBinInputs() {
-    const self = this.termsetting;
-    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
-    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
-    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
-    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
-    const trackBins = new Set(inputData);
-    if (!trackBins.size) return this.tw.q.lst;
-    const sortedBins = Array.from(trackBins).map(Number).sort((a, b) => a - b);
-    const data = [
-      // first bin: StartUnbounded type
-      {
-        startunbounded: true,
-        stop: sortedBins[0],
-        startinclusive: false,
-        stopinclusive,
-        label: inputs[0].value
-      }
-    ];
-    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
-    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q);
-    for (const [i, d] of sortedBins.entries()) {
-      let bin;
-      const label = inputs[i + 1]?.value || "";
-      if (i !== trackBins.size - 1) {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive,
-          stop: sortedBins[i + 1],
-          label
-          //range: ''
-        };
-      } else {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive: false,
-          stopunbounded: true,
-          label
-          //range: ''
-        };
-      }
-      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
-      if (bin.range === "" || bin.range === void 0) bin.range = get_bin_range_equation(bin, self.q);
-      data.push(bin);
-    }
-    return data;
-  }
-  getEditedQ(destroyDom = true) {
-    const lst = this.processCustomBinInputs();
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst
-    };
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.inputsDiv.selectAll("*").remove();
-    this.renderCustomBinInputs();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumCustomBinEditor
-};
-//# sourceMappingURL=chunk-MW3PIRGF.js.map

package/dist/chunk-MW3PIRGF.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termsetting/handlers/NumCustomBinEditor.ts"],
-  "sourcesContent": ["import { keyupEnter } from '#src/client'\nimport type { NumCustomBins } from '#tw'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor.ts'\nimport type { BoundaryOpts, LineData } from './NumericDensity.ts'\nimport type { TermSetting } from '../TermSetting.ts'\nimport type { CustomNumericBinConfig, CustomNumericBinConfigLst, StartUnboundedBin, StopUnboundedBin } from '#types'\nimport { get_bin_label, get_bin_range_equation } from '#shared/termdb.bins.js'\n\n// This is a bin editor for NumDiscreteEditor\n// NumericHandler (handler) -> NumDiscreteEditor (editor) -> NumCustomBinEditor (bin editor)\nexport class NumCustomBinEditor {\n\ttw: NumCustomBins\n\tq!: CustomNumericBinConfig\n\teditHandler: NumDiscreteEditor\n\ttermsetting: TermSetting\n\topts: any\n\tdom: {\n\t\t[elemName: string]: any\n\t} = {}\n\n\tconstructor(editHandler) {\n\t\tthis.editHandler = editHandler\n\t\tthis.opts = editHandler.opts\n\t\tthis.tw = editHandler.tw\n\t\tthis.termsetting = editHandler.termsetting\n\t}\n\n\tasync render(div) {\n\t\tif (this.q?.type != 'custom-bin') this.q = this.getDefaultQ()\n\t\tawait this.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\tif (this.dom.inputsDiv) {\n\t\t\tif (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return\n\t\t\telse {\n\t\t\t\tthis.dom.inputsDiv.remove()\n\t\t\t\tdelete this.dom.inputsDiv\n\t\t\t}\n\t\t}\n\t\tthis.dom.inputsDiv = div.append('div').style('display', 'flex').style('width', '100%')\n\t\tthis.renderCustomBinInputs()\n\t}\n\n\tgetBoundaryOpts(): BoundaryOpts {\n\t\treturn {\n\t\t\tvalues: this.q.lst.slice(1).map(bin => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),\n\t\t\tcallback: (d: LineData, value) => {\n\t\t\t\tconst boundaryValues = this.q.lst.slice(1).map(d => ('start' in d ? d.start : ''))\n\t\t\t\tboundaryValues[d.index] = value\n\t\t\t\tthis.dom.customBinBoundaryInput.text(boundaryValues.join(',\\n'))\n\t\t\t\tthis.handleInputChange('drag')\n\t\t\t\treturn 0\n\t\t\t}\n\t\t}\n\t}\n\n\tgetDefaultQ(): CustomNumericBinConfig {\n\t\tif (this.tw.q.mode == 'discrete' && this.tw.q.type == 