@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/Disco.UI-UDUXNCZX.js

@@ -1,239 +0,0 @@
-import {
-  launch
-} from "./chunk-EARMOT6Q.js";
-import {
-  makeBtn,
-  makeFileUpload,
-  makeGenomeDropDown,
-  makePrompt,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-5EBRF6Z7.js";
-import "./chunk-4WFXCUT4.js";
-import "./chunk-W2SBSEKT.js";
-import "./chunk-4E2F26CC.js";
-import "./chunk-LMONIWPI.js";
-import {
-  Tabs,
-  appear,
-  sayerror
-} from "./chunk-DPWSIN62.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KZ54E2FU.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-DOC3HBOV.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-6V7ITU5F.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-KUOXZIH4.js";
-import "./chunk-T2W4JHWJ.js";
-import "./chunk-2N345NXD.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/disco/Disco.UI.ts
-function init_discoplotUI(holder, genomes, debugmode) {
-  const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
-    "font-family",
-    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
-  ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true).classed("sjpp-disco-ui", true);
-  const obj = {
-    data: []
-  };
-  makePrompt(wrapper, "Select Genome").style("font-size", "1.15em").style("padding", "10px 0px").style("color", "#003366");
-  genomeSelection(wrapper, genomes, obj);
-  makePrompt(wrapper, "Provide Data").style("font-size", "1.15em").style("padding", "10px 0px 5px 0px").style("color", "#003366");
-  wrapper.append("div").style("opacity", 0.75).style("padding", "10px 10px 15px 20px").style("width", "65vw").style("line-height", "1.5em").html(
-    '<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>'
-  );
-  const dataTypeTabs_div = wrapper.append("div").style("margin-left", "2vw");
-  makeDataTypeTabs(dataTypeTabs_div, obj);
-  const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("padding", "15px 0px");
-  submitButton(controlBtns_div, obj, genomes, wrapper, holder);
-  makeResetBtn(controlBtns_div, obj, ".disco_input");
-  if (debugmode) window["doms"] = obj;
-  return obj;
-}
-function genomeSelection(div, genomes, obj) {
-  const genome_div = div.append("div").style("margin-left", "40px");
-  const g = makeGenomeDropDown(genome_div, genomes).style("border", "1px solid rgb(138, 177, 212)");
-  obj.genome = g.node();
-}
-function makeDataTypeTabs(dataTypeTabs_div, obj) {
-  const tabs = [
-    {
-      label: "SNV Indel",
-      active: true,
-      callback: async (event, dataTypeTab) => {
-        dataTypeTab.key = "snv";
-        const listHTML = `<ol>
-					<li>chr</li>
-					<li>position</li>
-					<li>gene</li>
-					<li>aachange</li>
-					<li>class</li>
-					<li>DNA total reads (optional)</li>
-					<li>DNA alt reads (optional)</li>
-					<li>RNA total reads (optional)</li>
-					<li>RNA alt reads (optional)</li></ol>
-					<p>Example:</p>
-<pre style="margin-left: 10px;">
-chr1	226252135	H3F3A	K28M	M	100	25	80	16
-chr2	98765432	TestGene	TestMutation	F
-</pre>`;
-        mainTabCallback(dataTypeTab, obj, listHTML);
-      }
-    },
-    {
-      label: "SV",
-      active: false,
-      callback: async (event, dataTypeTab) => {
-        dataTypeTab.key = "sv";
-        const listHTML = `<ol>
-					<li>chrA</li>
-					<li>posA</li>
-					<li>geneA (optional)</li>
-					<li>chrB</li>
-					<li>posB</li>
-					<li>geneB (optional)</li>
-				</ol>
-				<p>Example (with genes):</p>
-<pre style="margin-left: 10px;">
-chr6	3067605	MDC1	chr12	61521661	KMT2D
-</pre>
-				<p>Example (without genes):</p>
-<pre style="margin-left: 10px;">
-chr6	3067605	chr12	61521661
-</pre>`;
-        mainTabCallback(dataTypeTab, obj, listHTML);
-      }
-    },
-    {
-      label: "CNV",
-      active: false,
-      callback: async (event, dataTypeTab) => {
-        dataTypeTab.key = "cnv";
-        const listHTML = `<ol>
-				<li>chr</li>
-				<li>start</li>
-				<li>stop</li>
-				<li>value</li>
-				</ol>
-				<p>Example:</p>
-<pre style="margin-left: 10px;">
-chr1	1	100000000	0.5
-chr1	100000000	200000000	-0.5
-</pre>`;
-        mainTabCallback(dataTypeTab, obj, listHTML);
-      }
-    }
-  ];
-  new Tabs({ holder: dataTypeTabs_div, tabs, tabsPosition: "vertical", linePosition: "right" }).main();
-}
-function mainTabCallback(dataTypeTab, obj, listHTML) {
-  dataTypeTab.contentHolder.style("border", "none").style("display", "block").style("padding-left", "30px");
