@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-XFAL46LZ.js

@@ -0,0 +1,102 @@
+import {
+  __commonJS
+} from "./chunk-HFNDKYVF.js";
+
+// ../node_modules/debounce/index.js
+var require_debounce = __commonJS({
+  "../node_modules/debounce/index.js"(exports, module) {
+    function debounce(func, wait, immediate) {
+      var timeout, args, context, timestamp, result;
+      if (null == wait) wait = 100;
+      function later() {
+        var last = Date.now() - timestamp;
+        if (last < wait && last >= 0) {
+          timeout = setTimeout(later, wait - last);
+        } else {
+          timeout = null;
+          if (!immediate) {
+            result = func.apply(context, args);
+            context = args = null;
+          }
+        }
+      }
+      ;
+      var debounced = function() {
+        context = this;
+        args = arguments;
+        timestamp = Date.now();
+        var callNow = immediate && !timeout;
+        if (!timeout) timeout = setTimeout(later, wait);
+        if (callNow) {
+          result = func.apply(context, args);
+          context = args = null;
+        }
+        return result;
+      };
+      debounced.clear = function() {
+        if (timeout) {
+          clearTimeout(timeout);
+          timeout = null;
+        }
+      };
+      debounced.flush = function() {
+        if (timeout) {
+          result = func.apply(context, args);
+          context = args = null;
+          clearTimeout(timeout);
+          timeout = null;
+        }
+      };
+      return debounced;
+    }
+    debounce.debounce = debounce;
+    module.exports = debounce;
+  }
+});
+
+// termsetting/HandlerBase.ts
+var HandlerBase = class {
+  //tw: TwBase
+  constructor(opts) {
+    this.termsetting = opts.termsetting;
+  }
+  showEditMenu(_) {
+  }
+  getPillStatus(_) {
+    const tw = this.termsetting.tw;
+    return tw.getStatus?.() || { text: "" };
+  }
+  // this is equivalent to getPillNameDefault()
+  getPillName(d) {
+    const self = this.termsetting;
+    if (!self.opts.abbrCutoff) return d.name;
+    return d.name.length <= self.opts.abbrCutoff + 2 ? d.name : '<label title="' + d.name + '">' + d.name.substring(0, self.opts.abbrCutoff) + "...</label>";
+  }
+  applyEdits() {
+  }
+  undoEdits() {
+  }
+  /* a term with valueConversion{} stores its values in fromUnit (e.g. day) but shows them to
+  users in toUnit (e.g. year). the inputs of the numeric edit menus (bin boundaries, knots) are
+  in the stored unit, so tell the user which unit they are typing in */
+  mayShowValueconversionMsg(div) {
+    const vc = this.termsetting.tw?.term?.valueConversion;
+    if (!vc) return;
+    div.append("div").style("margin", "0px 0px 10px 10px").style("opacity", 0.6).text(`Note: using values by the unit of ${vc.toUnit}.`);
+  }
+  showLoading(_div) {
+    const self = this.termsetting;
+    const div = _div || self.dom.tip.d;
+    div.selectAll("*").remove();
+    this.dom.loadingDiv = div.append("div").style("margin", "15px").text("Loading ...");
+  }
+  hideLoading() {
+    this.dom.loadingDiv?.remove();
+  }
+};
+
+export {
+  require_debounce,
+  HandlerBase
+};
+//# sourceMappingURL=chunk-XFAL46LZ.js.map

package/dist/chunk-XFAL46LZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/debounce/index.js", "../termsetting/HandlerBase.ts"],
+  "sourcesContent": ["/**\n * Returns a function, that, as long as it continues to be invoked, will not\n * be triggered. The function will be called after it stops being called for\n * N milliseconds. If `immediate` is passed, trigger the function on the\n * leading edge, instead of the trailing. The function also has a property 'clear' \n * that is a function which will clear the timer to prevent previously scheduled executions. \n *\n * @source underscore.js\n * @see http://unscriptable.com/2009/03/20/debouncing-javascript-methods/\n * @param {Function} function to wrap\n * @param {Number} timeout in ms (`100`)\n * @param {Boolean} whether to execute at the beginning (`false`)\n * @api public\n */\nfunction debounce(func, wait, immediate){\n  var timeout, args, context, timestamp, result;\n  if (null == wait) wait = 100;\n\n  function later() {\n    var last = Date.now() - timestamp;\n\n    if (last < wait && last >= 0) {\n      timeout = setTimeout(later, wait - last);\n    } else {\n      timeout = null;\n      if (!immediate) {\n        result = func.apply(context, args);\n        context = args = null;\n      }\n    }\n  };\n\n  var debounced = function(){\n    context = this;\n    args = arguments;\n    timestamp = Date.now();\n    var callNow = immediate && !timeout;\n    if (!timeout) timeout = setTimeout(later, wait);\n    if (callNow) {\n      result = func.apply(context, args);\n      context = args = null;\n    }\n\n    return result;\n  };\n\n  debounced.clear = function() {\n    if (timeout) {\n      clearTimeout(timeout);\n      timeout = null;\n    }\n  };\n  \n  debounced.flush = function() {\n    if (timeout) {\n      result = func.apply(context, args);\n      context = args = null;\n      \n      clearTimeout(timeout);\n      timeout = null;\n    }\n  };\n\n  return debounced;\n};\n\n// Adds compatibility for ES modules\ndebounce.debounce = debounce;\n\nmodule.exports = debounce;\n", "import type { Handler, UseCase } from './types'\nimport type { TermSetting } from './TermSetting.ts'\nimport type { TwBase } from '#tw'\n\nexport class HandlerBase implements Handler {\n\ttermsetting: TermSetting\n\tdom!: {\n\t\t[name: string]: any\n\t}\n\t//tw: TwBase\n\n\tconstructor(opts) {\n\t\tthis.termsetting = opts.termsetting\n\t\t//this.tw = opts.termsetting.tw\n\t}\n\n\tshowEditMenu(_) {\n\t\t//ignore\n\t}\n\n\tgetPillStatus(_?: UseCase) {\n\t\tconst tw = this.termsetting.tw as any as TwBase\n\t\treturn tw.getStatus?.() || { text: '' }\n\t}\n\n\t// this is equivalent to getPillNameDefault()\n\tgetPillName(d) {\n\t\tconst self = this.termsetting\n\t\tif (!self.opts.abbrCutoff) return d.name\n\t\treturn d.name.length <= self.opts.abbrCutoff + 2\n\t\t\t? d.name\n\t\t\t: '<label title=\"' + d.name + '\">' + d.name.substring(0, self.opts.abbrCutoff) + '...' + '</label>'\n\t}\n\n\tapplyEdits() {\n\t\t// ignore\n\t}\n\n\tundoEdits() {\n\t\t// ignore\n\t}\n\n\t/* a term with valueConversion{} stores its values in fromUnit (e.g. day) but shows them to\n\tusers in toUnit (e.g. year). the inputs of the numeric edit menus (bin boundaries, knots) are\n\tin the stored unit, so tell the user which unit they are typing in */\n\tmayShowValueconversionMsg(div: any) {\n\t\tconst vc = (this.termsetting.tw as any)?.term?.valueConversion\n\t\tif (!vc) return\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('margin', '0px 0px 10px 10px')\n\t\t\t.style('opacity', 0.6)\n\t\t\t// the editors show and read values in the user-facing unit, so that is the unit to name\n\t\t\t.text(`Note: using values by the unit of ${vc.toUnit}.`)\n\t}\n\n\tshowLoading(_div?: any) {\n\t\tconst self = this.termsetting\n\t\tconst div = _div || self.dom.tip.d\n\t\tdiv.selectAll('*').remove()\n\t\tthis.dom.loadingDiv = div.append('div').style('margin', '15px').text('Loading ...')\n\t}\n\n\thideLoading() {\n\t\tthis.dom.loadingDiv?.remove()\n\t}\n}\n"],
+  "mappings": ";;;;;AAAA;AAAA;AAcA,aAAS,SAAS,MAAM,MAAM,WAAU;AACtC,UAAI,SAAS,MAAM,SAAS,WAAW;AACvC,UAAI,QAAQ,KAAM,QAAO;AAEzB,eAAS,QAAQ;AACf,YAAI,OAAO,KAAK,IAAI,IAAI;AAExB,YAAI,OAAO,QAAQ,QAAQ,GAAG;AAC5B,oBAAU,WAAW,OAAO,OAAO,IAAI;AAAA,QACzC,OAAO;AACL,oBAAU;AACV,cAAI,CAAC,WAAW;AACd,qBAAS,KAAK,MAAM,SAAS,IAAI;AACjC,sBAAU,OAAO;AAAA,UACnB;AAAA,QACF;AAAA,MACF;AAAC;AAED,UAAI,YAAY,WAAU;AACxB,kBAAU;AACV,eAAO;AACP,oBAAY,KAAK,IAAI;AACrB,YAAI,UAAU,aAAa,CAAC;AAC5B,YAAI,CAAC,QAAS,WAAU,WAAW,OAAO,IAAI;AAC9C,YAAI,SAAS;AACX,mBAAS,KAAK,MAAM,SAAS,IAAI;AACjC,oBAAU,OAAO;AAAA,QACnB;AAEA,eAAO;AAAA,MACT;AAEA,gBAAU,QAAQ,WAAW;AAC3B,YAAI,SAAS;AACX,uBAAa,OAAO;AACpB,oBAAU;AAAA,QACZ;AAAA,MACF;AAEA,gBAAU,QAAQ,WAAW;AAC3B,YAAI,SAAS;AACX,mBAAS,KAAK,MAAM,SAAS,IAAI;AACjC,oBAAU,OAAO;AAEjB,uBAAa,OAAO;AACpB,oBAAU;AAAA,QACZ;AAAA,MACF;AAEA,aAAO;AAAA,IACT;AAGA,aAAS,WAAW;AAEpB,WAAO,UAAU;AAAA;AAAA;;;ACjEV,IAAM,cAAN,MAAqC;AAAA;AAAA,EAO3C,YAAY,MAAM;AACjB,SAAK,cAAc,KAAK;AAAA,EAEzB;AAAA,EAEA,aAAa,GAAG;AAAA,EAEhB;AAAA,EAEA,cAAc,GAAa;AAC1B,UAAM,KAAK,KAAK,YAAY;AAC5B,WAAO,GAAG,YAAY,KAAK,EAAE,MAAM,GAAG;AAAA,EACvC;AAAA;AAAA,EAGA,YAAY,GAAG;AACd,UAAM,OAAO,KAAK;AAClB,QAAI,CAAC,KAAK,KAAK,WAAY,QAAO,EAAE;AACpC,WAAO,EAAE,KAAK,UAAU,KAAK,KAAK,aAAa,IAC5C,EAAE,OACF,mBAAmB,EAAE,OAAO,OAAO,EAAE,KAAK,UAAU,GAAG,KAAK,KAAK,UAAU,IAAI;AAAA,EACnF;AAAA,EAEA,aAAa;AAAA,EAEb;AAAA,EAEA,YAAY;AAAA,EAEZ;AAAA;AAAA;AAAA;AAAA,EAKA,0BAA0B,KAAU;AACnC,UAAM,KAAM,KAAK,YAAY,IAAY,MAAM;AAC/C,QAAI,CAAC,GAAI;AACT,QACE,OAAO,KAAK,EACZ,MAAM,UAAU,mBAAmB,EACnC,MAAM,WAAW,GAAG,EAEpB,KAAK,qCAAqC,GAAG,MAAM,GAAG;AAAA,EACzD;AAAA,EAEA,YAAY,MAAY;AACvB,UAAM,OAAO,KAAK;AAClB,UAAM,MAAM,QAAQ,KAAK,IAAI,IAAI;AACjC,QAAI,UAAU,GAAG,EAAE,OAAO;AAC1B,SAAK,IAAI,aAAa,IAAI,OAAO,KAAK,EAAE,MAAM,UAAU,MAAM,EAAE,KAAK,aAAa;AAAA,EACnF;AAAA,EAEA,cAAc;AACb,SAAK,IAAI,YAAY,OAAO;AAAA,EAC7B;AACD;",
