@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/DM-W7PXTIKY.js

@@ -1,90 +0,0 @@
-import {
-  appInit
-} from "./chunk-XRMUUWLS.js";
-import "./chunk-TXIQ5PHR.js";
-import "./chunk-WXX2YD4Q.js";
-import "./chunk-72P6O537.js";
-import "./chunk-MSSPT5YM.js";
-import "./chunk-KAY2ODXX.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-HKSRIEWJ.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.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";
-
-// gdc/DM.ts
-async function init(arg, holder, genomes) {
-  const useGenome = arg.genome || "hg38";
-  const useDslabel = arg.dslabel || "GDC";
-  const genome = genomes[useGenome];
-  const massApi = await appInit({
-    genome,
-    holder,
-    state: {
-      genome: useGenome,
-      dslabel: useDslabel,
-      termfilter: { filter0: arg.filter0 },
-      nav: { activeTab: 1, header_mode: "hidden" },
-      // an embedder may supply prebuilt groups, see config.groups[] in plots/DEinput.ts.
-      // DEinput is the group-building submission ui, shared with DE and switched by termType;
-      // it launches the 'differentialAnalysis' results chart once groups are submitted
-      plots: arg.state?.plots || [{ chartType: "DEinput", termType: "dnaMethylation" }]
-    },
-    opts: Object.assign(
-      {
-        // todo additional customizations
-        // dictionary:{header:'Select a variable to build Correlation Plot'}
-        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
-      },
-      arg.opts || {}
-    ),
-    app: arg.opts?.app || {}
-  });
-  const api = {
-    update: async (updateArg) => {
-      if (!massApi) return;
-      if ("filter0" in updateArg) {
-        massApi.dispatch({
-          type: "app_refresh",
-          subactions: [
-            {
-              type: "filter_replace",
-              filter0: updateArg.filter0
-            }
-          ]
-        });
-      }
-    },
-    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
-  };
-  return api;
-}
-export {
-  init
-};
-//# sourceMappingURL=DM-W7PXTIKY.js.map

package/dist/DifferentialAnalysis-SHMQHWJL.js

@@ -1,236 +0,0 @@
-import {
-  getDefaultGseaSettings
-} from "./chunk-KTKZSYIH.js";
-import {
-  DATermTypes,
-  PlotBase,
-  Tabs,
-  enabledTermTypes,
-  formatHeaderText,
-  getDefaultVolcanoSettings,
-  validateVolcanoSettings
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import {
-  importPlot
-} from "./chunk-DMWOK4DS.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import {
-  termType2label
-} from "./chunk-GMRIEUBW.js";
-import {
-  PROTEOME_DAP
-} from "./chunk-4EZLVENZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./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";
-
-// plots/diffAnalysis/view/DiffAnalysisView.ts
-var DiffAnalysisView = class {
-  constructor(app, config, dom) {
-    this.app = app;
-    this.config = config;
-    this.dom = dom;
-    setRenderers(this);
-    this.tabsData = this.getTabsOptions(this);
-    this.tabs = new Tabs({ holder: this.dom.tabsDiv, tabs: this.tabsData });
-    this.tabs.main();
-  }
-  update(plotConfig) {
-    const activeTabIndex = this.tabsData.findIndex((tab) => tab.id == plotConfig.childType);
-    this.tabs.update(activeTabIndex);
-  }
-};
-function setRenderers(self) {
-  self.getTabsOptions = (self2) => {
-    const tabs = [
-      {
-        active: self2.config.childType === "volcano",
-        id: "volcano",
-        label: "Volcano",
-        isVisible: () => true,
-        // isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,
-        getPlotConfig: () => {
-          return {
-            childType: "volcano"
-          };
-        },
-        callback: self2.tabCallback
-      },
-      {
-        active: self2.config.childType === "gsea",
-        id: "gsea",
-        label: "Gene Set Enrichment Analysis",
-        isVisible: () => self2.config.termType !== PROTEOME_DAP,
-        // isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,
-        getPlotConfig: () => {
-          return {
-            childType: "gsea"
-          };
-        },
-        callback: self2.tabCallback
-      }
-    ];
-    return tabs;
-  };
-  self.tabCallback = async (event, tab) => {
-    if (!event || !tab || !tab.id) return;
-    const plotConfig = tab.getPlotConfig();
-    await self.app.dispatch({
