@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/chunk-3DCABJHB.js

@@ -0,0 +1,381 @@
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.js";
+import {
+  mclass
+} from "./chunk-XYFDBYOY.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// plots/matrix/matrix.sorterUi.js
+var alphabet = `ABCDEFGHIJKLMNOPQRSTUVWXYZ`.split("");
+function getSorterUi(opts) {
+  const { controls, holder } = opts;
+  const parent = controls.parent;
+  const s = structuredClone(parent.config.settings.matrix);
+  const l = s.controlLabels;
+  const tip = new Menu({ padding: "", parent_menu: parent.app.tip?.d.node() });
+  let input, theads = [], sectionData, dragged = {};
+  const self = {
+    dom: { tip },
+    opts,
+    highlightColor: "none",
+    label: `Sort ${l.Samples}`,
+    title: `Set how to sort ${l.samples}`,
+    type: "custom",
+    expanded: opts.expanded || false,
+    expandedSection: opts.expandedSection || "",
+    init(overrides = {}, _opts = {}) {
+      tip.clear().hide();
+      if (parent.config.settings.matrix != s) copyMerge(s, parent.config.settings.matrix);
+      if (s !== overrides) copyMerge(s, overrides);
+      self.settings = s;
+      self.activeOption = structuredClone(s.sortOptions[s.sortSamplesBy]);
+      sectionData = [
+        {
+          label: `For each selected row, sort ${l.samples} by matching data`,
+          notDraggable: true,
+          tiebreakers: [],
+          handler: handleSelectedTerms
+        },
+        ...self.activeOption.sortPriority,
+        {
+          label: `Sort ${l.samples} by name, alphabetically`,
+          notDraggable: true,
+          tiebreakers: []
+        }
+      ];
+      Object.assign(opts, _opts);
+      opts.holder.selectAll("*").remove();
+      const topDiv = opts.holder.append("div").style("text-align", "right");
+      topDiv.append("button").html("Apply").on("click", apply);
+      topDiv.append("button").html("Reset").on("click", (event, d) => self.init());
+      const table = opts.holder.append("table");
+      const tr = table.append("thead");
+      tr.append("th").html("Priority").style("text-align", "left").style("max-width", "0px");
+      tr.append("th").html("Description");
+      tr.append("th").html("Action");
+      let i = 0, j = 0;
+      for (const sd of sectionData) {
+        const hasTbOrder = sd.tiebreakers?.[0]?.order || sd.handler;
+        const thead = table.append("thead").datum(sd).property("draggable", !sd.notDraggable).attr("droppable", true).on("dragstart", trackDraggedSection).on("dragover", highlightSection).on("dragleave", unhighlightSection).on("drop", adjustSortPriority);
+        theads.push(select_default(thead));
+        const tr2 = thead.append("tr").style("background-color", "#eee").on("mouseover", undoMouseoverHighlights);
+        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("font-weight", 400).html(alphabet[j++]).on("click", hasTbOrder ? toggleSection : null);
+        const td2 = tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "left").style("cursor", hasTbOrder ? "pointer" : "").on("click", hasTbOrder ? toggleSection : null);
+        td2.append("span").style("margin-right", "12px").style("font-weight", 400).html(sd.label);
+        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "center").style("font-weight", 400).style("cursor", hasTbOrder ? "pointer" : "").append("span").html(hasTbOrder ? "Details" : " ").on("click", hasTbOrder ? toggleSection : null);
+        const tbody = table.append("tbody").datum(sd).style("display", self.expandedSection == "all" || self.expandedSection == sd.label ? "" : "none");
+        for (const tb of sd.tiebreakers) {
+          if (tb.skip) continue;
+          if (!sd.types?.includes("geneVariant")) {
+            continue;
+          }
+          const tr3 = tbody.append("tr").on("mouseover", undoMouseoverHighlights).datum(tb).attr("draggable", !tb.disabled && sd.types?.length !== 0).attr("droppable", !tb.disabled && sd.types?.length !== 0).on("dragstart", trackDraggedTieBreaker).on("dragover", highlightTieBreaker).on("dragleave", unhighlightTieBreaker).on("drop", adjustTieBreakers);
+          if (!tb.disabled) i++;
+          const td1 = tr3.append("td").attr(
+            "title",
+            tb.disabled ? `This tiebreaker is currently not being used to sort ${l.cases}. Check the box to use.` : `The number indicates the order in which this tiebreaker is used. Unched the box to skip.`
+          ).datum(tb);
+          td1.style("padding", "5px").style("vertical-align", "top").style("text-align", "center");
+          td1.append("span").html(!tb.disabled ? i : "");
+          const td22 = tr3.append("td").style("opacity", tb.disabled ? 0.5 : 1).style("padding", "5px").style("vertical-align", "top").style("max-width", "500px");