+  "names": []
+}

package/dist/chunk-XIBY5I6F.js

@@ -0,0 +1,240 @@
+import {
+  make_radios
+} from "./chunk-K6OVOHIZ.js";
+import {
+  initBinConfig
+} from "./chunk-4USLEUNR.js";
+import {
+  toStoredUnit,
+  toUserUnit
+} from "./chunk-75T7ESEO.js";
+import {
+  format
+} from "./chunk-UJELJXJG.js";
+
+// termsetting/handlers/NumRegularBinEditor.ts
+var NumRegularBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  /* q holds bin boundaries in the unit the term's values are stored in, while the <input>s and the
+  density plot show them in the term's user-facing unit. toDisplay()/toStored() cross that boundary;
+  both are identity functions unless the term declares valueConversion{} */
+  toDisplay(v) {
+    return toUserUnit(v, this.tw.term);
+  }
+  toStored(v) {
+    return toStoredUnit(v, this.tw.term);
+  }
+  render(div) {
+    this.tw = this.editHandler.tw;
+    const isRemounting = !!this.dom.binsTable && this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node());
+    if (!isRemounting) this.q = this.getDefaultQ();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (isRemounting) return;
+    if (this.dom.binsTable) {
+      this.dom.binsTable.remove();
+      delete this.dom.binsTable;
+    }
+    const binsTable = div.append("table");
+    this.dom.binsTable = binsTable;
+    this.renderBinSizeInput(binsTable.append("tr"));
+    this.renderFirstBinInput(binsTable.append("tr"));
+    this.renderLastBinInputs(binsTable.append("tr"));
+  }
+  getDefaultQ() {
+    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
+    const t = this.tw.term;
+    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
+    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
+    const binConfig = initBinConfig(this.editHandler.handler.density_data);
+    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
+  }
+  renderBinSizeInput(tr) {
+    const handler = this.editHandler.handler;
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
+    const { min, max } = handler.density_data;
+    const q = this.q;
+    const origBinSize = this.toDisplay(q.bin_size);
+    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr(
+      "value",
+      handler.density.scaleFactor == 1 && "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : origBinSize
+    ).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
+      const newValue = this.toStored(Number(event.target.value));
+      if (newValue <= 0) {
+        window.alert("Please enter non-negative bin size.");
+        event.target.value = origBinSize;
+        return;
+      }
+      if ((max - min) / newValue > 100) {
+        window.alert("Bin size too small. Try setting a bigger value.");
+        event.target.value = origBinSize;
+        return;
+      }
+      q.bin_size = newValue;
+      this.dom.bin_size_input.style(
+        "color",
+        q.bin_size > max - min ? "red" : this.toDisplay(newValue) != origBinSize ? "green" : ""
+      );
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+  }
+  renderFirstBinInput(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    if (!q.first_bin) throw "missing q.first_bin";
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
+    const { min, max } = handler.density_data;
+    const origValue = this.toDisplay(q.first_bin.stop);
+    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
+      const newValue = this.toStored(Number(event.target.value));
+      if (Number(event.target.value) < this.toDisplay(min) || Number(event.target.value) > this.toDisplay(max)) {
+        window.alert("First bin stop value out of bound.");
+        event.target.value = origValue;
