@sjcrh/proteinpaint-client 2.224.2 → 2.225.0

package/dist/chunk-D2YPS46O.js

@@ -1,266 +0,0 @@
-import {
-  DATermTypes,
-  DMRCATE_DEFAULTS,
-  getOthersGroup
-} from "./chunk-ZIMAIUZD.js";
-import {
-  dofetch3
-} from "./chunk-ZUXXBQ7D.js";
-import {
-  DMR_SCAN_ELEMENT_TYPE
-} from "./chunk-R2H22S4J.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.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 {
-  /** TODO: This model is used in both the volcano and gsea.
-   * In the future, create base model in DA and use specific
-   * classes for the volcano and gsea. */
-  constructor(plot, termType) {
-    this.plot = plot;
-    this.app = plot.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 === DATermTypes.GENE_EXPRESSION) {
-      const body = await this.getGERequestBody();
-      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) {
-        response.daRequest = body;
-        this.setGroupSizes(response);
-      }
-      return response;
-    }
-    if (this.termType === DATermTypes.DNA_METHYLATION) {
-      const body = await this.getDMRequestBody();
-      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) {
-        response.daRequest = body;
-        this.setGroupSizes(response);
-      }
-      return response;
-    }
-    if (this.termType === DATermTypes.JUNCTION) {
-      const body = await this.getDSRequestBody();
-      const response = await dofetch3("termdb/diffSplice", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) {
-        response.daRequest = body;
-        this.setGroupSizes(response);
-      }
-      return response;
-    }
-    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
-      const body = await this.getSCCTRequestBody();
-      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
-    }
-    if (this.termType === DATermTypes.PROTEOME_DAP) {
-      const body = this.getDapRequestBody();
-      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
-    }
-    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
-    }
-    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
-  }
-  //Gene expression
-  async getGERequestBody() {
-    this.setOthersGroup(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()
-    };
-    const pseudobulk = this.config.tw?.pseudobulk;
-    if (pseudobulk) body.pseudobulk = pseudobulk;
-    this.addConfounderTw(body);
-    return body;
-  }
-  //DNA methylation
-  async getDMRequestBody() {
-    this.setOthersGroup(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,
-      exclude_sex_chr: this.settings.excludeSexChr,
-      /* Omitted rather than sent as 'promoter' when it is the default, so a request
-      from a promoter-only dataset is byte-identical to what this client sent before
-      the element picker existed. The server resolves an absent element_type to
-      'promoter'. This does NOT preserve cache keys -- the key object gained the
-      field server-side, so every pre-existing dm/ entry is orphaned on deploy
-      regardless of what the client sends. */
-      ...this.settings.elementType && this.settings.elementType != "promoter" ? { element_type: this.settings.elementType } : {},
-      // the scan's own knobs; the server ignores them for any other element type
-      ...this.settings.elementType == DMR_SCAN_ELEMENT_TYPE ? {
-        scan: {
-          ...this.settings.scanChromosome ? { chromosome: this.settings.scanChromosome } : {},
-          backgroundCorrection: !!this.settings.backgroundCorrection,
-          minCpgs: this.settings.minCpgs,
-          profileBinBp: this.settings.profileBinBp,
-          // only when changed: an explicit default would orphan every cached scan
-          ...this.settings.lambda != DMRCATE_DEFAULTS.lambda ? { lambda: this.settings.lambda } : {},
-          ...this.settings.C != DMRCATE_DEFAULTS.C ? { C: this.settings.C } : {},
-          ...this.settings.fdrCutoff != DMRCATE_DEFAULTS.fdrCutoff ? { fdrCutoff: this.settings.fdrCutoff } : {}
-        }
-      } : {},
-      volcanoRender: this.getVolcanoRender()
-    };
-    if (this.settings.elementType != DMR_SCAN_ELEMENT_TYPE) this.addConfounderTw(body);
-    return body;
-  }
-  //Splicing
-  async getDSRequestBody() {
-    this.setOthersGroup(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DS",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      method: this.settings.method,
-      /* leafcutter's own cluster filters, applied by the edgeR screen too so both engines
-      rank the same cluster set. Sent already scaled to cohort size by validateDSSettings --
-      as absolute counts they silently loosen as N grows. */
-      minSamplesPerIntron: this.settings.minSamplesPerIntron,
-      minSamplesPerGroup: this.settings.minSamplesPerGroup,
-      minCountsPerCluster: this.settings.minCountsPerCluster,
-      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);
-    const useDeltaBeta = this.termType === DATermTypes.DNA_METHYLATION && this.settings.xAxis == "delta_beta";
-    const render = {
-      significanceThresholds: {
-        pValueCutoff: this.settings.pValue,
-        pValueType: this.settings.pValueType,
-        foldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff
-      },
-      ...useDeltaBeta ? { xField: "delta_beta" } : {},
-      // Tied to the delta-beta axis: the control that sets it is only offered for
-      // methylation, and centering a log2 fold-change axis is a different conversation.
