@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-DHNXATHC.js

@@ -0,0 +1,158 @@
+import {
+  NumericDensity
+} from "./chunk-ICBNFAW4.js";
+import {
+  Tabs
+} from "./chunk-2YC6ZVE4.js";
+import {
+  HandlerBase
+} from "./chunk-LSEFWW72.js";
+
+// termsetting/handlers/NumericHandler.ts
+var NumericHandler = class extends HandlerBase {
+  constructor(opts) {
+    super(opts);
+    this.tabs = [];
+    this.handlerByMode = {};
+    this.dom = {};
+    this.opts = opts;
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+    this.tabs = this.setTabData();
+    this.density = new NumericDensity(opts);
+  }
+  getPillStatus() {
+    this.tw = this.termsetting.tw;
+    return this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
+  }
+  setTabData() {
+    const self = this.termsetting;
+    const tabs = [];
+    const callback = async (event, tabData) => {
+      if (event) event.stopPropagation();
+      try {
+        await this.setEditHandler(tabData);
+        await this.editHandler.showEditMenu(tabData.contentHolder);
+      } catch (e) {
+        this.dom.errdiv.style("display", "").text(e);
+      }
+    };
+    const numTabs = self.opts.numericEditMenuVersion.length;
+    if (self.opts.numericEditMenuVersion.includes("continuous")) {
+      tabs.push({
+        mode: "continuous",
+        label: self.term.type == "survival" ? "Time to Event" : "Continuous",
+        callback,
+        active: this.tw.q.mode === "continuous" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("discrete")) {
+      tabs.push({
+        mode: "discrete",
+        label: self.term.type == "survival" ? "Exit code" : "Discrete",
+        callback,
+        active: this.tw.q.mode === "discrete" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("spline")) {
+      tabs.push({
+        mode: "spline",
+        label: "Cubic spline",
+        callback,
+        active: this.tw.q.mode === "spline" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("binary")) {
+      tabs.push({
+        mode: "binary",
+        label: "Binary",
+        callback,
+        active: this.tw.q.mode === "binary" || numTabs === 1
+      });
+    }
+    return tabs;
+  }
+  async setEditHandler(tabData) {
+    if (!this.handlerByMode[tabData.mode]) {
+      switch (tabData.mode) {
+        case "continuous": {
+          const { NumContEditor } = await import("./NumContEditor-5PYW3OLY.js");
+          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
+          break;
+        }
+        case "discrete": {
+          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-N6OJYSJA.js");
+          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
+          break;
+        }
+        case "binary": {
+          const { NumBinaryEditor } = await import("./NumBinaryEditor-B3FXQAOH.js");
+          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
+          break;
+        }
+        case "spline": {
+          const { NumSplineEditor } = await import("./NumSplineEditor-XERKOACS.js");
+          this.handlerByMode.spline = new NumSplineEditor(this.opts, this);
+          break;
+        }
+        default:
+          throw `unexpected numeric tabData.mode='${tabData.mode}'`;
+          break;
+      }
+    }
+    this.editHandler = this.handlerByMode[tabData.mode];
+  }
+  async showEditMenu(div) {
+    try {
+      this.showLoading(div);
+      this.dom.errdiv = div.append("div").attr("class", "sja_errorbar").style("display", "none");
+      this.tw = this.termsetting.tw;
+      const self = this.tw;
+      for (const t of this.tabs) {
+        t.active = this.tabs.length === 1 || self.q.mode == t.mode || t.mode == "continuous" && !self.q.mode;
+      }
+      this.density_data = await this.density.setData();
+      await this.setEditHandler(this.tabs.find((t) => t.active));
+      this.dom.editDiv = div.append("div").attr("data-testid", "sjpp-num-ts-edit-div");
+      this.dom.btnDiv = div.append("div");
+      this.renderButtons(this.dom.btnDiv);
+      if (this.tabs.length > 1) {