+        return;
+      }
+      this.q.first_bin.stop = newValue;
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
+  }
+  renderLastBinInputs(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
+    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
+    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
+    const radio_div = td1.append("div");
+    const radios = make_radios({
+      holder: radio_div,
+      options: [
+        { label: "Automatic", value: "auto", checked: isAuto },
+        { label: "Fixed", value: "fixed", checked: !isAuto }
+      ],
+      callback: (v) => {
+        if (v == "auto") {
+          delete q.last_bin;
+          edit_div.style("display", "none");
+          handler.density.setBinLines(this.getBoundaryOpts());
+          return;
+        }
+        edit_div.style("display", "inline-block");
+        if (this.dom.last_start_input.property("value") == "") {
+          this.dom.last_start_input.property(
+            "value",
+            this.toDisplay(this.tw.q.last_bin?.start || handler.density_data.max)
+          );
+        }
+        this.setLastBinStart();
+      }
+    });
+    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
+    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
+    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", Number.isFinite(q.last_bin?.start) ? this.toDisplay(q.last_bin.start) : "").style("width", "100px").on("change", () => this.setLastBinStart());
+    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
+  }
+  setLastBinStart() {
+    const q = this.q;
+    const { max } = this.editHandler.handler.density_data;
+    const strInput = this.dom.last_start_input.property("value");
+    if (strInput === "") return;
+    const inputValue = this.toStored(Number(strInput));
+    if (q.first_bin && Number(strInput) <= this.toDisplay(q.first_bin.stop)) {
+      window.alert("Last bin start cannot be smaller than first bin stop.");
+      this.dom.last_start_input.property("value", this.toDisplay(max));
+      return;
+    }
+    if (Number(strInput) > this.toDisplay(max)) {
+      window.alert("Last bin start value out of bound.");
+      this.dom.last_start_input.property("value", this.toDisplay(max));
+      return;
+    }
+    if (q.last_bin) q.last_bin.start = inputValue;
+    else
+      q.last_bin = {
+        start: inputValue,
+        stopunbounded: true,
+        stopinclusive: false
+      };
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  getBoundaryOpts() {
+    const { min, max } = this.editHandler.handler.density_data;
+    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
+    const boundaryValues = [];
+    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
+      if (this.q.last_bin?.start === i) break;
+      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
+      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
+      boundaryValues.push({ x: this.toDisplay(i), isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
+    }
+    if (this.q.last_bin) {
+      boundaryValues.push({
+        x: this.toDisplay(this.q.last_bin.start),
+        isDraggable: true,
+        isLastVisibleLine: true,
+        movesWithLineIndex: -1
+      });
+    }
+    return {
+      values: boundaryValues,
+      // the dragged value arrives in display units, matching what the <input>s show
+      callback: (d, value) => {
+        if (d.index === 0) {
+          this.dom.first_stop_input.property("value", value);
+          this.q.first_bin.stop = this.toStored(value);
+        } else {
+          this.dom.last_start_input.property("value", value);
+          if (this.q.last_bin) this.q.last_bin.start = this.toStored(value);
+        }
+      }
+    };
+  }
+  getEditedQ(destroyDom = true) {
+    const bin_size = this.dom.bin_size_input.property("value");
+    const config = {
+      mode: "discrete",
+      type: "regular-bin",
+      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
+      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
+      bin_size: this.toStored(Number(bin_size)),
+      first_bin: {
+        startunbounded: true,
+        stop: this.toStored(Number(this.dom.first_stop_input.property("value")))