-      ...useDeltaBeta && this.settings.centerDeltaBeta ? { centerX: true } : {},
-      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
-    };
-    if (this.termType === DATermTypes.JUNCTION) {
-      render.xField = "delta_psi";
-      render.significanceThresholds.foldChangeCutoff = this.settings.deltaPsiCutoff;
-    }
-    return render;
-  }
-  //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()
-    };
-  }
-  /** The "others" group arrives as a placeholder with {in: false}. Replace it with the group that
-   * it stands for: the filter of the app without the samples of the other group, which the server
-   * resolves. */
-  setOthersGroup(samplelst) {
-    const i = samplelst.groups.findIndex((g) => !g.in);
-    if (i == -1) return;
-    const samplesGroup = samplelst.groups.find((g) => g.in);
-    samplelst.groups[i] = getOthersGroup(
-      { name: samplelst.groups[i].name, values: samplesGroup.values },
-      this.app.getState().termfilter
-    );
-  }
-  /** A group that the server resolved from a filter lists no sample here. Keep the number of its
-   * samples that the analysis ran on, where the group does not carry one, for getSampleNum(). */
-  setGroupSizes(response) {
-    for (const [i, g] of this.config.samplelst.groups.entries()) {
-      const n = response[`sample_size${i + 1}`];
-      if (!Array.isArray(g.values) && g.sampleCount === void 0 && Number.isFinite(n)) g.sampleCount = n;
-    }
-  }
-};
-
-export {
-  getGroupColors,
-  VolcanoModel
-};
-//# sourceMappingURL=chunk-D2YPS46O.js.map

package/dist/chunk-D2YPS46O.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/volcano/colors.ts", "../plots/volcano/model/VolcanoModel.ts"],
-  "sourcesContent": ["import { rgb } from 'd3-color'\n\n/** Resolve the case/control dot colors for a volcano plot in one place so the\n * interactive SVG overlay (VolcanoViewModel) and the server-rendered PNG\n * (VolcanoModel \u2192 Rust) paint each dot the same color.\n *\n * `caseColor` maps to points with `fold_change > 0` (group 2 in samplelst),\n * `controlColor` to `fold_change < 0` (group 1). Every returned color is a\n * `#rrggbb` hex string \u2014 CSS names like `'red'` are normalized via d3-color\n * so the Rust renderer's hex-only parser doesn't fall back to a muted tuple.\n */\nexport function getGroupColors(config: any): { caseColor: string; controlColor: string } {\n\tconst groups = config?.samplelst?.groups\n\tconst termValues = config?.tw?.term?.values\n\tconst rawDown = termValues?.[groups?.[0]?.name]?.color || 'red'\n\tconst rawUp = termValues?.[groups?.[1]?.name]?.color || 'blue'\n\treturn {\n\t\tcontrolColor: toHex(rawDown, 'red'),\n\t\tcaseColor: toHex(rawUp, 'blue')\n\t}\n}\n\n/** Normalize any CSS-accepted color string into `#rrggbb`. */\nexport function toHex(color: string | undefined, fallback: string): string {\n\tconst c = rgb(color || fallback)\n\treturn c.displayable() ? c.formatHex() : rgb(fallback).formatHex()\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { dofetch3 } from '#common/dofetch'\nimport type { DERequest, DiffMethRequest, TermdbSingleCellDEgenesRequest, VolcanoRenderRequest } from '#types'\nimport type { DiffSpliceRequest } from '#types'\nimport { DATermTypes as tt } from '../../diffAnalysis/enabledTermTypes'\nimport { DMR_SCAN_ELEMENT_TYPE } from '#types'\nimport { getGroupColors, toHex } from '../colors'\nimport { DMRCATE_DEFAULTS } from '../settings/defaults'\nimport { getOthersGroup } from '#mass/groups'\n// import type { Volcano } from '../Volcano'\n\nexport class VolcanoModel {\n\tplot: any\n\tapp: MassAppApi\n\tconfig!: any\n\tsettings!: any\n\ttermType: string\n\n\t/** TODO: This model is used in both the volcano and gsea.