+        this.dom.topBar = this.dom.editDiv.append("div").style("padding", "10px");
+        this.dom.topBar.append("span").html("Use as ");
+        new Tabs({
+          holder: this.dom.topBar.append("div").style("display", "inline-block"),
+          contentHolder: this.dom.editDiv.append("div"),
+          noTopContentStyle: true,
+          tabs: this.tabs
+        }).main();
+      } else {
+        await this.editHandler.showEditMenu(this.dom.editDiv);
+      }
+      this.dom.loadingDiv.style("display", "none");
+    } catch (e) {
+      this.hideLoading();
+      this.dom.errdiv.style("display", "").text(typeof e == "object" ? e.message || e.error || e : e);
+    }
+  }
+  renderButtons(btnDiv) {
+    btnDiv.append("button").style("margin", "5px").html("Apply").on("click", () => {
+      this.termsetting.q = this.editHandler.getEditedQ();
+      this.termsetting.dom.tip.hide();
+      this.termsetting.api.runCallback();
+    });
+    btnDiv.append("button").style("margin", "5px").html("Reset").on("click", () => {
+      this.editHandler.undoEdits();
+    });
+  }
+  destroy() {
+    for (const s of Object.values(this.dom)) {
+      if (typeof s.remove == "function") s.remove();
+    }
+    this.density.destroy();
+  }
+};
+
+export {
+  NumericHandler
+};
+//# sourceMappingURL=chunk-DHNXATHC.js.map

package/dist/chunk-DXHATYHE.js

@@ -0,0 +1,180 @@
+import {
+  NumericModes
+} from "./chunk-EGWVYY7K.js";
+
+// plots/proteomeAbundance.ts
+function renderAssayAndCohortRadios({
+  holder,
+  organisms,
+  selectedProteomeDetails,
+  onChange,
+  organismTitle = "Organism",
+  assayTitle = "Assay Type",
+  cohortTitle = "Cohort"
+}) {
+  const organismEntries = Object.entries(organisms || {});
+  if (!organismEntries.length) {
+    holder.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No proteome organisms available.");
+    return {
+      getSelected: () => ({ organism: void 0, assay: void 0, cohort: void 0 })
+    };
+  }
+  const initialProteomeDetails = selectedProteomeDetails || {};
+  const organismRadioName = `sjpp-proteome-organism-${Math.random().toString().slice(-6)}`;
+  const assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`;
+  const cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`;
+  let selectedOrganism = organisms[initialProteomeDetails.organism || ""] ? initialProteomeDetails.organism : organismEntries[0][0];
+  let selectedAssay = initialProteomeDetails.assay;
+  let selectedCohort = initialProteomeDetails.cohort;
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(organismTitle);
+  const organismListDiv = holder.append("div").style("margin-bottom", "10px");
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(assayTitle);
+  const assayListDiv = holder.append("div").style("margin-bottom", "10px");
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(cohortTitle);
+  const cohortListDiv = holder.append("div").style("max-height", "300px").style("overflow-y", "auto").style("border", "1px solid #ddd").style("border-radius", "4px").style("padding", "5px");
+  for (const [organismKey] of organismEntries) {
+    const organismLabel = organismListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+    organismLabel.append("input").attr("type", "radio").attr("name", organismRadioName).attr("value", organismKey).property("checked", organismKey === selectedOrganism).style("margin-right", "6px").on("change", () => {
+      selectedOrganism = organismKey;
+      selectedAssay = void 0;
+      selectedCohort = void 0;
+      renderAssayOptions();
+      renderCohortOptions();
+      onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+    });
+    organismLabel.append("span").text(organismKey);
+  }
+  renderAssayOptions();
+  renderCohortOptions();
+  onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+  return {
+    getSelected: () => ({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })
+  };
+  function renderAssayOptions() {
+    assayListDiv.selectAll("*").remove();