+      },
+      /* rounding formats the stored bin size, so it cannot be derived from the decimals of a
+      converted input. a converted term labels its bins through valueConversion instead */
+      rounding: this.editHandler.handler.density.scaleFactor != 1 ? ".0f" : bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
+    };
+    if (this.dom.fixed_radio.property("checked")) {
+      config.last_bin = {
+        start: this.toStored(Number(this.dom.last_start_input.property("value"))),
+        stopunbounded: true
+      };
+    }
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return config;
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.binsTable.selectAll("*").remove();
+    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
+    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
+    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumRegularBinEditor
+};
+//# sourceMappingURL=chunk-XIBY5I6F.js.map

package/dist/chunk-XIBY5I6F.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumRegularBinEditor.ts"],
+  "sourcesContent": ["import { format } from 'd3-format'\n//import { setDensityPlot } from './density'\nimport { make_radios } from '#dom'\nimport initBinConfig from '#shared/termdb.initbinconfig.js'\nimport { toUserUnit, toStoredUnit } from '#shared/helpers.js'\nimport type { NumRegularBin } from '#tw'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor.ts'\nimport type { BoundaryOpts, BoundaryValue, DraggedLineData } from './NumericDensity.ts'\nimport type { TermSetting } from '../TermSetting.ts'\nimport type { RegularNumericBinConfig } from '#types'\n\n// This is a bin editor for NumDiscreteEditor\n// NumericHandler (handler) -> NumDiscreteEditor (editor) -> NumRegularBinEditor (bin editor)\nexport class NumRegularBinEditor {\n\ttw: NumRegularBin\n\tq!: RegularNumericBinConfig\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\t/* q holds bin boundaries in the unit the term's values are stored in, while the <input>s and the\n\tdensity plot show them in the term's user-facing unit. toDisplay()/toStored() cross that boundary;\n\tboth are identity functions unless the term declares valueConversion{} */\n\ttoDisplay(v) {\n\t\treturn toUserUnit(v, this.tw.term)\n\t}\n\n\ttoStored(v) {\n\t\treturn toStoredUnit(v, this.tw.term)\n\t}\n\n\trender(div) {\n\t\tthis.tw = this.editHandler.tw as NumRegularBin\n\t\t// see the note in NumCustomBinEditor.render(): keep unapplied edits when returning to this tab\n\t\tconst isRemounting =\n\t\t\t!!this.dom.binsTable && this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())\n\t\tif (!isRemounting) this.q = this.getDefaultQ()\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\tif (isRemounting) return\n\t\tif (this.dom.binsTable) {\n\t\t\tthis.dom.binsTable.remove()\n\t\t\tdelete this.dom.binsTable\n\t\t}\n\t\tconst binsTable = div.append('table')\n\t\tthis.dom.binsTable = binsTable\n\t\tthis.renderBinSizeInput(binsTable.append('tr'))\n\t\tthis.renderFirstBinInput(binsTable.append('tr'))\n\t\tthis.renderLastBinInputs(binsTable.append('tr'))\n\t}\n\n\tgetDefaultQ(): RegularNumericBinConfig {\n\t\tif (this.tw.q.type == 'regular-bin') return JSON.parse(JSON.stringify(this.tw.q))\n\t\tconst t = this.tw.term\n\t\tconst defaultQ = (this.termsetting.opts.use_bins_less && t.bins?.less) || t.bins?.default\n\t\tif (defaultQ) return JSON.parse(JSON.stringify(defaultQ))\n\t\tconst binConfig = initBinConfig(this.editHandler.handler.density_data)\n\t\treturn typeof binConfig == 'string' ? JSON.parse(binConfig) : binConfig\n\t}\n\n\trenderBinSizeInput(tr: any) {\n\t\tconst handler = this.editHandler.handler\n\t\ttr.append('td').style('margin', '5px').style('opacity', 0.5).text('Bin Size')\n\n\t\tconst { min, max } = handler.density_data\n\t\tconst q = this.q\n\t\t// bin size is a span rather than a point, but converts the same way as one\n\t\tconst origBinSize = this.toDisplay(q.bin_size)\n\n\t\tthis.dom.bin_size_input = tr\n\t\t\t.append('td')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr(\n\t\t\t\t'value',\n\t\t\t\thandler.density.scaleFactor == 1 && 'rounding' in q ? format(q.rounding || '.0f')(q.bin_size) : origBinSize\n\t\t\t)\n\t\t\t.attr('data-testid', 'sjpp-num-reg-bin-editor-size')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.style('width', '100px')\n\t\t\t.style('color', () => (q.bin_size > Math.abs(max - min) ? 