\n\t * In the future, create base model in DA and use specific\n\t * classes for the volcano and gsea. */\n\tconstructor(plot: any, termType: string) {\n\t\tthis.plot = plot\n\t\tthis.app = plot.app\n\t\tthis.termType = termType\n\t}\n\n\t/** May use mapper instead as more termTypes are added */\n\tasync getData(config: any, settings: any) {\n\t\tthis.config = config\n\t\tthis.settings = settings\n\n\t\tif (this.termType === tt.GENE_EXPRESSION) {\n\t\t\tconst body = await this.getGERequestBody()\n\t\t\tconst response = await dofetch3('termdb/DE', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DE request so downstream plots (GSEA) can snapshot\n\t\t\t// it and later ask the server to recompute the DA cache if the\n\t\t\t// file is missing on a peer node or after TTL eviction.\n\t\t\tif (response && !response.error) {\n\t\t\t\tresponse.daRequest = body\n\t\t\t\tthis.setGroupSizes(response)\n\t\t\t}\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.DNA_METHYLATION) {\n\t\t\tconst body = await this.getDMRequestBody()\n\t\t\tconst response = await dofetch3('termdb/diffMeth', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DM request the same way the GE branch above does so\n\t\t\t// the GSEA tab can snapshot it and the server can recompute the DM\n\t\t\t// cache if the file is missing on a peer node or after TTL.\n\t\t\tif (response && !response.error) {\n\t\t\t\tresponse.daRequest = body\n\t\t\t\tthis.setGroupSizes(response)\n\t\t\t}\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.JUNCTION) {\n\t\t\tconst body = await this.getDSRequestBody()\n\t\t\tconst response = await dofetch3('termdb/diffSplice', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\tif (response && !response.error) {\n\t\t\t\tresponse.daRequest = body\n\t\t\t\tthis.setGroupSizes(response)\n\t\t\t}\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_CELLTYPE) {\n\t\t\tconst body = await this.getSCCTRequestBody()\n\t\t\treturn await dofetch3('termdb/singlecellDEgenes', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.PROTEOME_DAP) {\n\t\t\tconst body = this.getDapRequestBody()\n\t\t\treturn await dofetch3('termdb/dapVolcano', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_GENE_EXPRESSION) {\n\t\t\t//TODO\n\t\t}\n\t\tthrow new Error(`Volcano plot does not support route for termType='${this.termType}'`)\n\t}\n\n\t//Gene expression\n\tasync getGERequestBody() {\n\t\tthis.setOthersGroup(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DE',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tmethod: this.settings.method,\n\t\t\tmin_count: this.settings.minCount,\n\t\t\tmin_total_count: this.settings.minTotalCount,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tcpm_cutoff: this.settings.cpmCutoff,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DERequest> //remove Partial when storage_type is removed from DERequest\n\t\tconst pseudobulk = this.config.tw?.pseudobulk\n\t\tif (pseudobulk) body.pseudobulk = pseudobulk\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//DNA methylation\n\tasync getDMRequestBody() {\n\t\tthis.setOthersGroup(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DM',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmin_samples_per_group: this.settings.minSamplesPerGroup,\n\t\t\texclude_sex_chr: this.settings.excludeSexChr,\n\t\t\t/* Omitted rather than sent as 'promoter' when it is the default, so a request\n\t\t\tfrom a promoter-only dataset is byte-identical to what this client sent before\n\t\t\tthe element picker existed. The server resolves an absent element_type to\n\t\t\t'promoter'. This does NOT preserve cache keys -- the key object gained the\n\t\t\tfield server-side, so every pre-existing dm/ entry is orphaned on deploy\n\t\t\tregardless of what the client sends. */\n\t\t\t...(this.settings.elementType && this.settings.elementType != 'promoter'\n\t\t\t\t? { element_type: this.settings.elementType }\n\t\t\t\t: {}),\n\t\t\t// the scan's own knobs; the server ignores them for any other element type\n\t\t\t...(this.settings.elementType == DMR_SCAN_ELEMENT_TYPE\n\t\t\t\t? {\n\t\t\t\t\t\tscan: {\n\t\t\t\t\t\t\t...(this.settings.scanChromosome ? { chromosome: this.settings.scanChromosome } : {}),\n\t\t\t\t\t\t\tbackgroundCorrection: !!this.settings.backgroundCorrection,\n\t\t\t\t\t\t\tminCpgs: this.settings.minCpgs,\n\t\t\t\t\t\t\tprofileBinBp: this.settings.profileBinBp,\n\t\t\t\t\t\t\t// only when changed: an explicit default would orphan every cached scan\n\t\t\t\t\t\t\t...