+    const assays = organisms[selectedOrganism || ""]?.assays || {};
+    const assayEntries = Object.entries(assays);
+    if (!assayEntries.length) {
+      selectedAssay = void 0;
+      selectedCohort = void 0;
+      assayListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No assays available.");
+      return;
+    }
+    if (!selectedAssay || !assays[selectedAssay]) {
+      selectedAssay = assayEntries.some(([k]) => k === initialProteomeDetails.assay) ? initialProteomeDetails.assay : assayEntries[0][0];
+    }
+    for (const [assayKey] of assayEntries) {
+      const assayLabel = assayListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+      assayLabel.append("input").attr("type", "radio").attr("name", assayRadioName).attr("value", assayKey).property("checked", assayKey === selectedAssay).style("margin-right", "6px").on("change", () => {
+        selectedAssay = assayKey;
+        selectedCohort = void 0;
+        renderCohortOptions();
+        onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+      });
+      assayLabel.append("span").text(assayKey);
+    }
+  }
+  function renderCohortOptions() {
+    cohortListDiv.selectAll("*").remove();
+    const cohorts = Object.keys(organisms[selectedOrganism || ""]?.assays?.[selectedAssay || ""]?.cohorts || {});
+    if (!cohorts.length) {
+      selectedCohort = void 0;
+      cohortListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No cohorts available.");
+      return;
+    }
+    if (!selectedCohort || !organisms[selectedOrganism || ""]?.assays?.[selectedAssay || ""]?.cohorts?.[selectedCohort]) {
+      selectedCohort = cohorts.includes(initialProteomeDetails.cohort || "") ? initialProteomeDetails.cohort : cohorts[0];
+    }
+    for (const cohortKey of cohorts) {
+      const cohortLabel = cohortListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+      cohortLabel.append("input").attr("type", "radio").attr("name", cohortRadioName).attr("value", cohortKey).property("checked", cohortKey === selectedCohort).style("margin-right", "6px").on("change", () => {
+        selectedCohort = cohortKey;
+        onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+      });
+      cohortLabel.append("span").text(cohortKey);
+    }
+  }
+}
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.dom.tip.clear();
+  const organisms = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms || {};
+  const menuDiv = holder.append("div");
+  let selectedProteomeDetails;
+  const launchOption = menuDiv.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").style("display", "block").style("margin", "10px auto 10px").text("Select Protein").on("click", () => {
+    const current = selectedProteomeDetails;
+    if (!current?.organism || !current.assay || !current.cohort) return;
+    const { organism, assay, cohort } = current;
+    const assayCohortTitle = `${organism} ${assay}: ${cohort}`;
+    const chart = {
+      label: "Protein Abundance",
+      chartType: "proteomeAbundance",
+      usecase: {
+        target: "proteomeAbundance",
+        detail: "term",
+        proteomeDetails: { organism, assay, cohort },
+        label: `Organism: ${organism}; Assay: ${assay}; Cohort: ${cohort}`
+      },
+      processSelection: (termlst) => termlst,
+      updateActionBySelectedTerms: (action, termlst) => {
+        action.config.assayCohortTitle = assayCohortTitle;
+        const currentDetails = selectedProteomeDetails;
+        if (!currentDetails?.organism || !currentDetails.assay || !currentDetails.cohort) return;
+        const { organism: organism2, assay: assay2, cohort: cohort2 } = currentDetails;
+        action.config.proteomeDetails = { organism: organism2, assay: assay2, cohort: cohort2 };
+        const twlst = termlst.map((term) => {
+          const t = structuredClone(term);
+          t.proteomeDetails = { organism: organism2, assay: assay2, cohort: cohort2 };
+          return { term: t, q: { mode: NumericModes.continuous } };
+        });
+        if (twlst.length == 1) {
