@sjcrh/proteinpaint-client 2.191.3 → 2.191.4

package/dist/chunk-MBZ3D6T6.js

@@ -1,55 +0,0 @@
-import {
-  colorinframe
-} from "./chunk-APO4BA2P.js";
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-EBKERML3.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-MBZ3D6T6.js.map

package/dist/chunk-MEGBYD4U.js

@@ -1,182 +0,0 @@
-import {
-  dofetch3
-} from "./chunk-6VKTEMFV.js";
-import {
-  DNA_METHYLATION,
-  GENE_EXPRESSION,
-  PROTEOME_DAP,
-  SINGLECELL_CELLTYPE
-} from "./chunk-TVADJLMF.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-
-// plots/volcano/colors.ts
-function getGroupColors(config) {
-  const groups = config?.samplelst?.groups;
-  const termValues = config?.tw?.term?.values;
-  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
-  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
-  return {
-    controlColor: toHex(rawDown, "red"),
-    caseColor: toHex(rawUp, "blue")
-  };
-}
-function toHex(color, fallback) {
-  const c = rgb(color || fallback);
-  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
-}
-
-// plots/volcano/model/VolcanoModel.ts
-var VolcanoModel = class {
-  constructor(app, termType) {
-    this.app = app;
-    this.termType = termType;
-  }
-  /** May use mapper instead as more termTypes are added */
-  async getData(config, settings) {
-    this.config = config;
-    this.settings = settings;
-    if (this.termType === GENE_EXPRESSION) {
-      const body = await this.getGERequestBody();
-      const response = await dofetch3("termdb/DE", { body });
-      if (response && !response.error) response.daRequest = body;
-      return response;
-    }
-    if (this.termType === DNA_METHYLATION) {
-      const body = await this.getDMRequestBody();
-      const response = await dofetch3("termdb/diffMeth", { body });
-      if (response && !response.error) response.daRequest = body;
-      return response;
-    }
-    if (this.termType === SINGLECELL_CELLTYPE) {
-      const body = await this.getSCCTRequestBody();
-      return await dofetch3("termdb/singlecellDEgenes", { body });
-    }
-    if (this.termType === PROTEOME_DAP) {
-      const body = this.getDapRequestBody();
-      return await dofetch3("termdb/dapVolcano", { body });
-    }
-    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
-  }
-  //Gene expression
-  async getGERequestBody() {
-    await this.getOtherSamples(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DE",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      method: this.settings.method,
-      min_count: this.settings.minCount,
-      min_total_count: this.settings.minTotalCount,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      cpm_cutoff: this.settings.cpmCutoff,
-      volcanoRender: this.getVolcanoRender()
-    };
-    this.addConfounderTw(body);
-    return body;
-  }
-  //DNA methylation
-  async getDMRequestBody() {
-    await this.getOtherSamples(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DM",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      min_samples_per_group: this.settings.minSamplesPerGroup,
-      volcanoRender: this.getVolcanoRender()
-    };
-    this.addConfounderTw(body);
-    return body;
-  }
-  /** Parameters telling the server to run the `volcano` Rust renderer and return a
-   * volcano PNG + top-significant rows instead of the full dot list. */
-  getVolcanoRender() {
-    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
-    const { caseColor, controlColor } = getGroupColors(this.config);
-    return {
-      significanceThresholds: {
-        pValueCutoff: this.settings.pValue,
-        pValueType: this.settings.pValueType,
-        foldChangeCutoff: this.settings.foldChangeCutoff
-      },
-      pixelWidth: this.settings.width,
-      pixelHeight: this.settings.height,
-      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
-      colorSignificantUp: caseColor,
-      colorSignificantDown: controlColor,
-      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
-      dotRadius,
-      maxInteractiveDots: this.settings.maxInteractiveDots,
-      // Render the PNG at device-pixel resolution so it stays sharp on
-      // retina screens. The server reports the plot extent in CSS-space,
-      // so SVG overlay coords are unaffected.
-      //
-      // Oversample by 2× so the PNG also stays sharp when the user
-      // *zooms in after* the initial render (the captured DPR is frozen
-      // at fetch time — bigger headroom = more tolerable post-render
-      // zoom before pixelation appears). The server clamp keeps the
-      // bitmap memory bounded.
-      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
-    };
-  }
-  //This is a workaround until the server can accept an arr of confounder tws
-  addConfounderTw(body) {
-    const confounders = this.config?.confounderTws;
-    if (confounders?.length) {
-      body.tw = this.config.confounderTws[0];
-      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
-    }
-  }
-  //Single cell cell type
-  getSCCTRequestBody() {
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      sample: this.config.sample,
-      termId: this.config.termId,
-      categoryName: this.config.categoryName,
-      volcanoRender: this.getVolcanoRender()
-    };
-    return body;
-  }
-  getDapRequestBody() {
-    const { organism, assay, cohort } = this.config.proteomeDetails;
-    return {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      organism,
-      assay,
-      cohort,
-      volcanoRender: this.getVolcanoRender()
-    };
-  }
-  /** retrieve the sampleId/sampleName for samples in
-   * the "others" group instead of using {in: false} */
-  async getOtherSamples(samplelst) {
-    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
-    if (!othersSamplesGroup) return;
-    const state = this.app.getState();
-    const samplesGroup = samplelst.groups.find((g) => g.in);
-    othersSamplesGroup.values = [];
-    for (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
-      if (samplesGroup.values.indexOf((i) => i.sampleId == s.id) == -1) {
-        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
-      }
-    }
-    othersSamplesGroup.in = true;
-  }
-};
-
-export {
-  getGroupColors,
-  VolcanoModel
-};
-//# sourceMappingURL=chunk-MEGBYD4U.js.map