(this.settings.lambda != DMRCATE_DEFAULTS.lambda ? { lambda: this.settings.lambda } : {}),\n\t\t\t\t\t\t\t...(this.settings.C != DMRCATE_DEFAULTS.C ? { C: this.settings.C } : {}),\n\t\t\t\t\t\t\t...(this.settings.fdrCutoff != DMRCATE_DEFAULTS.fdrCutoff ? { fdrCutoff: this.settings.fdrCutoff } : {})\n\t\t\t\t\t\t}\n\t\t\t\t  }\n\t\t\t\t: {}),\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DiffMethRequest>\n\n\t\t/* The scan fits no covariates and the server rejects a scan request carrying them. Confounders\n\t\tchosen under an element class stay in the config when the class switches to the scan, so they\n\t\tare left off here rather than failing every scan until the user finds and clears them. */\n\t\tif (this.settings.elementType != DMR_SCAN_ELEMENT_TYPE) this.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//Splicing\n\tasync getDSRequestBody() {\n\t\tthis.setOthersGroup(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DS',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmethod: this.settings.method,\n\t\t\t/* leafcutter's own cluster filters, applied by the edgeR screen too so both engines\n\t\t\trank the same cluster set. Sent already scaled to cohort size by validateDSSettings --\n\t\t\tas absolute counts they silently loosen as N grows. */\n\t\t\tminSamplesPerIntron: this.settings.minSamplesPerIntron,\n\t\t\tminSamplesPerGroup: this.settings.minSamplesPerGroup,\n\t\t\tminCountsPerCluster: this.settings.minCountsPerCluster,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DiffSpliceRequest>\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t/** Parameters telling the server to run the `volcano` Rust renderer and return a\n\t * volcano PNG + top-significant rows instead of the full dot list. */\n\tgetVolcanoRender(): VolcanoRenderRequest {\n\t\t// Match the client overlay's radius (see VolcanoViewModel.setPointData)\n\t\t// so the PNG rings and the interactive overlay rings line up; otherwise\n\t\t// a smaller PNG ring sits inside the larger overlay ring and looks like\n\t\t// a stray dot at the center.\n\t\tconst dotRadius = Math.max(this.settings.width, this.settings.height) / 80\n\t\t// Resolve case/control colors via the shared helper (see colors.ts) so the\n\t\t// PNG and the SVG overlay paint each side with the exact same hex string.\n\t\tconst { caseColor, controlColor } = getGroupColors(this.config)\n\t\t/* Only differential methylation carries delta_beta, and only it offers the axis toggle, so\n\t\tother term types always fall through to fold_change. 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The server reports the plot extent in CSS-space,\n\t\t\t// so SVG overlay coords are unaffected.\n\t\t\t//\n\t\t\t// Oversample by 2\u00D7 so the PNG also stays sharp when the user\n\t\t\t// *zooms in after* the initial render (the captured DPR is frozen\n\t\t\t// at fetch time \u2014 bigger headroom = more tolerable post-render\n\t\t\t// zoom before pixelation appears). 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Replace it with the group that\n\t * it stands for: the filter of the app without the samples of the other group, which the server\n\t * resolves. */\n\tsetOthersGroup(samplelst) {\n\t\tconst i = samplelst.groups.findIndex(g => !g.in)\n\t\tif (i == -1) return\n\t\tconst samplesGroup = samplelst.groups.find(g => g.in)\n\t\tsamplelst.groups[i] = getOthersGroup(\n\t\t\t{ name: samplelst.groups[i].name, values: samplesGroup.values },\n\t\t\tthis.app.getState().termfilter\n\t\t)\n\t}\n\n\t/** A group that the server resolved from a filter lists no sample here. Keep the number of its\n\t * samples that the analysis ran on, where the group does not carry one, for getSampleNum(). */\n\tsetGroupSizes(response) {\n\t\tfor (const [i, g] of this.config.samplelst.groups.entries()) {\n\t\t\tconst n = response[`sample_size${i + 1}`]\n\t\t\tif (!Array.isArray(g.values) && g.sampleCount === undefined && Number.isFinite(n)) g.sampleCount = n\n\t\t}\n\t}\n}\n"],