+          action.config.chartType = "summary";
+          action.config.term = twlst[0];
+          const proteomeOverlayTerm = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms?.[organism2]?.overlayTerm;
+          if (proteomeOverlayTerm) action.config.term2 = { term: structuredClone(proteomeOverlayTerm), q: {} };
+          return;
+        }
+        if (twlst.length == 2) {
+          action.config.chartType = "summary";
+          action.config.term = twlst[0];
+          action.config.term2 = twlst[1];
+          return;
+        }
+        action.config.chartType = "hierCluster";
+        action.config.dataType = "proteomeAbundance";
+        action.config.termgroups = [{ name: "Protein Abundance Cluster", lst: twlst, type: "hierCluster" }];
+      }
+    };
+    chartsInstance.dom.tip.clear();
+    chartsInstance.showTree_selectlst(chart);
+  });
+  const syncLaunchButtonState = () => {
+    if (!launchOption) return;
+    if (selectedProteomeDetails?.cohort) launchOption.style("opacity", 1).style("pointer-events", "auto");
+    else launchOption.style("opacity", 0.5).style("pointer-events", "none");
+  };
+  renderAssayAndCohortRadios({
+    holder: menuDiv,
+    organisms,
+    onChange: (proteomeDetails) => {
+      selectedProteomeDetails = proteomeDetails;
+      syncLaunchButtonState();
+    }
+  });
+  syncLaunchButtonState();
+}
+function toTvslstFilter(filterConfig) {
+  if (filterConfig && Array.isArray(filterConfig) && filterConfig.length)
+    return {
+      type: "tvslst",
+      in: true,
+      join: filterConfig.length > 1 ? "and" : "",
+      lst: filterConfig.map((tvs) => ({ type: "tvs", tvs }))
+    };
+}
+
+export {
+  renderAssayAndCohortRadios,
+  makeChartBtnMenu,
+  toTvslstFilter
+};
+//# sourceMappingURL=chunk-DXHATYHE.js.map

package/dist/chunk-DXHATYHE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/proteomeAbundance.ts"],
+  "sourcesContent": ["import { NumericModes } from '#shared/terms.js'\nimport type { ProteomeDetails } from '#types'\n\ntype RenderAssayAndCohortRadiosOpts = {\n\tholder: any\n\torganisms: any\n\tselectedProteomeDetails?: Partial<ProteomeDetails>\n\tonChange?: (details: Partial<ProteomeDetails>) => void\n\torganismTitle?: string\n\tassayTitle?: string\n\tcohortTitle?: string\n}\n\nexport function renderAssayAndCohortRadios({\n\tholder,\n\torganisms,\n\tselectedProteomeDetails,\n\tonChange,\n\torganismTitle = 'Organism',\n\tassayTitle = 'Assay Type',\n\tcohortTitle = 'Cohort'\n}: RenderAssayAndCohortRadiosOpts) {\n\tconst organismEntries = Object.entries(organisms || {})\n\tif (!organismEntries.length) {\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('padding', '8px')\n\t\t\t.text('No proteome organisms available.')\n\t\treturn {\n\t\t\tgetSelected: () => ({ organism: undefined, assay: undefined, cohort: undefined })\n\t\t}\n\t}\n\n\tconst initialProteomeDetails = selectedProteomeDetails || {}\n\n\tconst organismRadioName = `sjpp-proteome-organism-${Math.random().toString().slice(-6)}`\n\tconst assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`\n\tconst cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`\n\n\tlet selectedOrganism = organisms[initialProteomeDetails.organism || '']\n\t\t? initialProteomeDetails.organism\n\t\t: organismEntries[0][0]\n\tlet selectedAssay = initialProteomeDetails.assay\n\tlet selectedCohort = initialProteomeDetails.cohort\n\n\tholder\n\t\t.append('div')\n\t\t.style('margin', '3px 5px')\n\t\t.style('padding', '3px 5px')\n\t\t.style('font-weight', 600)\n\t\t.text(organismTitle)\n\tconst organismListDiv = holder.append('div').style('margin-bottom', '10px')\n\n\tholder.append('div').style('margin', '3px 5px').style('padding', '3px 5px').style('font-weight', 600).text(assayTitle)\n\tconst assayListDiv = holder.append('div').style('margin-bottom', '10px')\n\n\tholder\n\t\t.append('div')\n\t\t.style('margin', '3px 5px')\n\t\t.style('padding', '3px 5px')\n\t\t.style('font-weight', 600)\n\t\t.text(cohortTitle)\n\tconst cohortListDiv = holder\n\t\t.append('div')\n\t\t.style('max-height', '300px')\n\t\t.style('overflow-y', 'auto')\n\t\t.style('border', '1px solid #ddd')\n\t\t.style('border-radius', '4px')\n\t\t.style('padding', '5px')\n\n\tfor (const [organismKey] of organismEntries) {\n\t\tconst organismLabel = organismListDiv\n\t\t\t.append('label')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('display', 'block')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.style('padding', '6px 8px')\n\t\t\t.style('border-radius', '4px')\n\n\t\torganismLabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'radio')\n\t\t\t.attr('name', organismRadioName)\n\t\t\t.attr('value', organismKey)\n\t\t\t.property('checked', organismKey === selectedOrganism)\n\t\t\t.style('margin-right', '6px')\n\t\t\t.on('change', () => {\n\t\t\t\tselectedOrganism = organismKey\n\t\t\t\tselectedAssay = undefined\n\t\t\t\tselectedCohort = undefined\n\t\t\t\trenderAssayOptions()\n\t\t\t\trenderCohortOptions()\n\t\t\t\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t\t\t})\n\t\torganismLabel.append('span').text(organismKey)\n\t}\n\n\trenderAssayOptions()\n\trenderCohortOptions()\n\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\n\treturn {\n\t\tgetSelected: () => ({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t}\n\n\tfunction renderAssayOptions() {\n\t\tassayListDiv.selectAll('*').remove()\n\t\tconst assays = organisms[selectedOrganism || '']?.assays || {}\n\t\tconst assayEntries = Object.entries(assays)\n\t\tif (!assayEntries.length) {\n\t\t\tselectedAssay = undefined\n\t\t\tselectedCohort = undefined\n\t\t\tassayListDiv.append('div').attr('class', 'sja_sharp_border').style('padding', '8px').text('No assays available.')\n\t\t\treturn\n\t\t}\n\n\t\tif (!selectedAssay || !assays[selectedAssay]) {\n\t\t\tselectedAssay = assayEntries.some(([k]) => k === initialProteomeDetails.assay)\n\t\t\t\t? initialProteomeDetails.assay\n\t\t\t\t: assayEntries[0][0]\n\t\t}\n\n\t\tfor (const [assayKey] of assayEntries) {\n\t\t\tconst assayLabel = assayListDiv\n\t\t\t\t.append('label')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('padding', '6px 8px')\n\t\t\t\t.style('border-radius', '4px')\n\n\t\t\tassayLabel\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'radio')\n\t\t\t\t.attr('name', assayRadioName)\n\t\t\t\t.attr('value', assayKey)\n\t\t\t\t.property('checked', assayKey === selectedAssay)\n\t\t\t\t.style('margin-right', '6px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tselectedAssay = assayKey\n\t\t\t\t\tselectedCohort = undefined\n\t\t\t\t\trenderCohortOptions()\n\t\t\t\t\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t\t\t\t})\n\t\t\tassayLabel.append('span').text(assayKey)\n\t\t}\n\t}\n\n\tfunction renderCohortOptions() {\n\t\tcohortListDiv.selectAll('*').remove()\n\t\tconst cohorts = Object.keys(organisms[selectedOrganism || '']?.assays?.[selectedAssay || '']?.cohorts || {})\n\t\tif (!cohorts.length) {\n\t\t\tselectedCohort = undefined\n\t\t\tcohortListDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '8px')\n\t\t\t\t.text('No cohorts available.')\n\t\t\treturn\n\t\t}\n\n\t\tif (!selectedCohort || !organisms[selectedOrganism || '']?.assays?.[selectedAssay || '']?.cohorts?.[selectedCohort]) {\n\t\t\tselectedCohort = cohorts.includes(initialProteomeDetails.cohort || '') ? initialProteomeDetails.cohort : cohorts[0]\n\t\t}\n\n\t\tfor (const cohortKey of cohorts) {\n\t\t\tconst cohortLabel = cohortListDiv\n\t\t\t\t.append('label')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('padding', '6px 8px')\n\t\t\t\t.style('border-radius', '4px')\n\t\t\tcohortLabel\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'radio')\n\t\t\t\t.attr('name', cohortRadioName)\n\t\t\t\t.attr('value', cohortKey)\n\t\t\t\t.property('checked', cohortKey === selectedCohort)\n\t\t\t\t.style('margin-right', '6px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tselectedCohort = cohortKey\n\t\t\t\t\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t\t\t\t})\n\n\t\t\tcohortLabel.append('span').text(cohortKey)\n\t\t}\n\t}\n}\n\nexport