@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

package/dist/chunk-Y4PX2ECH.js

@@ -1,299 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-PC4MFDHP.js";
-import {
-  dofetch3
-} from "./chunk-52QHIKH2.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-RUBZCKIX.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-747IK2EW.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-      if (arg.hidePdomain) {
-        for (const i of a.pdomains) {
-          m.domain_hidden[i.name + i.description] = 1;
-        }
-      }
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-IEFWFVS6.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-747IK2EW.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    aarange: arg.aarange,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-Y4PX2ECH.js.map

package/dist/chunk-YKM46UX5.js

@@ -1,170 +0,0 @@
-import {
-  getEmptyCell,
-  maySetEmptyCell,
-  setCellProps
-} from "./chunk-GVLWCGXX.js";
-import {
-  TermTypeGroups
-} from "./chunk-RUBZCKIX.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.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-YKM46UX5.js.map

package/dist/chunk-Z7AO6A7M.js

@@ -1,14 +0,0 @@
-// src/block.lazyload.js
-var Block;
-async function blocklazyload(arg) {
-  if (!Block) {
-    const b = await import("./block-747IK2EW.js");
-    Block = b.Block;
-  }
-  return new Block(arg);
-}
-
-export {
-  blocklazyload
-};
-//# sourceMappingURL=chunk-Z7AO6A7M.js.map

package/dist/chunk-ZENZ5H2Q.js

@@ -1,49 +0,0 @@
-import {
-  runproteinpaint
-} from "./chunk-LGR6CJTW.js";
-
-// test/front.helpers.js
-var serverData = /* @__PURE__ */ Object.create(null);
-function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
-  const host = window.testHost || _host;
-  const arg = {
-    host: window.testHost || _host,
-    noheader: 1,
-    nobox: true,
-    debug: 1,
-    norecover: true
-  };
-  if (appname == "mass" || appname == "termdb") {
-    defaultArgs.debounceInterval = 0;
-  }
-  if (appname) arg[appname] = defaultArgs;
-  else copyMerge(arg, defaultArgs);
-  const argStr = JSON.stringify(arg);
-  return function runpp(overrides = {}) {
-    const argCopy = JSON.parse(argStr);
-    if (appname) copyMerge(argCopy[appname], overrides);
-    else copyMerge(argCopy, overrides);
-    if (appname && defaultArgs.fetchOpts) {
-      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
-    }
-    return runproteinpaint(Object.assign(argCopy, { serverData }));
-  };
-}
-function copyMerge(base, ...args) {
-  const target = typeof base == "string" ? JSON.parse(base) : base;
-  for (const arg of args) {
-    if (arg) {
-      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
-      for (const key in source) {
-        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
-        else copyMerge(target[key], source[key]);
-      }
-    }
-  }
-  return target;
-}
-
-export {
-  getRunPp
-};
-//# sourceMappingURL=chunk-ZENZ5H2Q.js.map

package/dist/cohort-Q7TW5XTY.js

@@ -1,70 +0,0 @@
-import {
-  appInit,
-  vocabInit
-} from "./chunk-PC4MFDHP.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-HPAW7XDM.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-BZN2O76M.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-52QHIKH2.js";
-import "./chunk-A2ORIMUJ.js";
-import "./chunk-PPSWNLMG.js";
-import {
-  TermTypes
-} from "./chunk-RUBZCKIX.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// termdb/handlers/cohort.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const cohorts = this.app.vocabApi.app?.opts?.opts?.cohorts0;
-    if (!cohorts?.length) return;
-    const terms = cohorts.map((cohort) => {
-      const term = {
-        id: cohort.id,
-        name: cohort.name,
-        type: TermTypes.COHORT,
-        filter0: cohort.filter,
-        isleaf: true,
-        parent_id: null
-      };
-      return term;
-    });
-    const vocabApi = vocabInit({ vocab: { terms } });
-    appInit({
-      holder,
-      vocabApi,
-      state: {
-        nav: { header_mode: "hide_search" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback(term);
-        }
-      }
-    });
-  }
-};
-export {
-  SearchHandler
-};
-//# sourceMappingURL=cohort-Q7TW5XTY.js.map