-  makeDataInputTabs(dataTypeTab, obj);
-  dataTypeTab.contentHolder.append("div").style("padding", "15px 0px 0px 10px").style("opacity", 0.75).text(`Provide ${dataTypeTab.label} data in tab delimited format with the following columns:`).append("span").html(listHTML);
-  delete dataTypeTab.callback;
-}
-function makeDataInputTabs(dataTypeTab, obj) {
-  const width = 95;
-  const tabs = [
-    // //TODO: implement file upload and file path input once launch.adhoc is ready
-    {
-      label: "Select File",
-      active: true,
-      width,
-      callback: async (event, tab) => {
-        const key = dataTypeTab.key;
-        tab.contentHolder.style("border", "none").style("display", "block");
-        appear(tab.contentHolder);
-        tab.contentHolder.append("div").style("padding", "0px 0px 5px 15px").style("opacity", 0.65).text(`Select a local file`);
-        makeFileUpload2(tab, obj, key);
-        delete tab.callback;
-      }
-    },
-    // {
-    // 	label: 'File Path',
-    // 	active: false,
-    // 	width,
-    // 	callback: async (tab: Tab) => {
-    // 		const key = dataTypeTab.key
-    // 		tab.contentHolder.style('border', 'none').style('display', 'block')
-    // 		appear(tab.contentHolder)
-    // 		tab.contentHolder
-    // 			.append('div')
-    // 			.html(`<p style="margin-left: 10px; opacity: 0.65;">Provide a URL file path.</p>`)
-    // 		uiutils.makePrompt(tab.contentHolder, 'URL')
-    // 		makeTextEntryFilePathInput(tab.contentHolder, obj, key)
-    // 		delete tab.callback
-    // 	}
-    // },
-    {
-      label: "Paste Data",
-      active: false,
-      width,
-      callback: async (event, tab) => {
-        const key = dataTypeTab.key;
-        tab.contentHolder.style("border", "none").style("display", "block");
-        appear(tab.contentHolder);
-        makeCopyPasteInput(tab, obj, key);
-        delete tab.callback;
-      }
-    }
-  ];
-  new Tabs({ holder: dataTypeTab.contentHolder, tabs }).main();
-}
-function makeFileUpload2(tab, obj, key) {
-  const upload_div = tab.contentHolder.append("div").style("display", "inline-block");
-  const upload = makeFileUpload(upload_div).classed("disco_input", true);
-  upload.on("change", (event) => {
-    const file = event.target.files[0];
-    const reader = new FileReader();
-    reader.onload = (event2) => {
-      obj.data[key + "Text"] = event2.target.result;
-    };
-    reader.readAsText(file, "utf8");
-  });
-}
-function makeCopyPasteInput(tab, obj, key) {
-  const paste_div = tab.contentHolder.append("div").style("display", "block");
-  const paste = makeTextAreaInput({ div: paste_div, cols: 50 }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("disco_input", true).on("keyup", async () => {
-    obj.data[key + "Text"] = paste.property("value").trim();
-  });
-}
-function submitButton(div, obj, genomes, wrapper, holder) {
-  const submit = makeBtn({ div, text: "Create Disco Plot" });
-  const errorMessage_div = div.append("div");
-  submit.style("margin-right", "10px").style("font-size", "16px").classed("sjpp-ui-submitBtn", true).attr("type", "submit").on("click", () => {
-    if (!obj.data || obj.data == void 0) {
-      const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
-      sayerror(sayerrorDiv, "Please provide data");
-      setTimeout(() => sayerrorDiv.remove(), 2e3);
-    } else {
-      const genomeObj = genomes[obj.genome.options[obj.genome.selectedIndex].text];
-      wrapper.remove();
-      launch(obj.data, genomeObj, holder);
-      backButton(holder, genomes);
-    }
-  });
-}
-function backButton(holder, genomes) {
-  holder.append("button").html("&#171; Back").on("click", () => {
-    holder.selectAll("*").remove();
-    init_discoplotUI(holder, genomes, false);
-  });
-}
-export {
-  init_discoplotUI
-};
-//# sourceMappingURL=Disco.UI-UDUXNCZX.js.map

package/dist/DmrPlot-FZCD6FTX.js

@@ -1,366 +0,0 @@
-import {
-  DmrViewModel,
-  getDefaultDMRSettings
-} from "./chunk-XKWLP433.js";
-import {
-  PlotBase,
-  startElapsedTimer,
-  table2col
-} from "./chunk-DPWSIN62.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KZ54E2FU.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-DOC3HBOV.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3,
-  formatElapsedTime
-} from "./chunk-6V7ITU5F.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-KUOXZIH4.js";
-import "./chunk-T2W4JHWJ.js";