'custom-bin') {\n\t\t\tconst copy = JSON.parse(JSON.stringify(this.tw.q))\n\t\t\tcopy.lst.forEach(bin => {\n\t\t\t\tif (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion)\n\t\t\t\tbin.range = get_bin_range_equation(bin, this.tw.q)\n\t\t\t})\n\t\t\treturn copy\n\t\t}\n\t\tconst { min, max } = this.editHandler.handler.density_data\n\t\tconst defaultCustomBoundary =\n\t\t\t/* when no sample is annotated by this term,\n\t\t\tminvalue and maxvalue are both null\n\t\t\tsetting defaultCustomBoundary to arbitrary \"0\" will allow existing UI to work\n\t\t\tbut remains to be evaluated if is really okay to use 0\n\t\t\t*/\n\t\t\t!Number.isFinite(min) || !Number.isFinite(max)\n\t\t\t\t? 0\n\t\t\t\t: // minvalue and maxvalue is valid number\n\t\t\t\tmax != min\n\t\t\t\t? min + (max - min) / 2\n\t\t\t\t: max\n\n\t\tconst firstBin = {\n\t\t\tstartunbounded: true,\n\t\t\tstartinclusive: false,\n\t\t\tstopinclusive: false,\n\t\t\tstop: +defaultCustomBoundary.toFixed(this.tw.term.type == 'integer' ? 0 : 2)\n\t\t} satisfies StartUnboundedBin\n\n\t\tconst lastBin = {\n\t\t\tstopunbounded: true,\n\t\t\tstartinclusive: true,\n\t\t\tstopinclusive: false,\n\t\t\tstart: +defaultCustomBoundary.toFixed(this.tw.term.type == 'integer' ? 0 : 2)\n\t\t} satisfies StopUnboundedBin\n\n\t\treturn {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t// Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.\n\t\t\t\t// Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.\n\t\t\t\t{\n\t\t\t\t\t...firstBin,\n\t\t\t\t\tlabel: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),\n\t\t\t\t\trange: get_bin_range_equation(firstBin, this.tw.q)\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t...lastBin,\n\t\t\t\t\tlabel: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),\n\t\t\t\t\trange: get_bin_range_equation(lastBin, this.tw.q)\n\t\t\t\t} //satisfies StopUnboundedBin\n\t\t\t]\n\t\t}\n\t}\n\n\t/******************* Functions for Numerical Custom size bins *******************/\n\trenderCustomBinInputs() {\n\t\tconst q = this.q\n\t\t// boundaryDiv for entering bin boundaries\n\t\t// rangeAndLabelDiv for rendering ranges and labels\n\t\tconst boundaryDiv = this.dom.inputsDiv.append('div').style('margin-right', '20px')\n\t\tthis.dom.rangeAndLabelDiv = this.dom.inputsDiv.append('div')\n\n\t\tboundaryDiv.append('div').style('margin-bottom', '5px').style('color', 'rgb(136, 136, 136)').text('Bin boundaries')\n\n\t\tthis.dom.customBinBoundaryInput = boundaryDiv\n\t\t\t.append('textarea')\n\t\t\t.style('width', '100px')\n\t\t\t.style('height', '70px')\n\t\t\t.text(\n\t\t\t\tq.lst\n\t\t\t\t\t.slice(1)\n\t\t\t\t\t.map(d => ('start' in d ? d.start : ''))\n\t\t\t\t\t.join('\\n')\n\t\t\t)\n\t\t\t.on('change', () => this.handleInputChange())\n\t\t\t.on('keyup', async (event: any) => {\n\t\t\t\t// enter or backspace/delete\n\t\t\t\t// i don't think backspace works\n\t\t\t\tif (!keyupEnter(event) && event.key != 8 && event.key != 'Enter') return\n\t\t\t\tif (!this.dom.inputsDiv.selectAll('input').node().value) return\n\t\t\t\t// Fix for if user hits enter with no values. Reverts to default cutoff.\n\t\t\t\tthis.handleInputChange()\n\t\t\t})\n\n\t\t// help note\n\t\tboundaryDiv\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('margin-left', '1px')\n\t\t\t.style('color', '#858585')\n\t\t\t.html('Enter numeric values </br>seperated by ENTER')\n\n\t\tthis.renderBoundaryInputDivs()\n\n\t\t// add help message for custom bin labels\n\t}\n\n\trenderBoundaryInputDivs() {\n\t\tconst data = this.q.lst\n\t\tconst holder = this.dom.rangeAndLabelDiv\n\t\tholder.selectAll('*').remove()\n\n\t\tconst grid = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'grid')\n\t\t\t.style('grid-template-columns', 'auto auto')\n\t\t\t.style('column-gap', '20px')\n\t\t\t.style('align-items', 'center')\n\n\t\tgrid.append('div').style('margin-bottom', '3px').style('color', 'rgb(136, 136, 136)').text('Range')\n\n\t\tgrid.append('div').style('margin-bottom', '3px').style('color', 'rgb(136, 136, 136)').text('Bin label')\n\n\t\tfor (const d of data) {\n\t\t\tgrid.append('div').attr('name', 'range').html(d.range)\n\n\t\t\tgrid\n\t\t\t\t.append('div')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'text')\n\t\t\t\t.style('margin', '2px 0px')\n\t\t\t\t.property('value', d.label)\n\t\t\t\t.on('change', function (this: any) {\n\t\t\t\t\td.label = this.value\n\t\t\t\t})\n\t\t}\n\n\t\tthis.