package/dist/chunk-MEY5OBDJ.js

@@ -1,170 +0,0 @@
-import {
-  getEmptyCell,
-  maySetEmptyCell,
-  setCellProps
-} from "./chunk-JEZIKGZI.js";
-import {
-  TermTypeGroups
-} from "./chunk-EBKERML3.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.serieses.js
-var matrix_serieses_exports = {};
-__export(matrix_serieses_exports, {
-  getSerieses: () => getSerieses
-});
-function getSerieses(data) {
-  const s = this.settings.matrix;
-  const serieses = [];
-  const { colw, dx, dy, xMin, xMax } = this.dimensions;
-  const dvt = this.config.divideBy || {};
-  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
-  const legendGroups = {};
-  this.colorScaleByTermId = {};
-  for (const t of this.termOrder) {
-    const $id = t.tw.$id;
-    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
-    const isDivideByTerm = termid === divideByTermId;
-    const emptyGridCells = [];
-    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
-    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
-    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
-    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
-    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
-    const series = {
-      t,
-      tw: t.tw,
-      cells: [],
-      y,
-      hoverY0,
-      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
-    };
-    for (const so of this.unfilteredSampleOrder) {
-      const { totalIndex, grpIndex, row } = so;
-      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
-      const anno = row[$id];
-      const cellTemplate = {
-        s: so,
-        sample: row.sample,
-        tw: t.tw,
-        term: t.tw.term,
-        termid,
-        $id,
-        totalIndex,
-        grpIndex,
-        row,
-        t,
-        seriesY: y
-      };
-      if (!anno) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      const key = anno.key;
-      const values = anno.filteredValues || anno.values || [anno.value];
-      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
-      const height = !s.transpose ? s.rowh / numRects : colw;
-      const width = !s.transpose ? colw : colw / values.length;
-      const siblingCells = [];
-      if (!anno || !anno.renderedValues?.length) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      for (const [i, value] of values.entries()) {
-        const cell = Object.assign({ key, siblingCells }, cellTemplate);
-        cell.valueIndex = i;
-        let legend;
-        if (typeof t.tw.setCellProps == "function") {
-          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
-        } else {
-          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
-          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
-        }
-        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
-        if (legend) {
-          for (const l of [legendGroups, so.grp.legendGroups]) {
-            if (!l) continue;
-            if (!l[legend.group]) {
-              l[legend.group] = {
-                ref: legend.ref,
-                values: {},
-                order: legend.order,
-                $id,
-                origin: legend.entry.origin
-              };
-              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
-            }
-            const lg = l[legend.group];
-            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
-            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
-            if (!lg.values[legendK]) {
-              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
-              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
-            }
-            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
-            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
-              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
-            } else lg.values[legendK].samples.add(row.sample);
-            if (isDivideByTerm) {
-              lg.values[legend.value].isExcluded = so.grp.isExcluded;
-            }
-          }
-        }
-        if (!so.grp.isExcluded) {
-          if (anno.renderedValues.includes(value)) series.cells.push(cell);
-          siblingCells.push(cell);
-        }
-      }
-      if (s.showGrid == "rect" && !so.grp.isExcluded) {
-        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
-        if (cell) emptyGridCells.push(cell);
-      }
-    }
-    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
-    if (series.cells.length) serieses.push(series);
-  }
-  addAllHiddenLegendGroups(legendGroups, this);
-  this.legendData = this.getLegendData(legendGroups, data.refs, this);
-  for (const grp of this.sampleGroups) {
-    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
-  }
-  return serieses;
-}
-function addAllHiddenLegendGroups(legendGroups, self) {
-  for (const valueFilter of self.config.legendValueFilter.lst) {
-    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
-      legendGroups[valueFilter.legendGrpName] = {
-        ref: {},
-        values: {},
-        dt: [valueFilter.tvs.values[0].dt],
-        origin: valueFilter.tvs.values[0].origin
-      };
-    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    }
-  }
-}
-
-export {
-  getSerieses,
-  matrix_serieses_exports
-};
-//# sourceMappingURL=chunk-MEY5OBDJ.js.map

package/dist/chunk-MHOVJLLC.js

@@ -1,102 +0,0 @@
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist,
-  getDNAMethUnit,
-  sayerror
-} from "./chunk-APO4BA2P.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  DNA_METHYLATION
-} from "./chunk-TVADJLMF.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-WGOA676W.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-MHOVJLLC.js.map

package/dist/chunk-N4PSYVGO.js

@@ -1,14 +0,0 @@
-// src/block.lazyload.js
-var Block;
-async function blocklazyload(arg) {
-  if (!Block) {
-    const b = await import("./block-WGOA676W.js");
-    Block = b.Block;
-  }
-  return new Block(arg);
-}
-
-export {
-  blocklazyload
-};
-//# sourceMappingURL=chunk-N4PSYVGO.js.map