+          td22.append("span").html(tb.label || "");
+          if (!tb.disabled) {
+            const label = td22.append("label");
+            label.append("span").html("<br>(use data list order ");
+            if (!tb.isOrdered) tb.isOrdered = false;
+            const checkbox = label.append("input").datum(tb).attr("type", "checkbox").property("checked", tb.isOrdered).style("vertical-align", "bottom").on("change", toggleTieBreakerIsOrdered);
+            label.append("span").html(")");
+            const order = tb.order;
+            td22.append("div").attr("class", "sjpp-matrix-sorter-ui-value").selectAll("div").data(
+              order.map((key, index) => ({
+                lstName: "order",
+                key,
+                cls: mclass[key],
+                tb,
+                dragstart: trackDraggedValue,
+                dragover: highlightValue,
+                dragleave: unhighlightValue,
+                drop: adjustValueOrder,
+                filterByClass: s.filterByClass,
+                index
+              }))
+            ).enter().append("div").style("display", tb.isOrdered ? "block" : "inline-block").each(setValueDiv);
+            if (tb.notUsed?.length) {
+              const notUsed = td22.append("div");
+              notUsed.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-add").style("display", "inline-block").style("padding", "5x").style("vertical-align", "top").style("padding", "3px 5px").style("cursor", "pointer").html(`+Add`).on("click", showNotUsedValues);
+            }
+          }
+          const td3 = tr3.append("td").style("text-align", "center").style("vertical-align", "top");
+          if (tb.mayToggle) {
+            td3.append("button").datum(tb).html(tb.disabled ? "Enable" : "Disable").on("click", toggleTieBreakerDisabled);
+          }
+        }
+        const lastTr = tbody.append("tr").attr("draggable", true).on("mouseover", undoMouseoverHighlights);
+        lastTr.append("td").html("&nbsp;");
+        const tdNew = lastTr.append("td").style("text-align", "left").html(sd.details && !sd.order?.length ? sd.details : "&nbsp;");
+        if (sd.handler) sd.handler(tdNew, lastTr, tbody);
+        lastTr.append("td").html("&nbsp;");
+      }
+    },
+    toggleSection,
+    trackDraggedSection,
+    highlightSection,
+    unhighlightSection,
+    adjustSortPriority,
+    trackDraggedTieBreaker,
+    highlightTieBreaker,
+    unhighlightTieBreaker,
+    adjustTieBreakers,
+    trackDraggedValue,
+    highlightValue,
+    unhighlightValue,
+    adjustValueOrder,
+    apply
+  };
+  function toggleSection(event, d = { label: "all" }) {
+    self.expandedSection = self.expandedSection === d.label ? "" : d.label;
+    self.expanded = !!self.expandedSection;
+    self.init();
+  }
+  function trackDraggedSection(event, d) {
+    dragged.type = "sortPriority";
+    dragged.data = d;
+    dragged.index = self.activeOption.sortPriority.indexOf(d);
+  }
+  function highlightSection(event, d) {
+    if (dragged.type != "sortPriority" || d == dragged.data) return;
+    event.preventDefault();
+    const i = self.activeOption.sortPriority.indexOf(d);
+    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
+    if (!borderSide) return;
+    select_default(this).selectAll("th").style(borderSide, "2px solid blue");
+  }
+  function unhighlightSection(event, d) {
+    if (dragged.type != "sortPriority") return;
+    event.preventDefault();
+    select_default(this).selectAll("th").style("border", "none");
+  }
+  function adjustSortPriority(event, d) {
+    if (d == dragged.data) return;
+    const i = self.activeOption.sortPriority.indexOf(d);
+    const s2 = parent.config.settings.matrix;
+    self.activeOption.sortPriority.splice(dragged.index, 1);
+    self.activeOption.sortPriority.splice(i, 0, dragged.data);
+    self.init({
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function trackDraggedTieBreaker(event, d) {
+    dragged.type = "tiebreaker";
+    dragged.data = d;
+    dragged.sectionData = event.target.closest("tbody").__data__;
+    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
+    dragged.index = dragged.sectionData.tiebreakers.indexOf(d);
+  }
+  function highlightTieBreaker(event, d) {
+    if (dragged.type != "tiebreaker" || d == dragged.data) return;
+    event.preventDefault();
+    const i = dragged.sectionData.tiebreakers.indexOf(d);
+    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
+    if (!borderSide) return;
+    select_default(this).selectAll("td:nth-child(2)").style(borderSide, "2px solid blue");
+  }
+  function unhighlightTieBreaker(event, d) {
+    if (dragged.type != "tiebreaker") return;
