@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/Disco.UI-UNPUBQCN.js

@@ -1,239 +0,0 @@
-import {
-  launch
-} from "./chunk-TEFWF3SK.js";
-import {
-  makeBtn,
-  makeFileUpload,
-  makeGenomeDropDown,
-  makePrompt,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-5EBRF6Z7.js";
-import "./chunk-FK5NL2DF.js";
-import "./chunk-CTFHEDG2.js";
-import "./chunk-4E2F26CC.js";
-import "./chunk-SKMFMGCD.js";
-import {
-  Tabs,
-  appear,
-  sayerror
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.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-UNPUBQCN.js.map

package/dist/DmrPlot-27NGDMT4.js

@@ -1,358 +0,0 @@
-import {
-  DmrViewModel,
-  getDefaultDMRSettings
-} from "./chunk-QYCPIVCX.js";
-import {
-  PlotBase,
-  table2col
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3,
-  formatElapsedTime
-} from "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.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,
-        backend: settings.dmr.backend,
-        element_type: this.config.elementType
-      }
-    });
-  }
-};
-
-// 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-RQ3HTJVP.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.fdr.filter((f) => f < fdr_cutoff).length;
-    const minDeltaBeta = 0.05;
-    const sigDualCount = probes.fdr.filter((f, i) => {
-      if (f >= fdr_cutoff) 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");
-  }
-  showLoessNote(show) {
-    this.dom.note.selectAll("*").remove();
-    if (show) {
-      this.dom.note.append("div").attr("class", "sjpp-loess-note").style("color", "#888").style("font-size", ".8em").style("padding", "4px 0").text("Zoom in to see per-CpG dots.");
-    }
-  }
-};
-
-// plots/dmr/DmrPlot.ts
-var DmrPlot = class _DmrPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _DmrPlot.type;
-    this.blockInstance = null;
-    this.analyzedRegion = null;
-    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)");
-    const toggleDiv = opts.holder.append("div").style("padding", "2px 0");
-    const initBackend = opts.state?.config?.settings?.dmr?.backend || "rust";
-    const toggleBtn = toggleDiv.append("button").style("font-size", "11px").text(`Backend: ${initBackend === "rust" ? "Rust" : "R (DMRCate)"}`).on("click", () => {
-      const config = this.state.config;
-      const curr = config.settings.dmr.backend || "rust";
-      const next = curr === "rust" ? "r" : "rust";
-      toggleBtn.text(`Backend: ${next === "rust" ? "Rust" : "R (DMRCate)"}`);
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { settings: { dmr: { ...config.settings.dmr, backend: next } } }
-      });
-    });
-    this.dom = {
-      header: opts?.header,
-      holder: wrapper.append("div"),
-      loadingOverlay,
-      error: opts.holder.append("div"),
-      note: opts.holder.append("div"),
-      loading: opts.holder.append("div").text("Running DMR analysis\u2026"),
-      diagnosticPanel: opts.holder.append("div").style("display", "none")
-    };
-    this.view = new DmrView(this.dom);
-  }
-  static {
-    this.type = "dmr";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw new Error(`No plot with id='${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();
-      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.showLoessNote(!vm.viewData.showDots);
-        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;
-      }
-      this.view.hideOverlay();
-    } else {
-      this.dom.holder.selectAll("*").remove();
-      this.dom.loading.style("display", "block");
-      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.showLoessNote(!vm.viewData.showDots);
-        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.dom.loading.style("display", "none");
-        throw e;
-      }
-      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-27NGDMT4.js.map

