@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/chunk-H7F6DMJA.js

@@ -0,0 +1,70 @@
+import {
+  junctionCustomTermSource
+} from "./chunk-MANAUI7R.js";
+import {
+  mayRenderFractionSelection
+} from "./chunk-WD7FZ5EE.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-H7F6DMJA.js.map

package/dist/chunk-HH3NUAR2.js

@@ -0,0 +1,96 @@
+import {
+  keyupEnter,
+  require_debounce
+} from "./chunk-WD7FZ5EE.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import {
+  dofetch,
+  dofetch3
+} from "./chunk-4TJO2DGU.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// src/gene.js
+var import_debounce = __toESM(require_debounce(), 1);
+var tip;
+function gene_searchbox(p) {
+  if (!tip) {
+    tip = new Menu({ padding: "" });
+    tip.d.style("z-index", 1e3);
+  }
+  const input = p.div.append("input").attr("placeholder", "Search gene").style("width", p.width || "100px");
+  const printdiv = p.resultdiv || (p.tip ? p.tip.d : tip.d);
+  function fold() {
+    if (p.resultdiv) {
+      p.resultdiv.selectAll("*").remove();
+    } else if (p.tip) {
+      p.tip.hide();
+    } else {
+      tip.hide();
+    }
+  }
+  input.on("keyup", (event) => {
+    const str = event.target.value;
+    if (str.length <= 1) {
+      fold();
+      return;
+    }
+    if (keyupEnter(event)) {
+      const hitgene = printdiv.select(".sja_menuoption");
+      if (hitgene.size() > 0) {
+        p.callback(hitgene.text());
+        fold();
+      }
+      return;
+    }
+    debouncer();
+  });
+  input.node().focus();
+  function genesearch() {
+    dofetch("genelookup", { genome: p.genome, input: input.property("value") }).then((data) => {
+      if (data.error) throw data.error;
+      if (!data.hits) throw ".hits[] missing";
+      if (p.resultdiv) {
+        p.resultdiv.selectAll("*").remove();
+      } else if (p.tip) {
+        p.tip.clear().showunder(input.node());
+      } else {
+        tip.clear().showunder(input.node());
+      }
+      for (const name of data.hits) {
+        printdiv.append("div").attr("class", "sja_menuoption").text(name).on("click", () => {
+          p.callback(name);
+          fold();
+        });
+      }
+    }).catch((err) => {
+      printdiv.append("div").text(err.message || err);
+      if (err.stack) console.log(err.stack);
+    });
+  }
+  const debouncer = (0, import_debounce.debounce)(genesearch, 300);
+}
+function findgenemodel_bysymbol(genome, str) {
+  return dofetch3("genelookup", {
+    body: {
+      deep: 1,
+      input: str,
+      genome
+    }
+  }).then((data) => {
+    if (data.error) throw data.error;
+    if (!data.gmlst || data.gmlst.length == 0) return null;
+    return data.gmlst;
+  }).catch((e) => {
+    throw e;
+  });
+}
+
+export {
+  gene_searchbox,
+  findgenemodel_bysymbol
+};
+//# sourceMappingURL=chunk-HH3NUAR2.js.map

package/dist/chunk-HRTPGNOG.js

@@ -0,0 +1,159 @@
+import {
+  NumericDensity
+} from "./chunk-WY3IORKG.js";
+import {
+  HandlerBase,
+  Tabs
+} from "./chunk-WD7FZ5EE.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;
+    const status = this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
+    if (this.tw.term.type == "geneExpression" && this.tw.term.sampleTypeLabel)
+      status.text += ` (${this.tw.term.sampleTypeLabel})`;
+    return status;
+  }
+  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-6CURFOCH.js");
+          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
+          break;
+        }
+        case "discrete": {
+          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-U7Z2QNYP.js");
+          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
+          break;
+        }
+        case "binary": {
+          const { NumBinaryEditor } = await import("./NumBinaryEditor-DSRP4OOU.js");
+          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
+          break;
+        }
+        case "spline": {
+          const { NumSplineEditor } = await import("./NumSplineEditor-U43D5NBJ.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").style("margin", "0px 0px 5px 5px");
+      this.renderButtons(this.dom.btnDiv);
+      if (this.tabs.length > 1) {
+        this.dom.topBar = this.dom.editDiv.append("div").attr("data-testid", "sja-ts-numeric-edit-top-bar").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").attr("data-testId", "sjpp_numeric_edit_apply").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").attr("data-testId", "sjpp_numeric_edit_reset").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-HRTPGNOG.js.map