function makeChartBtnMenu(holder: any, chartsInstance: any): void {\n\tchartsInstance.dom.tip.clear()\n\tconst organisms = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms || {}\n\tconst menuDiv = holder.append('div')\n\n\tlet selectedProteomeDetails: Partial<ProteomeDetails> | undefined\n\tconst launchOption = menuDiv\n\t\t.append('button')\n\t\t.attr('class', 'sjpp_apply_btn sja_filter_tag_btn sja_sharp_border')\n\t\t.style('display', 'block')\n\t\t.style('margin', '10px auto 10px')\n\t\t.text('Select Protein')\n\t\t.on('click', () => {\n\t\t\tconst current = selectedProteomeDetails\n\t\t\tif (!current?.organism || !current.assay || !current.cohort) return\n\t\t\tconst { organism, assay, cohort } = current\n\t\t\tconst assayCohortTitle = `${organism} ${assay}: ${cohort}`\n\t\t\tconst chart = {\n\t\t\t\tlabel: 'Protein Abundance',\n\t\t\t\tchartType: 'proteomeAbundance',\n\t\t\t\tusecase: {\n\t\t\t\t\ttarget: 'proteomeAbundance',\n\t\t\t\t\tdetail: 'term',\n\t\t\t\t\tproteomeDetails: { organism, assay, cohort },\n\t\t\t\t\tlabel: `Organism: ${organism}; Assay: ${assay}; Cohort: ${cohort}`\n\t\t\t\t},\n\t\t\t\tprocessSelection: (termlst: any[]) => termlst,\n\t\t\t\tupdateActionBySelectedTerms: (action: any, termlst: any[]) => {\n\t\t\t\t\taction.config.assayCohortTitle = assayCohortTitle\n\t\t\t\t\tconst currentDetails = selectedProteomeDetails\n\t\t\t\t\tif (!currentDetails?.organism || !currentDetails.assay || !currentDetails.cohort) return\n\t\t\t\t\tconst { organism, assay, cohort } = currentDetails\n\t\t\t\t\taction.config.proteomeDetails = { organism, assay, cohort }\n\t\t\t\t\tconst twlst = termlst.map(term => {\n\t\t\t\t\t\tconst t = structuredClone(term)\n\t\t\t\t\t\tt.proteomeDetails = { organism, assay, cohort }\n\t\t\t\t\t\treturn { term: t, q: { mode: NumericModes.continuous } }\n\t\t\t\t\t})\n\n\t\t\t\t\tif (twlst.length == 1) {\n\t\t\t\t\t\taction.config.chartType = 'summary'\n\t\t\t\t\t\taction.config.term = twlst[0]\n\t\t\t\t\t\tconst proteomeOverlayTerm =\n\t\t\t\t\t\t\tchartsInstance.state.termdbConfig?.queries?.proteome?.organisms?.[organism]?.overlayTerm\n\t\t\t\t\t\tif (proteomeOverlayTerm) action.config.term2 = { term: structuredClone(proteomeOverlayTerm), q: {} }\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tif (twlst.length == 2) {\n\t\t\t\t\t\taction.config.chartType = 'summary'\n\t\t\t\t\t\taction.config.term = twlst[0]\n\t\t\t\t\t\taction.config.term2 = twlst[1]\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\taction.config.chartType = 'hierCluster'\n\t\t\t\t\taction.config.dataType = 'proteomeAbundance'\n\t\t\t\t\taction.config.termgroups = [{ name: 'Protein Abundance Cluster', lst: twlst, type: 'hierCluster' }]\n\t\t\t\t}\n\t\t\t}\n\t\t\tchartsInstance.dom.tip.clear()\n\t\t\tchartsInstance.showTree_selectlst(chart)\n\t\t})\n\n\tconst syncLaunchButtonState = () => {\n\t\tif (!launchOption) return\n\t\tif (selectedProteomeDetails?.cohort) launchOption.style('opacity', 1).style('pointer-events', 'auto')\n\t\telse launchOption.style('opacity', 0.5).style('pointer-events', 'none')\n\t}\n\n\trenderAssayAndCohortRadios({\n\t\tholder: menuDiv,\n\t\torganisms,\n\t\tonChange: proteomeDetails => {\n\t\t\tselectedProteomeDetails = proteomeDetails\n\t\t\tsyncLaunchButtonState()\n\t\t}\n\t})\n\n\tsyncLaunchButtonState()\n}\n\nexport function toTvslstFilter(filterConfig: any): any {\n\tif (filterConfig && Array.isArray(filterConfig) && filterConfig.length)\n\t\treturn {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: filterConfig.length > 1 ? 'and' : '',\n\t\t\tlst: filterConfig.map((tvs: any) => ({ type: 'tvs', tvs }))\n\t\t}\n}"],
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+  "names": ["organism", "assay", "cohort"]
+}

package/dist/chunk-E3BI23UK.js

@@ -0,0 +1,229 @@
+import {
+  keyupEnter
+} from "./chunk-2YC6ZVE4.js";
+import {
+  get_bin_label,
+  get_bin_range_equation
+} from "./chunk-ZYY54HBU.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-E3BI23UK.js.map