-      type: "plot_edit",
-      id: self.config.id,
-      config: plotConfig
-    });
-  };
-}
-
-// plots/diffAnalysis/DifferentialAnalysis.ts
-var { SINGLECELL_CELLTYPE } = DATermTypes;
-var DifferentialAnalysis = class _DifferentialAnalysis extends PlotBase {
-  static {
-    this.type = "differentialAnalysis";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _DifferentialAnalysis.type;
-    this.components = {
-      plots: {}
-    };
-    this.termType = opts.termType;
-    const holder = opts.holder.classed("sjpp-diff-analysis-main", true);
-    const controls = opts.controls ? holder : holder.append("div");
-    const div = holder.append("div").style("padding", "5px").style("display", "inline-block").style("vertical-align", "top");
-    const tabsDiv = div.append("div").attr("id", "sjpp-diff-analysis-tabs").style("display", "inline-block");
-    const plots = div.append("div").attr("id", "sjpp-diff-analysis-tabs-content");
-    this.dom = {
-      controls: controls.style("display", "inline-block"),
-      div,
-      tabsDiv,
-      plots,
-      tip: new Menu({ padding: "" })
-    };
-    if (opts.header) this.dom.header = opts.header;
-    this.plotsControlsDiv = {};
-    this.plotsDiv = {};
-    if (opts.parentId) this.parentId = opts.parentId;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw new Error(
-        `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
-      );
-    }
-    return {
-      config
-    };
-  }
-  reactsTo(action) {
-    if (action.type.startsWith("plot_")) {
-      return action.id === this.id || action.id == this.parentId;
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.plotTabs = new DiffAnalysisView(this.app, config, this.dom);
-    if (this.dom.header) {
-      const text = config?.headerText || (config.tw?.term?.name ?? "");
-      const typeStr = termType2label(config.termType).toUpperCase();
-      formatHeaderText({
-        header: this.dom.header,
-        chartType: `DIFFERENTIAL ${typeStr} ANALYSIS`,
-        text
-      });
-    }
-  }
-  async setComponent(config) {
-    this.plotsControlsDiv[config.childType] = this.dom.controls.append("div");
-    this.plotsDiv[config.childType] = this.dom.plots.append("div");
-    const opts = {
-      app: this.app,
-      holder: this.plotsDiv[config.childType],
-      id: this.id,
-      parent: this.api,
-      controls: this.plotsControlsDiv[config.childType],
-      termType: config.termType
-    };
-    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
-    this.components.plots[config.childType] = await _.componentInit(opts);
-  }
-  async main() {
-    const config = structuredClone(this.state.config);
-    if (config.chartType != this.type) return;
-    if (!this.components.plots[config.childType]) await this.setComponent(config);
-    for (const childType in this.components.plots) {
-      const chart = this.components.plots[childType];
-      if (chart.type != config.childType) {
-        this.plotsDiv[chart.type].style("display", "none");
-        this.plotsControlsDiv[chart.type].style("display", "none");
-      }
-    }
-    this.plotsDiv[config.childType].style("display", "");
-    this.plotsControlsDiv[config.childType].style("display", "");
-    if (this.plotTabs) this.plotTabs.update(config);
-  }
-};
-var DiffAnalysisInit = getCompInit(DifferentialAnalysis);
-var componentInit = DiffAnalysisInit;
-function getPlotConfig(opts, app) {
-  if (!opts.termType) throw new Error(".termType is required");
-  if (!enabledTermTypes.has(opts.termType))
-    throw new Error(`termType = '${opts.termType}' not supported by Differential Analysis`);
-  const config = {
-    chartType: "differentialAnalysis",
-    childType: "volcano",
-    termType: opts.termType,
-    settings: {},
-    highlightedData: opts.highlightedData || [],
-    hidePlotFilter: true
-    //TODO: Support filtering and reactivity in child plots
-  };
-  if (opts?.tw?.term?.name && opts.headerText)
-    throw new Error("Cannot provide both tw.term.name and headerText. Please choose one to use as the plot title.");
-  if (opts.termType == SINGLECELL_CELLTYPE) {
-    Object.assign(config, {
-      categoryName: opts.categoryName || "",
-      termId: opts.termId || "",
-      sample: opts.sample || { sID: "", eID: "" }
-    });
-  }