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package/dist/chunk-DVSTBGZT.js

@@ -1,182 +0,0 @@
-import {
-  Tabs,
-  addGeneSearchbox,
-  make_one_checkbox,
-  make_radios
-} from "./chunk-ZIMAIUZD.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  termType2label
-} from "./chunk-5FD6NRGE.js";
-import {
-  TermTypeGroups
-} from "./chunk-R2H22S4J.js";
-
-// termdb/handlers/pseudobulk.ts
-var SearchHandler = class {
-  async init(opts) {
-    const pseudobulkTerms = this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    this.genome = opts.genomeObj;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    this.multiSelect = opts?.usecase?.target == "aggregateMatrix";
-    this.selectedTerm = void 0;
-    this.map = this.buildRenderingDataMap(pseudobulkTerms);
-    this.renderPseudobulkSearch(holder);
-  }
-  validateOpts(opts) {
-    if (!opts) throw new Error("opts is required");
-    if (!opts.app) throw new Error("opts.app is required");
-    if (!opts.holder) throw new Error("opts.holder is required");
-    if (opts.genomeObj == null || typeof opts.genomeObj !== "object") throw new Error("genomeObj is required");
-    if (!opts.callback) throw new Error("opts.callback is required");
-    const pseudobulkTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.PSEUDOBULK];
-    if (!pseudobulkTerms?.length) {
-      throw new Error(
-        `termType2terms[${TermTypeGroups.PSEUDOBULK}]:[] is required in termdbConfig for pseudobulk handler`
-      );
-    }
-    return pseudobulkTerms;
-  }
-  /** Builds a map from assay to memberId to terms */
-  buildRenderingDataMap(pseudobulkTerms) {
-    const map = /* @__PURE__ */ new Map();
-    for (const term of pseudobulkTerms) {
-      const { assay, memberId } = term;
-      if (!map.has(assay)) map.set(assay, /* @__PURE__ */ new Map());
-      const assayMap = map.get(assay);
-      if (!assayMap.has(memberId)) assayMap.set(memberId, []);
-      assayMap.get(memberId).push(term);
-    }
-    return map;
-  }
-  /** If more than one assay, render tabs for each assay. Member IDs within
-   * an assay are rendered as tabs when there is more than one. */
-  renderPseudobulkSearch(holder) {
-    if (!this.map || this.map.size < 1) throw new Error("map is not initialized");
-    if (this.map.size === 1) {
-      const label = termType2label(this.map.keys().next().value);
-      holder.append("div").style("padding-bottom", "10px").text("Single-cell pseudobulk " + label);
-      this.renderMemberIdsByAssay(holder.append("div"), this.map);
-      return;
-    }
-    const tabs = this.buildTabsOpts(this.map);
-    new Tabs({ holder, tabs, tabsPosition: "vertical" }).main();
-  }
-  buildTabsOpts(map) {
-    const tabs = [];
-    for (const [key, valuesMap] of map.entries()) {
-      const label = termType2label(key);
-      tabs.push({
-        label,
-        active: false,
-        callback: (_, tab) => {
-          this.renderMemberIdsByAssay(tab.contentHolder, /* @__PURE__ */ new Map([[key, valuesMap]]));
-        }
-      });
-    }
-    return tabs;
-  }
-  renderMemberIdsByAssay(holder, map) {
-    const memberIdMap = map.values().next().value;
-    holder.selectAll("*").remove();
-    this.renderTermdByMemberId(holder, memberIdMap);
-  }
-  renderTermdByMemberId(holder, memberIdMap) {
-    const layout = holder.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "30px");
-    const pseudoTermsWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-terms-wrapper");
-    const geneSearchWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-gene-search-wrapper");
-    this.renderPseudobulkTerms(pseudoTermsWrapper, memberIdMap, geneSearchWrapper);
-  }
-  renderPseudobulkTerms(holder, memberIdMap, geneSearchHolder) {
-    if (memberIdMap.size === 1) {
-      const [memberId, terms] = memberIdMap.entries().next().value;
-      if (this.multiSelect) {
-        this.renderCategoriesAsTerms(holder, terms);
-      } else this.renderCategoryRadios(holder, memberId, terms, geneSearchHolder);