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name=\"range\"]').data(data)\n\t\tthis.dom.customBinLabelInput = this.dom.inputsDiv.selectAll('input').data(data)\n\t}\n\n\thandleInputChange(eventType = '') {\n\t\tconst self = this.tw\n\t\tconst inputs = this.dom.inputsDiv.selectAll('input')\n\t\tinputs.property('value', '')\n\t\tconst data = this.processCustomBinInputs()\n\t\tif (data == undefined) {\n\t\t\t// alert('Enter custom bin value(s)')\n\t\t\treturn\n\t\t}\n\t\t// update self.q.lst and render bin lines only if bin boundry changed\n\t\t//const q = self.numqByTermIdModeType[self.term.id].discrete[self.q.type!]\n\t\tif (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues\n\t\tif (this.binsChanged(data, this.q.lst)) {\n\t\t\tthis.q.lst = data\n\t\t}\n\t\tthis.renderBoundaryInputDivs()\n\t\tif (eventType != 'drag') this.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\t//self.q.lst = q.lst //store the new ranges in self.q, the mode is initialized when selecting the tab\n\t}\n\n\tbinsChanged(data, qlst) {\n\t\tif (data.length != qlst.length) return true\n\t\tif (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true\n\t\tfor (const [i, bin] of qlst.entries()) {\n\t\t\tfor (const k of Object.keys(bin)) {\n\t\t\t\tif (bin[k] && bin[k] !== data[i][k]) {\n\t\t\t\t\treturn true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn false\n\t}\n\n\tprocessCustomBinInputs() {\n\t\tconst self = this.termsetting\n\t\tconst startinclusive = this.editHandler.boundaryInclusion == 'startinclusive'\n\t\tconst stopinclusive = this.editHandler.boundaryInclusion == 'stopinclusive'\n\t\tconst inputs = this.dom.inputsDiv.node().querySelectorAll('input')\n\n\t\tconst inputData = this.dom.customBinBoundaryInput\n\t\t\t.property('value')\n\t\t\t.split('\\n')\n\t\t\t.filter((d: any) => d != '' && !isNaN(d))\n\n\t\t// Fix for when user enters in the same number more than once.\n\t\t// UI will ignore duplicate entries completely.\n\t\tconst trackBins = new Set(inputData)\n\t\tif (!trackBins.size) return this.tw.q.lst\n\n\t\tconst sortedBins = Array.from(trackBins)\n\t\t\t.map(Number)\n\t\t\t.sort((a, b) => a - b)\n\n\t\tconst data: CustomNumericBinConfigLst = [\n\t\t\t// first bin: StartUnbounded type\n\t\t\t{\n\t\t\t\tstartunbounded: true,\n\t\t\t\tstop: sortedBins[0],\n\t\t\t\tstartinclusive: false,\n\t\t\t\tstopinclusive,\n\t\t\t\tlabel: inputs[0].value\n\t\t\t}\n\t\t]\n\t\t// first bin\n\t\tif (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion)\n\t\tif (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q)\n\t\tfor (const [i, d] of sortedBins.entries()) {\n\t\t\tlet bin\n\t\t\tconst label = inputs[i + 1]?.value || ''\n\t\t\tif (i !== trackBins.size - 1) {\n\t\t\t\t// intermediate bin: FullyBounded type\n\t\t\t\tbin = {\n\t\t\t\t\tstart: +d,\n\t\t\t\t\tstartinclusive,\n\t\t\t\t\tstopinclusive,\n\t\t\t\t\tstop: sortedBins[i + 1],\n\t\t\t\t\tlabel\n\t\t\t\t\t//range: ''\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// last bin: StopUnbounded type\n\t\t\t\tbin = {\n\t\t\t\t\tstart: +d,\n\t\t\t\t\tstartinclusive,\n\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\tstopunbounded: true,\n\t\t\t\t\tlabel\n\t\t\t\t\t//range: ''\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (bin.label === '' || bin.label === undefined) bin.label = get_bin_label(bin, self.q, self.term.valueConversion)\n\t\t\tif (bin.range === '' || bin.range === undefined) bin.range = get_bin_range_equation(bin, self.q)\n\t\t\tdata.push(bin)\n\t\t}\n\t\treturn data\n\t}\n\n\tgetEditedQ(destroyDom = true): CustomNumericBinConfig {\n\t\tconst lst = this.processCustomBinInputs()\n\t\tif (destroyDom) {\n\t\t\tfor (const name of Object.keys(this.dom)) {\n\t\t\t\tthis.dom[name].remove()\n\t\t\t\tdelete this.dom[name]\n\t\t\t}\n\t\t}\n\t\treturn {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst\n\t\t}\n\t}\n\n\tundoEdits() {\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.dom.inputsDiv.selectAll('*').remove()\n\t\tthis.renderCustomBinInputs()\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n}\n"],