package/dist/DmrPlot-27NGDMT4.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/dmr/model/DmrModel.ts", "../plots/dmr/view/DmrView.ts", "../plots/dmr/DmrPlot.ts"],
-  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport type { TermdbDmrResponse } from '#types'\nimport type { DmrConfig } from '../DmrTypes.ts'\n\nexport class DmrModel {\n\tprivate config: DmrConfig\n\tprivate vocab: { genome: string; dslabel: string }\n\n\tconstructor(config: DmrConfig, vocab: { genome: string; dslabel: string }) {\n\t\tthis.config = config\n\t\tthis.vocab = vocab\n\t}\n\n\tasync fetchDmr(chr: string, start: number, stop: number, signal?: AbortSignal): Promise<TermdbDmrResponse> {\n\t\tconst { group1, group2, settings } = this.config\n\t\tconst { genome, dslabel } = this.vocab\n\t\treturn dofetch3('termdb/dmr', {\n\t\t\tsignal,\n\t\t\tbody: {\n\t\t\t\tgenome,\n\t\t\t\tdslabel,\n\t\t\t\tchr,\n\t\t\t\tstart,\n\t\t\t\tstop,\n\t\t\t\tgroup1,\n\t\t\t\tgroup2,\n\t\t\t\tlambda: settings.dmr.lambda,\n\t\t\t\tC: settings.dmr.C,\n\t\t\t\tfdr_cutoff: settings.dmr.fdr_cutoff,\n\t\t\t\tgroup1Name: this.config.group1Name,\n\t\t\t\tgroup2Name: this.config.group2Name,\n\t\t\t\tblockWidth: settings.dmr.blockWidth,\n\t\t\t\tdevicePixelRatio: typeof window !== 'undefined' ? window.devicePixelRatio : 1,\n\t\t\t\tmaxLoessRegion: settings.dmr.maxLoessRegion,\n\t\t\t\tcolors: settings.dmr.colors,\n\t\t\t\tbackend: settings.dmr.backend,\n\t\t\t\telement_type: this.config.elementType\n\t\t\t}\n\t\t}) as Promise<TermdbDmrResponse>\n\t}\n}\n", "import { table2col } from '#dom'\nimport { formatElapsedTime } from '#shared'\nimport type { DmrDiagnostic } from '#types'\nimport type { DmrDom, LegendRow, DmrViewData } from '../DmrTypes.ts'\n\nexport class DmrView {\n\tprivate dom: DmrDom\n\n\tconstructor(dom: DmrDom) {\n\t\tthis.dom = dom\n\t}\n\n\tasync renderBlock(\n\t\tviewData: DmrViewData,\n\t\tgenomeObj: any,\n\t\tsettings: { blockWidth: number },\n\t\tchr: string,\n\t\tstart: number,\n\t\tstop: number,\n\t\tonCoordinateChange: (rglst: { chr: string; start: number; stop: number }[]) => void\n\t) {\n\t\tconst { Block } = await import('#src/block')\n\t\treturn new Block({\n\t\t\tholder: this.dom.holder,\n\t\t\tgenome: genomeObj,\n\t\t\tchr,\n\t\t\tstart,\n\t\t\tstop,\n\t\t\ttklst: viewData.tklst,\n\t\t\tnobox: true,\n\t\t\twidth: settings.blockWidth,\n\t\t\tonCoordinateChange\n\t\t})\n\t}\n\n\tupdateTracks(viewData: DmrViewData, blockInstance: any) {\n\t\tfor (const tk of blockInstance.tklst) {\n\t\t\tconst updated = viewData.tklst.find((t: any) => t.name === tk.name)\n\t\t\tif (!updated) continue\n\t\t\tif (tk.type === 'bedj' && updated.bedItems) {\n\t\t\t\ttk.bedItems = updated.bedItems\n\t\t\t\tblockInstance.tk_load(tk)\n\t\t\t} else if (tk.type === 'bigwig' && updated.imgData) {\n\t\t\t\ttk.imgData = updated.imgData\n\t\t\t\tblockInstance.tk_load(tk)\n\t\t\t}\n\t\t}\n\t}\n\n\tupdateLegend(blockInstance: any, legendRows: LegendRow[]) {\n\t\tif (!blockInstance?.legend?.holder) return\n\t\tconst labels = ['Per-CpG Means', 'DMR', 'Sig. CpGs']\n\t\tblockInstance.legend.holder\n\t\t\t.selectAll('tr')\n\t\t\t.filter((_d: any, i: number, nodes: any) => {\n\t\t\t\tconst td = nodes[i].querySelector('td')\n\t\t\t\treturn td && labels.includes(td.textContent)\n\t\t\t})\n\t\t\t.remove()\n\t\tthis.renderLegend(blockInstance, legendRows)\n\t}\n\n\trenderLegend(blockInstance: any, legendRows: LegendRow[]) {\n\t\tif (!blockInstance?.legend?.holder) return\n\t\tconst { legendcolor, vpad } = blockInstance.legend\n\n\t\tfor (const row of legendRows) {\n\t\t\tconst tr = blockInstance.legend.holder.append('tr')\n\t\t\ttr.append('td')\n\t\t\t\t.text(row.label)\n\t\t\t\t.attr('style', `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (const entry of