-import "./chunk-2N345NXD.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/dmr/model/DmrModel.ts
-var DmrModel = class {
-  constructor(config, vocab) {
-    this.config = config;
-    this.vocab = vocab;
-  }
-  async fetchDmr(chr, start, stop, signal) {
-    const { group1, group2, settings } = this.config;
-    const { genome, dslabel } = this.vocab;
-    return dofetch3("termdb/dmr", {
-      signal,
-      body: {
-        genome,
-        dslabel,
-        chr,
-        start,
-        stop,
-        group1,
-        group2,
-        lambda: settings.dmr.lambda,
-        C: settings.dmr.C,
-        fdr_cutoff: settings.dmr.fdr_cutoff,
-        group1Name: this.config.group1Name,
-        group2Name: this.config.group2Name,
-        blockWidth: settings.dmr.blockWidth,
-        devicePixelRatio: typeof window !== "undefined" ? window.devicePixelRatio : 1,
-        maxLoessRegion: settings.dmr.maxLoessRegion,
-        colors: settings.dmr.colors,
-        scanChromosomes: this.config.scanChromosomes,
-        backgroundCorrection: this.config.backgroundCorrection,
-        minCpgs: this.config.minCpgs,
-        yAxis: this.config.yAxis,
-        filter0: this.config.filter0
-      }
-    });
-  }
-};
-
-// plots/dmr/view/DmrView.ts
-var DmrView = class {
-  constructor(dom) {
-    this.dom = dom;
-  }
-  async renderBlock(viewData, genomeObj, settings, chr, start, stop, onCoordinateChange) {
-    const { Block } = await import("./block-YGQFUK5L.js");
-    return new Block({
-      holder: this.dom.holder,
-      genome: genomeObj,
-      chr,
-      start,
-      stop,
-      tklst: viewData.tklst,
-      nobox: true,
-      width: settings.blockWidth,
-      onCoordinateChange
-    });
-  }
-  updateTracks(viewData, blockInstance) {
-    for (const tk of blockInstance.tklst) {
-      const updated = viewData.tklst.find((t) => t.name === tk.name);
-      if (!updated) continue;
-      if (tk.type === "bedj" && updated.bedItems) {
-        tk.bedItems = updated.bedItems;
-        blockInstance.tk_load(tk);
-      } else if (tk.type === "bigwig" && updated.imgData) {
-        tk.imgData = updated.imgData;
-        blockInstance.tk_load(tk);
-      }
-    }
-  }
-  updateLegend(blockInstance, legendRows) {
-    if (!blockInstance?.legend?.holder) return;
-    const labels = ["Per-CpG Means", "DMR", "Sig. CpGs"];
-    blockInstance.legend.holder.selectAll("tr").filter((_d, i, nodes) => {
-      const td = nodes[i].querySelector("td");
-      return td && labels.includes(td.textContent);
-    }).remove();
-    this.renderLegend(blockInstance, legendRows);
-  }
-  renderLegend(blockInstance, legendRows) {
-    if (!blockInstance?.legend?.holder) return;
-    const { legendcolor, vpad } = blockInstance.legend;
-    for (const row of legendRows) {
-      const tr = blockInstance.legend.holder.append("tr");
-      tr.append("td").text(row.label).attr("style", `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`);
-      const td = tr.append("td");
-      for (const entry of row.items) {
-        const item = td.append("div").attr("style", `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`);
-        if (entry.style === "shaded") {
-          item.append("div").attr(
-            "style",
-            `display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`
-          );
-        } else if (entry.style === "dashed") {
-          item.append("div").attr(
-            "style",
-            `display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`
-          );
-        } else {
-          item.append("div").attr(
-            "style",
-            `display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`
-          );
-        }
-        item.append("div").attr("style", "display:inline-block;color:#555;font-size:.8em").text(entry.text);
-      }
-    }
-  }
-  renderDiagnostics(diagnostic, dmrs, fdr_cutoff) {
-    const panel = this.dom.diagnosticPanel;
-    panel.selectAll("*").remove();
-    panel.style("display", "block");
-    const { probes } = diagnostic;
-    const toggle = panel.append("div").attr("style", "cursor:default;font-size:12px;color:#888;padding:2px 0");
-    const statsContent = panel.append("div").style("display", "none");
-    let expanded = false;
-    toggle.text("+ Diagnostic details").on("click", () => {
-      expanded = !expanded;
-      toggle.text((expanded ? "\u2212 " : "+ ") + "Diagnostic details");