+    event.preventDefault();
+    select_default(this).selectAll("td:nth-child(2)").style("border", "none");
+  }
+  function toggleTieBreakerIsOrdered(event, tb) {
+    event.stopPropagation();
+    tb.isOrdered = !tb.isOrdered;
+    self.init({
+      sortOptions: {
+        [s.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function toggleTieBreakerDisabled(event, tb) {
+    event.stopPropagation();
+    tb.disabled = !tb.disabled;
+    self.init({
+      sortOptions: {
+        [s.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function adjustTieBreakers(event, d) {
+    if (dragged.type != "tiebreaker" || d == dragged.data) return;
+    event.preventDefault();
+    const i = dragged.sectionData.tiebreakers.indexOf(d);
+    const s2 = parent.config.settings.matrix;
+    dragged.sectionData.tiebreakers.splice(dragged.index, 1);
+    dragged.sectionData.tiebreakers.splice(i, 0, dragged.data);
+    self.init({
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function setValueDiv(d) {
+    const title = [];
+    if (d.tb.notUsed?.includes(d.key)) title.push(`- Click on this label to include in used data values.`);
+    if (d.filterByClass[d.key])
+      title.unshift("- Click on the corresponding entry in the matrix legend or Mutation/CNV menus to unhide");
+    if (title.length) title.unshift(`To use this data value for sorting ${l.samples}:`);
+    const skipped = d.tb.notUsed?.includes(d.key);
+    const opacity = d.filterByClass[d.key] == "value" ? 0.5 : 1;
+    const div = select_default(this).attr("aria-label", title.length ? title.join("\n") : `Click to not use this data value to sort ${l.samples}`).attr("draggable", d.tb.isOrdered ? true : false).attr("droppable", d.tb.isOrdered ? true : false).style("width", "fit-content").style("margin-right", "10px").style("overflow", "hidden").style("white-space", "nowrap").style("opacity", opacity).style("cursor", "pointer").on("dragstart", d.dragstart).on("dragover", d.dragover).on("dragleave", d.dragleave).on("drop", d.drop).on("mouseenter", () => toggle.style("opacity", 1)).on("mouseleave", () => toggle.style("opacity", 0)).on("click", () => {
+      if (title.length) {
+        const cls = "sjpp-matrix-sorter-value-note";
+        div.selectAll(`.${cls}`).remove();
+        const note = div.append("div").attr("class", cls).style("max-width", "200px").style("padding", "5px");
+        note.html(title.join("<br>"));
+        if (d.filterByClass[d.key]) return;
+      }
+      const targetLstName = d.lstName == "order" ? "notUsed" : "order";
+      if (!d.tb[targetLstName]) d.tb[targetLstName] = [];
+      const targetLst = d.tb[targetLstName];
+      d.tb[d.lstName].splice(d.index, 1);
+      if (d.lstName == "order") targetLst.unshift(d.key);
+      else targetLst.push(d.key);
+      self.init({
+        sortOptions: {
+          [s.sortSamplesBy]: self.activeOption
+        }
+      });
+    });
+    div.append("div").style("display", "inline-block").style("cursor", "pointer").style("width", "12px").style("height", "12px").style("margin-right", "3px").style("background-color", d.cls.color);
+    div.append("span").style("cursor", "pointer").style("text-decoration", d.filterByClass[d.key] == "case" ? "line-through" : "").html(d.cls.label + (d.filterByClass[d.key] ? " (<i>not used since this value is hidden</i>)" : ""));
+    const toggle = div.append("div").style("display", "inline-block").style("width", "12px").style("cursor", "pointer").style("opacity", 0).style("color", d.lstName == "order" ? "red" : "green").html(d.lstName == "order" ? "&cross;" : "&check;");
+  }
+  function trackDraggedValue(event, d) {
+    event.stopPropagation?.();
+    dragged.type = "value";
+    dragged.data = d;
+    dragged.sectionData = event.target.closest("tbody").__data__;
+    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
+    dragged.tiebreaker = event.target.closest("tr").__data__;
+    dragged.tbIndex = dragged.sectionData.tiebreakers.indexOf(dragged.priorityIndex);
+    dragged.order = dragged.tiebreaker.order;
+  }
+  function highlightValue(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value" || d == dragged.data) return;
+    if (d.tb != dragged.data.tb) return;
+    event.preventDefault();
+    const i = dragged.order.indexOf(d);
+    select_default(this).style("border", "2px solid blue");
+  }
+  function unhighlightValue(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value") return;
+    event.preventDefault();
+    select_default(this).style("border", "none");
+  }
+  function adjustValueOrder(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value" || d == dragged.data) return;
+    event.preventDefault();
+    const s2 = self.settings;
+    dragged.data.tb[dragged.data.lstName].splice(dragged.data.index, 1);