-  config.settings.volcano = getDefaultVolcanoSettings(opts.overrides, { ...opts, app: opts.app || app });
-  config.settings.gsea = getDefaultGseaSettings(opts.overrides, opts);
-  validateVolcanoSettings(config, opts);
-  return copyMerge(config, opts);
-}
-export {
-  DiffAnalysisInit,
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=DifferentialAnalysis-SHMQHWJL.js.map

package/dist/DifferentialAnalysis-SHMQHWJL.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/diffAnalysis/view/DiffAnalysisView.ts", "../plots/diffAnalysis/DifferentialAnalysis.ts"],
-  "sourcesContent": ["import type { MassAppApi } from '#mass/types/mass'\nimport { Tabs, type RenderedTab } from '#dom'\nimport type { DiffAnalysisDom, DiffAnalysisPlotConfig } from '../DiffAnalysisTypes'\nimport { PROTEOME_DAP } from '#types'\n\nexport class DiffAnalysisView {\n\tapp: MassAppApi\n\tconfig: DiffAnalysisPlotConfig\n\tdom: DiffAnalysisDom\n\ttabs: Tabs\n\ttabsData: RenderedTab[]\n\tgetTabsOptions: any\n\tconstructor(app: MassAppApi, config: DiffAnalysisPlotConfig, dom: DiffAnalysisDom) {\n\t\tthis.app = app\n\t\tthis.config = config\n\t\tthis.dom = dom\n\t\tsetRenderers(this)\n\t\tthis.tabsData = this.getTabsOptions(this)\n\t\tthis.tabs = new Tabs({ holder: this.dom.tabsDiv, tabs: this.tabsData })\n\t\tthis.tabs.main()\n\t}\n\n\tupdate(plotConfig) {\n\t\tconst activeTabIndex = this.tabsData.findIndex(tab => tab.id == plotConfig.childType)\n\t\tthis.tabs.update(activeTabIndex)\n\t}\n}\n\nfunction setRenderers(self) {\n\tself.getTabsOptions = self => {\n\t\tconst tabs = [\n\t\t\t{\n\t\t\t\tactive: self.config.childType === 'volcano',\n\t\t\t\tid: 'volcano',\n\t\t\t\tlabel: 'Volcano',\n\t\t\t\tisVisible: () => true,\n\t\t\t\t// isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchildType: 'volcano'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tcallback: self.tabCallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tactive: self.config.childType === 'gsea',\n\t\t\t\tid: 'gsea',\n\t\t\t\tlabel: 'Gene Set Enrichment Analysis',\n\t\t\t\tisVisible: () => self.config.termType !== PROTEOME_DAP,\n\t\t\t\t// isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchildType: 'gsea'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tcallback: self.tabCallback\n\t\t\t}\n\t\t]\n\t\treturn tabs\n\t}\n\n\tself.tabCallback = async (event, tab) => {\n\t\t/** When loading a mass session file, the callback for the\n\t\t * tab will trigger before the plot component is initialized.\n\t\t * check for the event before triggering an app.dispatch.*/\n\t\tif (!event || !tab || !tab.id) return\n\t\tconst plotConfig = tab.getPlotConfig()\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.config.id,\n\t\t\tconfig: plotConfig\n\t\t})\n\t}\n}\n", "import type { BasePlotConfig, MassState } from '#mass/types/mass'\nimport type { Div } from '../../types/d3'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '../PlotBase'\nimport { importPlot } from '../importPlot.js'\nimport { Menu, formatHeaderText } from '#dom'\nimport { termType2label } from '#shared/terms.js'\nimport type { DiffAnalysisDom, /*DiffAnalysisOpts,*/ DiffAnalysisPlotConfig } from './DiffAnalysisTypes'\nimport { DiffAnalysisView } from './view/DiffAnalysisView'\nimport { getDefaultVolcanoSettings, validateVolcanoSettings } from '../volcano/settings/defaults.ts'\nimport { getDefaultGseaSettings } from '#plots/gsea/settings/defaults.ts'\nimport { DATermTypes, enabledTermTypes } from './enabledTermTypes'\n\nconst { SINGLECELL_CELLTYPE } = DATermTypes\n\nclass DifferentialAnalysis extends PlotBase implements RxComponent {\n\tstatic type = 'differentialAnalysis'\n\n\ttype: string\n\tcomponents: {\n\t\tplots: { [key: string]: any }\n\t}\n\tdom: DiffAnalysisDom\n\tparentId?: string\n\tplotTabs?: DiffAnalysisView\n\tplotsDiv: { [key: string]: Div }\n\tplotsControlsDiv: { [key: string]: Div }\n\ttermType: string\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = DifferentialAnalysis.type\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t\tthis.termType = opts.termType\n\t\tconst holder = opts.holder.classed('sjpp-diff-analysis-main', true)\n\t\tconst controls = opts.controls ? holder : holder.append('div')\n\t\tconst div = holder\n\t\t\t.append('div')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\tconst tabsDiv = div.append('div').attr('id', 