'red' : ''))\n\t\t\t.on('change', event => {\n\t\t\t\tconst newValue = this.toStored(Number(event.target.value))\n\t\t\t\t// must validate input value\n\t\t\t\tif (newValue <= 0) {\n\t\t\t\t\twindow.alert('Please enter non-negative bin size.')\n\t\t\t\t\t// must reset value in <input>, otherwise the wrong value will be recorded in self.q upon clicking Submit\n\t\t\t\t\tevent.target.value = origBinSize\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif ((max - min) / newValue > 100) {\n\t\t\t\t\t// avoid rendering too many svg lines and lock up browser\n\t\t\t\t\twindow.alert('Bin size too small. Try setting a bigger value.')\n\t\t\t\t\tevent.target.value = origBinSize\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tq.bin_size = newValue\n\t\t\t\tthis.dom.bin_size_input.style(\n\t\t\t\t\t'color',\n\t\t\t\t\tq.bin_size > max - min ? 'red' : this.toDisplay(newValue) != origBinSize ? 'green' : ''\n\t\t\t\t)\n\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t})\n\t}\n\n\trenderFirstBinInput(tr: any) {\n\t\tconst handler = this.editHandler.handler\n\t\tconst q = this.q\n\t\tif (!q.first_bin) throw 'missing q.first_bin'\n\n\t\ttr.append('td').style('margin', '5px').style('opacity', 0.5).text('First Bin Stop')\n\n\t\tconst { min, max } = handler.density_data\n\t\tconst origValue = this.toDisplay(q.first_bin.stop)\n\n\t\tthis.dom.first_stop_input = tr\n\t\t\t.append('td')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', origValue)\n\t\t\t.style('width', '100px')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.on('change', event => {\n\t\t\t\tconst newValue = this.toStored(Number(event.target.value))\n\t\t\t\t// bounds are compared in the unit the value was typed in, see setLastBinStart()\n\t\t\t\tif (Number(event.target.value) < this.toDisplay(min) || Number(event.target.value) > this.toDisplay(max)) {\n\t\t\t\t\twindow.alert('First bin stop value out of bound.')\n\t\t\t\t\tevent.target.value = origValue\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\t// first_bin should have already been set; adding the check just to skip the tsc error...\n\t\t\t\tthis.q.first_bin.stop = newValue\n\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t})\n\n\t\ttr.append('td')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('display', handler.density.no_density_data ? 'none' : 'block')\n\t\t\t.text('Indicated by left-most red line. Drag to change.')\n\t}\n\n\trenderLastBinInputs(tr) {\n\t\tconst handler = this.editHandler.handler\n\t\tconst q = this.q\n\t\t// tell if last bin is automatic (not fixed)\n\t\tconst isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start)\n\n\t\ttr.append('td')\n\t\t\t.style('padding-top', '4px')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.text('Last Bin Start')\n\n\t\tconst td1 = tr.append('td').style('padding-left', '15px').style('vertical-align', 'top')\n\t\tconst radio_div = td1.append('div')\n\n\t\tconst radios = make_radios({\n\t\t\tholder: radio_div,\n\t\t\toptions: [\n\t\t\t\t{ label: 'Automatic', value: 'auto', checked: isAuto },\n\t\t\t\t{ label: 'Fixed', value: 'fixed', checked: !isAuto }\n\t\t\t],\n\t\t\tcallback: v => {\n\t\t\t\tif (v == 'auto') {\n\t\t\t\t\tdelete q.last_bin\n\t\t\t\t\t// if just deleting last_bin.start and keeps q.last_bin{}, density plot may set last_bin.bin='last' and will break bin validation\n\t\t\t\t\tedit_div.style('display', 'none')\n\t\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// v is \"fixed\", to assign a number to self.q.last_bin.start\n\t\t\t\tedit_div.style('display', 'inline-block')\n\t\t\t\tif (this.dom.last_start_input.property('value') == '') {\n\t\t\t\t\t// blank input, fill max\n\t\t\t\t\tthis.dom.last_start_input.property(\n\t\t\t\t\t\t'value',\n\t\t\t\t\t\tthis.toDisplay(this.tw.q.last_bin?.start || handler.density_data.max)\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\tthis.setLastBinStart()\n\t\t\t}\n\t\t})\n\n\t\tthis.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1)\n\n\t\tconst edit_div = tr\n\t\t\t.append('td')\n\t\t\t.append('div')\n\t\t\t.style('display', isAuto ? 