+    d.tb[d.lstName].splice(d.index, 0, dragged.data.key);
+    const j = s2.hiddenVariants.indexOf(dragged.data.key);
+    const hiddenVariants = structuredClone(s2.hiddenVariants);
+    const filterByClass = structuredClone(s2.filterByClass);
+    if (j != -1) {
+      hiddenVariants.splice(j, 1);
+      filterByClass[dragged.data.key] = false;
+    }
+    self.init({
+      hiddenVariants,
+      filterByClass,
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function showNotUsedValues(event, tb) {
+    event?.stopPropagation();
+    const availDiv = tip.clear().d.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-vals").style("margin-top", "3px").style("vertical-align", "top").style("padding-left", "12px");
+    availDiv.selectAll("div").data(
+      tb.notUsed.map((key, index) => ({
+        lstName: "notUsed",
+        key,
+        cls: mclass[key],
+        tb,
+        dragstart: trackDraggedValue,
+        dragover: highlightValue,
+        dragleave: unhighlightValue,
+        drop: adjustValueOrder,
+        filterByClass: s.filterByClass,
+        index
+      }))
+    ).enter().append("div").style("display", "block").each(setValueDiv);
+    tip.showunder(event.target);
+  }
+  function apply() {
+    parent.app.tip?.hide();
+    parent.app.dispatch({
+      type: "plot_edit",
+      id: parent.id,
+      config: {
+        settings: {
+          matrix: {
+            sortOptions: {
+              [s.sortSamplesBy]: self.activeOption
+            }
+          }
+        }
+      }
+    });
+  }
+  function undoMouseoverHighlights() {
+  }
+  function handleSelectedTerms(td, tr) {
+    if (!parent.selectedTermsToSortAgainst?.length) {
+      td.html(`Click on a matrix row label and the left triangle to add an entry here`);
+      return;
+    }
+    const selectedTerms = parent.selectedTermsToSortAgainst.map((t) => {
+      return {
+        t,
+        label: t.tw.term.name + (t.tw.term.type == "geneVariant" ? " alterations" : " values")
+      };
+    });
+    const tbody = select_default(tr.node().parentNode);
+    tbody.selectAll("tr").remove();
+    tbody.selectAll("tr").data(selectedTerms).enter().append("tr").selectAll("td").data((d, i) => [
+      { label: i + 1, textAlign: "center", cursor: "", t: d.t },
+      { label: d.label, textAlign: "left", cursor: "" },
+      {
+        label: "Delete",
+        textAlign: "center",
+        cursor: "pointer",
+        click: parent.unsortSamplesAgainstTerm,
+        data: d
+      }
+    ]).enter().append("td").style("text-align", (d) => d.textAlign).style("cursor", (d) => d.cursor).html((d) => d.label).on("click", (event, d) => d.click?.(event, d));
+  }
+  self.init();
+  self.api = {
+    main: self.init,
+    destroy: () => {
+      opts.holder.selectAll("*").remove();
+    }
+  };
+  if (opts.debug) self.api.Inner = self;
+  return self.api;
+}
+
+export {
+  getSorterUi
+};
+//# sourceMappingURL=chunk-3DCABJHB.js.map

package/dist/chunk-3MMKHYUM.js

@@ -0,0 +1,95 @@
+import {
+  keyupEnter
+} from "./chunk-NVB7MQLH.js";
+import {
+  dofetch,
+  dofetch3
+} from "./chunk-7RN3L2BX.js";
+import {
+  require_debounce
+} from "./chunk-LSEFWW72.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.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-3MMKHYUM.js.map

package/dist/chunk-3PRPMJTG.js

@@ -0,0 +1,55 @@
+import {
+  colorinframe
+} from "./chunk-NVB7MQLH.js";
+import {
+  IN_frame,
+  OUT_frame
+} from "./chunk-XYFDBYOY.js";
+
+// src/spliceevent.phrase.js
+function spliceevent_phrase_default(evt) {
+  const htmls = [];
+  if (evt.isaltexon || evt.isskipexon) {
+    const exonstart = Math.min(...evt.skippedexon);
+    const exonstop = Math.max(...evt.skippedexon);
+    htmls.push(
+      '<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
+    );
+    if (evt.isaltexon) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
+      );
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
+    }
+    if (evt.junctionB.data) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
+      );
+    }
+    htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
+    if (evt.framenocheck) {
+      if (evt.utr3) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
+      } else if (evt.utr5) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
+      }
+    } else if (evt.frame == IN_frame) {
+      htmls.push(
+        '<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
+      );
+    } else if (evt.frame == OUT_frame) {
+      htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
+    }
+  } else {
+    return "unknown event type!!";
+  }
+  return htmls.join(" ");
+}
+
+export {
+  spliceevent_phrase_default
+};
+//# sourceMappingURL=chunk-3PRPMJTG.js.map