-      statsContent.style("display", expanded ? "block" : "none");
-    });
-    const spacings = diagnostic.probe_spacings;
-    const medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0;
-    const maxGap = spacings.length ? Math.max(...spacings) : 0;
-    const gapsOver1kb = spacings.filter((s) => s > 1e3).length;
-    const density = probes.positions.length > 1 ? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1e3) : 0;
-    const sigFdrCount = probes.sig.filter(Boolean).length;
-    const minDeltaBeta = 0.05;
-    const sigDualCount = probes.sig.filter((s, i) => {
-      if (!s) return false;
-      const m1 = probes.mean_group1[i];
-      const m2 = probes.mean_group2[i];
-      if (m1 == null || m2 == null) return false;
-      return Math.abs(m2 - m1) >= minDeltaBeta;
-    }).length;
-    const t = table2col({ holder: statsContent, disableScroll: true });
-    for (const [k, v] of [
-      ["Probes in region", String(probes.positions.length)],
-      ["FDR significant", `${sigFdrCount} (FDR < ${fdr_cutoff})`],
-      ["FDR + effect size", `${sigDualCount} (FDR < ${fdr_cutoff} & |\u0394\u03B2| \u2265 ${minDeltaBeta})`],
-      ["Probe density", `${density.toFixed(1)} probes/kb`],
-      ["Median spacing", `${medianSpacing.toFixed(0)} bp`],
-      ["Max gap", `${maxGap.toFixed(0)} bp`],
-      ["Gaps > 1kb", String(gapsOver1kb)],
-      ["DMRs called", String(dmrs.length)],
-      ...diagnostic.total_probes_analyzed ? [["Probes analyzed (genome-wide)", diagnostic.total_probes_analyzed.toLocaleString()]] : [],
-      ...diagnostic.elapsed_ms != null ? [["Analysis time", formatElapsedTime(diagnostic.elapsed_ms)]] : [],
-      ...diagnostic.peak_memory_mb != null ? [["Peak memory", `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : []
-    ]) {
-      t.addRow(k, v);
-    }
-  }
-  showOverlay() {
-    this.dom.loadingOverlay.style("display", "");
-  }
-  hideOverlay() {
-    this.dom.loadingOverlay.style("display", "none");
-  }
-  clearDiagnostics() {
-    this.dom.diagnosticPanel.selectAll("*").remove();
-    this.dom.diagnosticPanel.style("display", "none");
-  }
-  /** The view model's notes, one line each, under the plot */
-  showNotes(notes) {
-    this.dom.note.selectAll("*").remove();
-    for (const text of notes)
-      this.dom.note.append("div").attr("class", "sjpp-dmr-note").style("color", "#666").style("font-size", ".85em").style("padding", "4px 0").style("max-width", "900px").text(text);
-  }
-};
-
-// plots/dmr/DmrPlot.ts
-var LOADING_TEXT = "Running DMR analysis\u2026 A comparison not yet cached first runs DMRcate over the whole genome, which can take minutes.";
-var DmrPlot = class _DmrPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _DmrPlot.type;
-    this.blockInstance = null;
-    this.analyzedRegion = null;
-    /** counts the requests that showed the loading text; see showLoading() */
-    this.loadingRequest = 0;
-    const wrapper = opts.holder.append("div").style("position", "relative");
-    const loadingOverlay = wrapper.append("div").attr("class", "sjpp-spinner").style("display", "none").style("position", "absolute").style("z-index", "10").style("background-color", "rgba(255,255,255,0.65)");
-    this.dom = {
-      header: opts?.header,
-      holder: wrapper.append("div"),
-      loadingOverlay,
-      error: opts.holder.append("div"),
-      note: opts.holder.append("div"),
-      loading: opts.holder.append("div").style("display", "none"),
-      diagnosticPanel: opts.holder.append("div").style("display", "none")
-    };
-    this.view = new DmrView(this.dom);
-  }
-  static {
-    this.type = "dmr";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw new Error(`No plot with id='${this.id}' found`);
-    return { config };
-  }
-  async init(appState) {
-    const { config } = this.getState(appState);
-    validateConfig(config);
-    if (this.dom.header) this.dom.header.text(config.headerText || "DMR Analysis");
-    this.genomeObj = this.app.opts.genome;
-    this.model = new DmrModel(config, this.app.vocabApi.vocab);
-  }
-  async main() {
-    const config = this.state.config;
-    this.model = new DmrModel(config, this.app.vocabApi.vocab);
-    const c = config.coordinateOverride;
-    if (!c) return;
-    const pad = config.settings.dmr.pad;
-    const chr = c.chr;
-    const start = Math.max(0, Number(c.start) - pad);
-    const stop = Number(c.stop) + pad;