-      return;
-    }
-    const memberEntries = Array.from(memberIdMap.entries());
-    const tabs = memberEntries.map(([memberId, terms]) => ({
-      label: memberId,
-      active: false,
-      testid: `sjpp-pseudobulk-member-${memberId}`,
-      callback: (_, tab) => {
-        geneSearchHolder.selectAll("*").remove();
-        tab.contentHolder.selectAll("*").remove();
-        if (this.multiSelect) this.renderCategoriesAsTerms(tab.contentHolder, terms);
-        else this.renderCategoryRadios(tab.contentHolder, memberId, terms, geneSearchHolder);
-      }
-    }));
-    new Tabs({ holder, tabs, tabsPosition: "vertical" }).main();
-  }
-  renderCategoryRadios(holder, memberId, terms, geneSearchHolder) {
-    if (!terms || terms.length < 1) throw new Error("No terms found for memberId");
-    const options = terms.map((term) => ({
-      label: term.name,
-      value: term.id,
-      checked: false,
-      testid: `sjpp-pseudobulk-category-${term.id}`
-    }));
-    make_radios({
-      holder,
-      inputName: `sjpp-pseudobulk-category-radios-${memberId}`,
-      options,
-      styles: { display: "block", padding: "3px 5px" },
-      callback: (value) => {
-        const term = terms.find((term2) => term2.id == value);
-        if (!term) throw new Error(`No pseudobulk term found for category ${value}`);
-        this.selectedTerm = term;
-        this.renderGeneSelection(geneSearchHolder);
-      }
-    });
-  }
-  renderGeneSelection(holder) {
-    holder.selectAll("*").remove();
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: this.genome,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => {
-        if (!geneSearch.geneSymbol) throw new Error("No gene selected");
-        if (!this.selectedTerm) throw new Error("No pseudobulk cell type selected");
-        this.callback(createPseudobulkTerm(this.selectedTerm, geneSearch.geneSymbol));
-      }
-    });
-  }
-  /** Mimics the style and functionality of pills created in tree.js.
-   * Returns the term object(s) from termdbConfig.termType2terms.[TermTypeGroups.PSEUDOBULK]
-   * without the gene. */
-  renderCategoriesAsTerms(holder, terms) {
-    holder.style("padding", "0px 10px");
-    make_one_checkbox({
-      holder,
-      labeltext: "Select all",
-      divstyle: { opacity: "0.7" },
-      callback: () => this.callback(terms)
-    });
-    const wrapper = holder.append("div").style("display", "block").style("padding", "10px 15px 0px");
-    wrapper.selectAll(".pseudobulk-term").data(terms, (term) => term.id).join((enter) => {
-      const row = enter.append("div").attr("class", "pseudobulk-term");
-      row.append("div").attr("class", "termlabel sja_filter_tag_btn sja_tree_click_term ts_pill").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text((term) => term.name).on("click", async (_, term) => {
-        await this.callback(term);
-      });
-      return row;
-    });
-  }
-};
-function createPseudobulkTerm(selectedTerm, gene) {
-  const category = selectedTerm.category || selectedTerm.id;
-  const name = `${selectedTerm.assay} ${category} ${gene}`;
-  return { ...selectedTerm, id: name, category, gene, name };
-}
-
-export {
-  SearchHandler,
-  createPseudobulkTerm
-};
-//# sourceMappingURL=chunk-DVSTBGZT.js.map

package/dist/chunk-EIO6DMIQ.js

@@ -1,31 +0,0 @@
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-R2H22S4J.js";
-
-// src/spliceevent.exonskip.getdefault.js
-function spliceevent_exonskip_getdefault_default(events) {
-  let evt2showidx = 0;
-  for (let i = 1; i < events.length; i++) {
-    const e = events[i];
-    const e2show = events[evt2showidx];
-    if (e.isskipexon && e2show.isaltexon) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == OUT_frame && e2show.framenocheck) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == IN_frame && e2show.frame != IN_frame) {
-      evt2showidx = i;
-      continue;
-    }
-  }
-  return evt2showidx;
-}
-
-export {
-  spliceevent_exonskip_getdefault_default
-};
-//# sourceMappingURL=chunk-EIO6DMIQ.js.map