row.items) {\n\t\t\t\tconst item = td\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('style', `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`)\n\t\t\t\tif (entry.style === 'shaded') {\n\t\t\t\t\t// Shaded region with line marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`\n\t\t\t\t\t\t)\n\t\t\t\t} else if (entry.style === 'dashed') {\n\t\t\t\t\t// Dashed line marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`\n\t\t\t\t\t\t)\n\t\t\t\t} else {\n\t\t\t\t\t// Default square marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\titem.append('div').attr('style', 'display:inline-block;color:#555;font-size:.8em').text(entry.text)\n\t\t\t}\n\t\t}\n\t}\n\n\trenderDiagnostics(\n\t\tdiagnostic: DmrDiagnostic,\n\t\tdmrs: { start: number; stop: number; direction: string }[],\n\t\tfdr_cutoff: number\n\t) {\n\t\tconst panel = this.dom.diagnosticPanel\n\t\tpanel.selectAll('*').remove()\n\t\tpanel.style('display', 'block')\n\n\t\tconst { probes } = diagnostic\n\n\t\tconst toggle = panel.append('div').attr('style', 'cursor:default;font-size:12px;color:#888;padding:2px 0')\n\t\tconst statsContent = panel.append('div').style('display', 'none')\n\t\tlet expanded = false\n\t\ttoggle.text('+ Diagnostic details').on('click', () => {\n\t\t\texpanded = !expanded\n\t\t\ttoggle.text((expanded ? '\\u2212 ' : '+ ') + 'Diagnostic details')\n\t\t\tstatsContent.style('display', expanded ? 'block' : 'none')\n\t\t})\n\n\t\tconst spacings = diagnostic.probe_spacings\n\t\tconst medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0\n\t\tconst maxGap = spacings.length ? Math.max(...spacings) : 0\n\t\tconst gapsOver1kb = spacings.filter(s => s > 1000).length\n\t\tconst density =\n\t\t\tprobes.positions.length > 1\n\t\t\t\t? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1000)\n\t\t\t\t: 0\n\t\tconst sigFdrCount = probes.fdr.filter(f => f < fdr_cutoff).length\n\t\tconst minDeltaBeta = 0.05\n\t\tconst sigDualCount = probes.fdr.filter((f, i) => {\n\t\t\tif (f >= fdr_cutoff) return false\n\t\t\tconst m1 = probes.mean_group1[i]\n\t\t\tconst m2 = probes.mean_group2[i]\n\t\t\tif (m1 == null || m2 == null) return false\n\t\t\treturn Math.abs(m2 - m1) >= minDeltaBeta\n\t\t}).length\n\n\t\tconst t = table2col({ holder: statsContent, disableScroll: true })\n\t\tfor (const [k, v] of [\n\t\t\t['Probes in region', String(probes.positions.length)],\n\t\t\t['FDR significant', `${sigFdrCount} (FDR < ${fdr_cutoff})`],\n\t\t\t['FDR + effect size', `${sigDualCount} (FDR < ${fdr_cutoff} & |\\u0394\\u03B2| \\u2265 ${minDeltaBeta})`],\n\t\t\t['Probe density', `${density.toFixed(1)} probes/kb`],\n\t\t\t['Median spacing', `${medianSpacing.toFixed(0)} bp`],\n\t\t\t['Max gap', `${maxGap.toFixed(0)} bp`],\n\t\t\t['Gaps > 1kb', String(gapsOver1kb)],\n\t\t\t['DMRs called', String(dmrs.length)],\n\t\t\t...(diagnostic.total_probes_analyzed\n\t\t\t\t? [['Probes analyzed (genome-wide)', diagnostic.total_probes_analyzed.toLocaleString()]]\n\t\t\t\t: []),\n\t\t\t...(diagnostic.elapsed_ms != null ? [['Analysis time', formatElapsedTime(diagnostic.elapsed_ms)]] : []),\n\t\t\t...(diagnostic.peak_memory_mb != null ? [['Peak memory', `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : [])\n\t\t] as [string, string][]) {\n\t\t\tt.addRow(k, v)\n\t\t}\n\t}\n\n\tshowOverlay() {\n\t\tthis.dom.loadingOverlay.style('display', '')\n\t}\n\n\thideOverlay() {\n\t\tthis.dom.loadingOverlay.style('display', 'none')\n\t}\n\n\tclearDiagnostics() {\n\t\tthis.dom.diagnosticPanel.selectAll('*').remove()\n\t\tthis.dom.diagnosticPanel.style('display', 'none')\n\t}\n\n\tshowLoessNote(show: boolean) {\n\t\tthis.dom.note.selectAll('*').remove()\n\t\tif (show) {\n\t\t\tthis.dom.note\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-loess-note')\n\t\t\t\t.style('color', '#888')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('padding', '4px 0')\n\t\t\t\t.text('Zoom in to see per-CpG dots.')