'none' : 'inline-block')\n\n\t\tthis.dom.last_start_input = edit_div\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', Number.isFinite(q.last_bin?.start) ? this.toDisplay(q.last_bin!.start) : '')\n\t\t\t.style('width', '100px')\n\t\t\t.on('change', () => this.setLastBinStart())\n\n\t\tedit_div\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('display', handler.density.no_density_data ? 'none' : 'block')\n\t\t\t.text('Indicated by right-most red line. Drag to change.')\n\t}\n\n\tsetLastBinStart() {\n\t\tconst q = this.q\n\t\tconst { max } = this.editHandler.handler.density_data\n\t\t// only get value from <input>\n\t\tconst strInput = this.dom.last_start_input.property('value')\n\t\tif (strInput === '') return\n\t\tconst inputValue = this.toStored(Number(strInput))\n\n\t\t/* the bounds are compared in the unit the value was typed in, which is also the unit this\n\t\tinput is filled in. converting a displayed value back is lossy, so the converted maximum is\n\t\tnot the maximum it came from: comparing there would reject the value filled in by the radio\n\t\tcallback above, which is the converted maximum */\n\t\t// TODO first_bin should be required\n\t\tif (q.first_bin && Number(strInput) <= this.toDisplay(q.first_bin.stop)) {\n\t\t\twindow.alert('Last bin start cannot be smaller than first bin stop.')\n\t\t\tthis.dom.last_start_input.property('value', this.toDisplay(max))\n\t\t\treturn\n\t\t}\n\t\tif (Number(strInput) > this.toDisplay(max)) {\n\t\t\twindow.alert('Last bin start value out of bound.')\n\t\t\tthis.dom.last_start_input.property('value', this.toDisplay(max))\n\t\t\treturn\n\t\t}\n\t\tif (q.last_bin) q.last_bin.start = inputValue\n\t\telse\n\t\t\tq.last_bin = {\n\t\t\t\tstart: inputValue,\n\t\t\t\tstopunbounded: true,\n\t\t\t\tstopinclusive: false\n\t\t\t}\n\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n\n\tgetBoundaryOpts(): BoundaryOpts {\n\t\tconst { min, max } = this.editHandler.handler.density_data\n\t\tconst binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0)\n\t\tconst boundaryValues: BoundaryValue[] = []\n\t\tfor (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {\n\t\t\tif (this.q.last_bin?.start === i) break\n\t\t\tif (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true\n\t\t\tconst isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1\n\t\t\t// non-draggable lines should move with the first bin boundary line\n\t\t\t// the loop runs in stored units; the plot is drawn in display units\n\t\t\tboundaryValues.push({ x: this.toDisplay(i), isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 })\n\t\t}\n\t\tif (this.q.last_bin) {\n\t\t\tboundaryValues.push({\n\t\t\t\tx: this.toDisplay(this.q.last_bin.start),\n\t\t\t\tisDraggable: true,\n\t\t\t\tisLastVisibleLine: true,\n\t\t\t\tmovesWithLineIndex: -1\n\t\t\t})\n\t\t}\n\n\t\treturn {\n\t\t\tvalues: boundaryValues,\n\t\t\t// the dragged value arrives in display units, matching what the <input>s show\n\t\t\tcallback: (d: DraggedLineData, value) => {\n\t\t\t\t//d.scaledX = Math.round(xscale(value))\n\t\t\t\tif (d.index === 0) {\n\t\t\t\t\tthis.dom.first_stop_input.property('value', value)\n\t\t\t\t\tthis.q.first_bin.stop = this.toStored(value)\n\t\t\t\t} else {\n\t\t\t\t\t// the input belongs to this bin editor; NumericHandler.dom never holds it\n\t\t\t\t\tthis.dom.last_start_input.property('value', value)\n\t\t\t\t\t//if (!this.q.last_bin) this.q.last_bin = {}\n\t\t\t\t\tif (this.q.last_bin) this.q.last_bin.start = this.toStored(value)\n\t\t\t\t\t//middleLines.style('display', (c: any) => (d.draggedX && c.scaledX >= d.draggedX ? 'none' : ''))\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tgetEditedQ(destroyDom = true): RegularNumericBinConfig {\n\t\tconst bin_size = this.dom.bin_size_input.property('value')\n\t\tconst config: RegularNumericBinConfig = {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'regular-bin',\n\t\t\tstartinclusive: this.editHandler.boundaryInclusion == 'startinclusive',\n\t\t\tstopinclusive: this.editHandler.boundaryInclusion == 'stopinclusive',\n\t\t\tbin_size: this.toStored(Number(bin_size)),\n\t\t\tfirst_bin: {\n\t\t\t\tstartunbounded: true,\n\t\t\t\tstop: this.toStored(Number(this.dom.first_stop_input.property('value')))\n\t\t\t},\n\t\t\t/* rounding formats the stored bin size, so it cannot be derived from the decimals of a\n\t\t\tconverted input. a converted term labels its bins through valueConversion instead */\n\t\t\trounding:\n\t\t\t\tthis.editHandler.handler.density.scaleFactor != 1\n\t\t\t\t\t? '.0f'\n\t\t\t\t\t: bin_size.includes('.') && !bin_size.endsWith('.')