@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

package/dist/chunk-D5ETVOOE.js

@@ -0,0 +1,158 @@
+import {
+  NumericDensity
+} from "./chunk-F4DM3WS4.js";
+import {
+  Tabs
+} from "./chunk-C3HEDQPT.js";
+import {
+  HandlerBase
+} from "./chunk-KV4W2ACA.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-3V76ZSEY.js");
+          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
+          break;
+        }
+        case "discrete": {
+          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-DFOJ7AIH.js");
+          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
+          break;
+        }
+        case "binary": {
+          const { NumBinaryEditor } = await import("./NumBinaryEditor-GYHOYPQL.js");
+          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
+          break;
+        }
+        case "spline": {
+          const { NumSplineEditor } = await import("./NumSplineEditor-PUXJF2RW.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").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-D5ETVOOE.js.map

package/dist/chunk-DANF4CC5.js

@@ -0,0 +1,102 @@
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist,
+  getDNAMethUnit,
+  sayerror
+} from "./chunk-C3HEDQPT.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  DNA_METHYLATION
+} from "./chunk-SB36AUG7.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-XGK6TEGH.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-DANF4CC5.js.map