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-  "names": ["d"]
-}

package/dist/chunk-NNMOXQTU.js

@@ -1,102 +0,0 @@
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist,
-  getDNAMethUnit,
-  sayerror
-} from "./chunk-6FF5VLGO.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  DNA_METHYLATION
-} from "./chunk-TVADJLMF.js";
-
-// termdb/handlers/dnaMethylation.ts
-var SearchHandler = class {
-  init(opts) {
-    this.opts = opts;
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("margin", "10px 0px");
-    this.dom = {};
-    this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
-    this.dom.geneSearchDiv = holder.append("div");
-    this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: this.dom.geneSearchDiv,
-      callback: async () => {
-        try {
-          this.dom.errDiv.style("display", "none");
-          await this.handleGeneSearch(geneSearch);
-        } catch (e) {
-          this.dom.errDiv.style("display", "block");
-          sayerror(this.dom.errDiv, "Error: " + (e.message || e));
-          if (e.stack) console.log(e.stack);
-        }
-      }
-    });
-  }
-  async handleGeneSearch(geneSearch) {
-    if (geneSearch.geneSymbol) {
-      const { chr, start, stop } = geneSearch;
-      if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
-        throw new Error("unable to retrieve gene coordinate");
-      this.dom.blockDiv.selectAll("*").remove();
-      this.dom.blockDiv.style("display", "block");
-      this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
-      const arg = {
-        holder: this.dom.blockDiv,
-        genome: this.opts.genomeObj,
-        // genome obj
-        chr,
-        start,
-        stop,
-        tklst: [],
-        nobox: true,
-        width: 500,
-        hidegenelegend: true,
-        debugmode: this.opts.debug
-      };
-      first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
-      const _ = await import("./block-7UW7QCRX.js");
-      this.blockInstance = new _.Block(arg);
-      this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
-        const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
-        const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
-        await this.callback(term);
-      });
-    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
-      const { chr } = geneSearch;
-      let { start, stop } = geneSearch;
-      if (geneSearch.actualposition?.len <= 1) {
-        start = geneSearch.actualposition.position;
-        stop = start + 1;
-      }
-      const term = this.makeTerm({ chr, start, stop });
-      await this.callback(term);
-    } else {
-      throw new Error("invalid gene search input");
-    }
-  }
-  makeTerm(opts) {
-    const { chr, start, stop } = opts;
-    if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
-    const unit = getDNAMethUnit("region", this.app.vocabApi);
-    const term = {
-      chr,
-      start,
-      stop,
-      type: DNA_METHYLATION,
-      unit,
-      genomicFeatureType: "region"
-    };
-    return term;
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-NNMOXQTU.js.map

package/dist/chunk-NV6JVKDN.js

@@ -1,291 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-VXKO2ONI.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-6FF5VLGO.js";
-import {
-  copyMerge
-} from "./chunk-5V43Y2RC.js";
-import {
-  isDictionaryType
-} from "./chunk-TVADJLMF.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-EBKERML3.js";
-
-// plots/matrix/matrix.config.js
-async function getPlotConfig(opts = {}, app) {
-  const controlLabels = structuredClone(defaultUiLabels);
-  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
-  const config = {
-    // data configuration
-    termgroups: [],
-    samplegroups: [],
-    divideBy: null,
-    legendValueFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    legendGrpFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    filter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    // cnvCutoffs: {},