\n\t\t\t\t\t? `.${bin_size.split('.')[1].length}f`\n\t\t\t\t\t: '.0f'\n\t\t}\n\n\t\tif (this.dom.fixed_radio.property('checked')) {\n\t\t\tconfig.last_bin = {\n\t\t\t\tstart: this.toStored(Number(this.dom.last_start_input.property('value'))),\n\t\t\t\tstopunbounded: true\n\t\t\t}\n\t\t}\n\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\n\t\treturn config\n\t}\n\n\tundoEdits() {\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.dom.binsTable.selectAll('*').remove()\n\t\tthis.renderBinSizeInput(this.dom.binsTable.append('tr'))\n\t\tthis.renderFirstBinInput(this.dom.binsTable.append('tr'))\n\t\tthis.renderLastBinInputs(this.dom.binsTable.append('tr'))\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/chunk-XJBSBIZ4.js

@@ -0,0 +1,70 @@
+import {
+  junctionCustomTermSource
+} from "./chunk-MGGAWPTR.js";
+import {
+  mayRenderFractionSelection
+} from "./chunk-K6OVOHIZ.js";
+
+// termdb/handlers/junction.ts
+var SearchHandler = class {
+  async init(opts) {
+    if (!opts?.holder) throw new Error("opts.holder is required");
+    if (typeof opts.callback != "function") throw new Error("opts.callback is required");
+    const entries = getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms);
+    render(opts, entries);
+  }
+};
+function getJunctionCustomTerms(customTerms) {
+  if (!Array.isArray(customTerms)) return [];
+  return customTerms.filter((term) => term?.source === junctionCustomTermSource && term.tw?.term);
+}
+function render(opts, entries) {
+  const holder = opts.holder;
+  holder.selectAll("*").remove();
+  const div = holder.append("div").style("padding", "10px 0px");
+  if (!entries.length) {
+    div.append("div").text("Junctions selected from genome browser will be shown here.");
+    return;
+  }
+  const listDiv = div.append("div");
+  const fractionDiv = div.append("div");
+  for (const entry of entries) {
+    if (entry.eventlabel) renderJunctionEvent(listDiv, fractionDiv, entry, opts);
+    else renderJunction(listDiv, entry, opts);
+  }
+  listDiv.append("div").style("font-size", ".7em").style("margin-top", "10px").style("opacity", 0.7).text("Select additional junctions from genome browser.");
+}
+function renderJunction(holder, entry, opts) {
+  const choice = holder.append("div");
+  choice.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.tw.term.name).on("click", () => opts.callback(entry.tw.term));
+  addDeleteButton(choice, entry, opts);
+}
+function renderJunctionEvent(holder, fractionDiv, entry, opts) {
+  const eventHolder = holder.append("div");
+  const pillRow = eventHolder.append("div");
+  pillRow.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.eventlabel).on("click", () => selectJunctionEvent(holder, fractionDiv, entry, opts));
+  addDeleteButton(pillRow, entry, opts);
+  eventHolder.append("div").style("margin-left", "10px").style("font-size", ".7em").selectAll("div").data(entry.tw.term.termlst, (term) => term.id).enter().append("div").text((term) => term.name);
+}
+function selectJunctionEvent(listDiv, fractionDiv, entry, opts) {
+  const isStaged = mayRenderFractionSelection({
+    term: entry.tw.term,
+    selectionMode: opts.termCollectionSelectionMode,
+    listDiv,
+    fractionDiv,
+    callback: (tw) => opts.callback(tw)
+  });
+  if (!isStaged) opts.callback(entry.tw.term);
+}
+function addDeleteButton(holder, entry, opts) {
+  holder.append("button").attr("data-testid", "sjpp-junction-delete").style("margin-left", "4px").attr("aria-label", `Delete ${entry.name}`).text("\xD7").on("click", async () => {
+    await opts.app.vocabApi.deleteCustomTermById(entry.id);
+    render(opts, getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms));
+  });
+}
+
+export {
+  SearchHandler,
+  getJunctionCustomTerms
+};
+//# sourceMappingURL=chunk-XJBSBIZ4.js.map