-    const a = this.analyzedRegion;
-    const coordsChanged = a && (chr !== a.chr || start !== a.start || stop !== a.stop);
-    if (a && coordsChanged) {
-      this.view.showOverlay();
-      const hideLoading = this.showLoading();
-      try {
-        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
-        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
-        if ("error" in dmrResult) throw new Error(dmrResult.error);
-        this.analyzedRegion = { chr, start, stop };
-        const blkRegion = this.blockInstance?.rglst?.[0];
-        const viewStart = blkRegion?.start ?? start;
-        const viewStop = blkRegion?.stop ?? stop;
-        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop);
-        this.view.updateTracks(vm.viewData, this.blockInstance);
-        this.view.updateLegend(this.blockInstance, vm.viewData.legendRows);
-        this.view.showNotes(vm.viewData.notes);
-        this.view.clearDiagnostics();
-        if (vm.viewData.diagnostic)
-          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
-      } catch (e) {
-        if (this.app.isAbortError(e)) return;
-        this.view.hideOverlay();
-        throw e;
-      } finally {
-        hideLoading();
-      }
-      this.view.hideOverlay();
-    } else {
-      this.dom.holder.selectAll("*").remove();
-      const hideLoading = this.showLoading();
-      this.blockInstance = null;
-      try {
-        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
-        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
-        if ("error" in dmrResult) throw new Error(dmrResult.error);
-        this.analyzedRegion = { chr, start, stop };
-        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop);
-        this.blockInstance = await this.view.renderBlock(
-          vm.viewData,
-          this.genomeObj,
-          config.settings.dmr,
-          chr,
-          start,
-          stop,
-          (rglst) => this.onBlockCoordinateChange(rglst)
-        );
-        this.view.renderLegend(this.blockInstance, vm.viewData.legendRows);
-        this.view.showNotes(vm.viewData.notes);
-        if (vm.viewData.diagnostic)
-          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
-      } catch (e) {
-        if (this.app.isAbortError(e)) return;
-        throw e;
-      } finally {
-        hideLoading();
-      }
-    }
-  }
-  /** Shows the loading text with its elapsed timer. The returned cleanup stops this request's timer and hides the text
-   * only when no newer request has shown it since: an aborted request ending late must not hide a newer one's. */
-  showLoading() {
-    const request = ++this.loadingRequest;
-    this.dom.loading.style("display", "block");
-    const stopTimer = startElapsedTimer(this.dom.loading, LOADING_TEXT);
-    return () => {
-      stopTimer();
-      if (request == this.loadingRequest) this.dom.loading.style("display", "none");
-    };
-  }
-  onBlockCoordinateChange(rglst) {
-    if (!this.analyzedRegion || !rglst.length) return;
-    const r = rglst[0];
-    if (r.start >= r.stop || r.start < 0) return;
-    const a = this.analyzedRegion;
-    if (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return;
-    this.app.dispatch({
-      type: "plot_edit",
-      id: this.id,
-      config: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }
-    });
-  }
-};
-var componentInit = getCompInit(DmrPlot);
-function getPlotConfig(opts, app) {
-  validateConfig(opts);
-  const config = {
-    settings: {
-      // app is passed through so the defaults can tell a CpG-level dataset from an
-      // element-level one; opts alone does not carry termdbConfig
-      dmr: getDefaultDMRSettings({ ...opts, app })
-    }
-  };
-  return copyMerge(config, opts);
-}
-function validateConfig(opts) {
-  if (!opts.coordinateOverride) throw new Error("coordinateOverride (chr/start/stop) is required for DMR plot");
-  if (!opts.group1) throw new Error("group1 is required for DMR plot");
-  if (!opts.group2) throw new Error("group2 is required for DMR plot");
-}
-function checkRegionSize(span, maxRegionSize) {
-  if (span > maxRegionSize) {
-    const mbLimit = (maxRegionSize / 1e6).toFixed(0);
-    const mbSpan = (span / 1e6).toFixed(1);
-    throw new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`);
-  }
-}
-export {
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=DmrPlot-FZCD6FTX.js.map