-    // rendering options
-    settings: {
-      matrix: {
-        svgCanvasSwitch: 1e3,
-        // the number of samples to trigger switching between svg and canvas
-        useMinPixelWidth: true,
-        // canvas may be hazy if false, but more accurately reflects column density
-        cellEncoding: "",
-        // can be "oncoprint" | "stacked" | "single"
-        margin: {
-          top: 10,
-          right: 5,
-          bottom: 20,
-          left: 50
-        },
-        // set any dataset-defined sample limits and sort priority, otherwise undefined
-        // put in settings, so that later may be overridden by a user
-        maxGenes: opts.settings?.maxGenes || 50,
-        maxSample: opts.settings?.maxSample || 1e3,
-        sampleNameFilter: "",
-        sortSamplesBy: "a",
-        sortPriority: void 0,
-        // will be filled-in
-        // sortByMutation: 'consequence', computed
-        // sortByCNV: true, computed
-        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
-        sortSampleGrpsBy: "name",
-        // 'hits' | 'name' | 'sampleCount'
-        sortSamplesTieBreakers: [{
-          $id: "sample",
-          sortSamples: {}
-          /*split: {char: '', index: 0}*/
-        }],
-        sortTermsBy: "sampleCount",
-        // or 'as listed'
-        // do not show number of samples at hiercluster gene row labels
-        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
-        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
-        geneVariantCountSamplesSkipMclass: [],
-        cellbg: "#ececec",
-        showGrid: "",
-        // false | 'pattern' | 'rect'
-        // whether to show these controls buttons
-        addMutationCNVButtons: false,
-        truncatingMutations,
-        proteinChangingMutations,
-        synonymousMutations,
-        mutationClasses,
-        CNVClasses,
-        gridStroke: "#fff",
-        outlineStroke: "#ccc",
-        beamStroke: "#f00",
-        colw: 0,
-        colwMin: 0.1 / devicePixelRatio,
-        colwMax: 16,
-        colspace: 1,
-        colgspace: 8,
-        colglabelpos: true,
-        collabelpos: "bottom",
-        collabelvisible: true,
-        collabelgap: 5,
-        collabelpad: 1,
-        collabelmaxchars: 32,
-        rowh: 18,
-        //use 0 to auto-compute row height, previous default=18,
-        rowhMin: 1,
-        rowhMax: 20,
-        rowspace: 1,
-        rowgspace: 8,
-        rowlabelpos: "left",
-        // | 'right'
-        rowlabelgap: 5,
-        rowlabelvisible: true,
-        rowlabelpad: 1,
-        rowlabelmaxchars: 32,
-        legendGrpLabelMaxChars: 26,
-        grpLabelFontSize: 12,
-        minLabelFontSize: 6,
-        maxLabelFontSize: 14,
-        transpose: false,
-        sampleLabelsToggle: opts.chartType === "hierCluster" ? "hide" : "auto",
-        // 'auto' | 'hide'
-        sampleLabelOffset: 120,
-        sampleGrpLabelOffset: 120,
-        sampleGrpLabelMaxChars: 32,
-        termLabelOffset: 80,
-        termGrpLabelOffset: 80,
-        termGrpLabelMaxChars: 32,
-        duration: 0,
-        zoomLevel: 1,
-        zoomCenterPct: 0,
-        zoomIndex: 0,
-        zoomGrpIndex: 0,
-        zoomMin: 0.5,
-        zoomIncrement: 0.1,
-        zoomStep: 1,
-        // renderedWMax should not be exposed as a user-input
-        // 60000 pixels is based on laptop and external monitor tests,
-        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
-        imgWMax: 6e4 / devicePixelRatio,
-        scrollHeight: 12,
-        controlLabels,
-        cnvUnit: "log2ratio",
-        ignoreCnvValues: false,
-        //will ignore numeric CNV values if true
-        barh: 32,
-        // default bar height for continuous terms,
-        // possible string entries:
-        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
-        // - may add other optional hints later
-        showHints: [],
-        genesetEditUiVersion: "",
-        // '' | 'withTabs'
-        // settings for a specific tw
-        twSpecificSettings: {},