'sjpp-diff-analysis-tabs').style('display', 'inline-block')\n\t\tconst plots = div.append('div').attr('id', 'sjpp-diff-analysis-tabs-content')\n\t\tthis.dom = {\n\t\t\tcontrols: controls.style('display', 'inline-block'),\n\t\t\tdiv,\n\t\t\ttabsDiv,\n\t\t\tplots: plots,\n\t\t\ttip: new Menu({ padding: '' })\n\t\t}\n\t\tif (opts.header) this.dom.header = opts.header\n\t\tthis.plotsControlsDiv = {}\n\t\tthis.plotsDiv = {}\n\n\t\tif (opts.parentId) this.parentId = opts.parentId\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn action.id === this.id || action.id == this.parentId\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t}\n\n\tasync init(appState: MassState) {\n\t\tconst state = this.getState(appState)\n\t\tconst config = structuredClone(state.config) as DiffAnalysisPlotConfig\n\n\t\tthis.plotTabs = new DiffAnalysisView(this.app, config, this.dom)\n\n\t\tif (this.dom.header) {\n\t\t\tconst text = config?.headerText || (config.tw?.term?.name ?? '')\n\t\t\tconst typeStr = termType2label(config.termType).toUpperCase()\n\t\t\tformatHeaderText({\n\t\t\t\theader: this.dom.header,\n\t\t\t\tchartType: `DIFFERENTIAL ${typeStr} ANALYSIS`,\n\t\t\t\ttext\n\t\t\t})\n\t\t}\n\t}\n\n\tasync setComponent(config: DiffAnalysisPlotConfig) {\n\t\tthis.plotsControlsDiv[config.childType] = this.dom.controls.append('div')\n\t\tthis.plotsDiv[config.childType] = this.dom.plots.append('div')\n\t\tconst opts = {\n\t\t\tapp: this.app,\n\t\t\tholder: this.plotsDiv[config.childType],\n\t\t\tid: this.id,\n\t\t\tparent: this.api,\n\t\t\tcontrols: this.plotsControlsDiv[config.childType],\n\t\t\ttermType: config.termType\n\t\t}\n\t\tconst _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`)\n\t\tthis.components.plots[config.childType] = await _.componentInit(opts)\n\t}\n\n\tasync main() {\n\t\tconst config = structuredClone(this.state.config)\n\t\tif (config.chartType != this.type) return\n\n\t\t//TODO: Change to use parentId instead\n\t\tif (!this.components.plots[config.childType]) await this.setComponent(config)\n\n\t\tfor (const childType in this.components.plots) {\n\t\t\tconst chart = this.components.plots[childType]\n\t\t\tif (chart.type != config.childType) {\n\t\t\t\tthis.plotsDiv[chart.type].style('display', 'none')\n\t\t\t\tthis.plotsControlsDiv[chart.type].style('display', 'none')\n\t\t\t}\n\t\t}\n\t\tthis.plotsDiv[config.childType].style('display', '')\n\t\tthis.plotsControlsDiv[config.childType].style('display', '')\n\n\t\tif (this.plotTabs) this.plotTabs.update(config)\n\t}\n}\n\nexport const DiffAnalysisInit = getCompInit(DifferentialAnalysis)\nexport const componentInit = DiffAnalysisInit\n\n/* `app` is supplied by the mass store (store.ts calls getPlotConfig(savedPlot, app, activeCohort))\nand is threaded into the volcano defaults below, which read the dataset's preferred starting\nelement class off termdbConfig. Without it that lookup silently returns undefined and every\ndataset falls back to the legacy 'promoter' matrix. */\nexport function getPlotConfig(opts: any, app?: any) {\n\tif (!opts.termType) throw new Error('.termType is required')\n\tif (!enabledTermTypes.has(opts.termType))\n\t\tthrow new Error(`termType = '${opts.termType}' not supported by Differential Analysis`)\n\n\tconst config = {\n\t\tchartType: 'differentialAnalysis',\n\t\tchildType: 'volcano',\n\t\ttermType: opts.termType,\n\t\tsettings: {},\n\t\thighlightedData: opts.highlightedData || [],\n\t\thidePlotFilter: true //TODO: Support filtering and reactivity in child plots\n\t} as any\n\n\tif (opts?.tw?.term?.name && opts.headerText)\n\t\tthrow new Error('Cannot provide both tw.term.name and headerText. Please choose one to use as the plot title.')\n\n\t/** TODO: Fix this config. This only applies to the\n\t * gdc and won't work long term for terms */\n\tif (opts.termType == SINGLECELL_CELLTYPE) {\n\t\tObject.assign(config, {\n\t\t\tcategoryName: opts.categoryName || '',\n\t\t\ttermId: opts.termId || '',\n\t\t\tsample: opts.sample || { sID: '', eID: '' }\n\t\t})\n\t}\n\n\tconfig.settings.volcano = getDefaultVolcanoSettings(opts.overrides, { ...opts, app: opts.app || app })\n\tconfig.settings.gsea = getDefaultGseaSettings(opts.overrides, opts)\n\n\tvalidateVolcanoSettings(config, opts)\n\n\treturn copyMerge(config, opts)\n}\n"],
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