-        oncoPrintSNVindelCellBorder: false,
-        // whether to show white cell border for SNVindel in oncoPrint mode
-        cnvValues: {
-          //Properties match the args for the ColorScales
-          //numericInput arg
-          cutoffMode: "percentile",
-          defaultPercentile: 99,
-          min: null,
-          max: null,
-          percentile: 99
-        }
-      }
-    }
-  };
-  const s = config.settings;
-  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
-  s.legend = {
-    ontop: false,
-    lineh: 25,
-    padx: 5,
-    padleft: 0,
-    //150,
-    padright: 20,
-    padbtm: 30,
-    fontsize,
-    iconh: fontsize - 2,
-    iconw: fontsize - 2,
-    hangleft: 1,
-    linesep: false
-  };
-  const overrides = app.vocabApi.termdbConfig.matrix || {};
-  copyMerge(config.settings.matrix, overrides.settings);
-  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
-  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
-  if (overrides.filter) config.filter = overrides.filter;
-  if (opts.name) {
-    const data = await app.vocabApi.getMatrixByName(opts.name);
-    if (!data) throw "error from getMatrixByName()";
-    if (data.error) throw data.error;
-    copyMerge(config, data);
-  }
-  const os = opts?.settings?.matrix;
-  if (os) {
-    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
-      os.sortSamplesBy = "a";
-    }
-    if (os.sortOptions) {
-      delete os.sortOptions.custom;
-      delete os.sortOptions.asListed;
-    }
-  }
-  copyMerge(config, opts);
-  const m = config.settings.matrix;
-  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
-  m.duration = 0;
-  m.colw = 0;
-  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
-  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
-  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
-  if (window.location.hostname == "localhost") {
-    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
-  }
-  for (const grp of config.termgroups) {
-    const promises = [];
-    for (const tw of grp.lst) {
-      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
-        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
-          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
-          tw.id = tw.term.id;
-        }
-        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    grp.lst = await Promise.all(promises);
-  }
-  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
-  return config;
-}
-function setComputedConfig(config) {
-  const s = config.settings.matrix;
-  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
-  s.filterByClass = { isAtomic: true };
-  for (const f of config.legendGrpFilter.lst) {
-    if (!f.dt) continue;
-    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
-      s.filterByClass[key2] = "value";
-    });
-  }
-  for (const f of config.legendValueFilter.lst) {
-    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
-    if (f.tvs.values?.[0].mclasslst)
-      f.tvs.values[0].mclasslst.forEach((key2) => {
-        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
-      });
-    else if (f.tvs.values)
-      f.tvs.values.forEach((v) => {
-        s.filterByClass[key] = "value";
-      });
-    else throw `unhandled tvs from legendValueFilter`;
-  }
-  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
-  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
-  s.hiddenCNVs = [...hiddenCNVs];
-  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
-  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
-  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
-  s.hiddenMutations = [...hiddenMutations];
-  const PCset = new Set(s.proteinChangingMutations);
-  const TMset = new Set(s.truncatingMutations);
-  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
-  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
-  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
-  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
-  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
-}
-
-export {
-  getPlotConfig,
-  setComputedConfig
-};
-//# sourceMappingURL=chunk-NV6JVKDN.js.map