\n\t\t}\n\t}\n}\n", "import { PlotBase } from '../PlotBase.ts'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport type { DmrConfig, DmrDom } from './DmrTypes.ts'\nimport { getDefaultDMRSettings } from './settings/defaults.ts'\nimport { DmrModel } from './model/DmrModel.ts'\nimport { DmrViewModel } from './viewModel/DmrViewModel.ts'\nimport { DmrView } from './view/DmrView.ts'\n\nclass DmrPlot extends PlotBase implements RxComponent {\n\tstatic type = 'dmr'\n\n\ttype = DmrPlot.type\n\tdeclare dom: DmrDom\n\tblockInstance: InstanceType<any> | null = null\n\tanalyzedRegion: { chr: string; start: number; stop: number } | null = null\n\tview!: DmrView\n\tprivate model!: DmrModel\n\tprivate genomeObj: any\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tconst wrapper = opts.holder.append('div').style('position', 'relative')\n\t\tconst loadingOverlay = wrapper\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-spinner')\n\t\t\t.style('display', 'none')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('z-index', '10')\n\t\t\t.style('background-color', 'rgba(255,255,255,0.65)')\n\t\t// Backend toggle button (temporary \u2014 for R vs Rust validation)\n\t\tconst toggleDiv = opts.holder.append('div').style('padding', '2px 0')\n\t\tconst initBackend = opts.state?.config?.settings?.dmr?.backend || 'rust'\n\t\tconst toggleBtn = toggleDiv\n\t\t\t.append('button')\n\t\t\t.style('font-size', '11px')\n\t\t\t.text(`Backend: ${initBackend === 'rust' ? 'Rust' : 'R (DMRCate)'}`)\n\t\t\t.on('click', () => {\n\t\t\t\tconst config = this.state.config as DmrConfig\n\t\t\t\tconst curr = config.settings.dmr.backend || 'rust'\n\t\t\t\tconst next = curr === 'rust' ? 'r' : 'rust'\n\t\t\t\ttoggleBtn.text(`Backend: ${next === 'rust' ? 'Rust' : 'R (DMRCate)'}`)\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: { settings: { dmr: { ...config.settings.dmr, backend: next } } }\n\t\t\t\t})\n\t\t\t})\n\n\t\tthis.dom = {\n\t\t\theader: opts?.header,\n\t\t\tholder: wrapper.append('div'),\n\t\t\tloadingOverlay,\n\t\t\terror: opts.holder.append('div'),\n\t\t\tnote: opts.holder.append('div'),\n\t\t\tloading: opts.holder.append('div').text('Running DMR analysis\\u2026'),\n\t\t\tdiagnosticPanel: opts.holder.append('div').style('display', 'none')\n\t\t}\n\t\tthis.view = new DmrView(this.dom)\n\t}\n\n\tgetState(appState: { plots: DmrConfig[] }): { config: DmrConfig } {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw new Error(`No plot with id='${this.id}' found`)\n\t\treturn { config }\n\t}\n\n\tasync init(appState: any) {\n\t\tconst { config } = this.getState(appState)\n\t\tvalidateConfig(config)\n\t\tif (this.dom.header) this.dom.header.text(config.headerText || 'DMR Analysis')\n\t\tthis.genomeObj = this.app.opts.genome\n\t\tthis.model = new DmrModel(config, this.app.vocabApi.vocab)\n\n\t\t/* No fetch here. main() runs right after init and its full-rebuild branch does the first\n\t\trender, so there is one code path for rendering and, more to the point, one for failing:\n\t\tan error thrown from main() is shown by the framework (PlotBase.printError) and re-shown on\n\t\tevery update until it is resolved, where an error caught inside init and written into\n\t\tdom.error was wiped by the very next update() before anyone saw it. */\n\t}\n\n\tasync main() {\n\t\tconst config = this.state.config as DmrConfig\n\t\tthis.model = new DmrModel(config, this.app.vocabApi.vocab)\n\n\t\tconst c = config.coordinateOverride\n\t\tif (!c) return\n\t\tconst pad = config.settings.dmr.pad\n\t\tconst chr = c.chr\n\t\tconst start = Math.max(0, Number(c.start) - pad)\n\t\tconst stop = Number(c.stop) + pad\n\n\t\tconst a = this.analyzedRegion\n\t\tconst coordsChanged = a && (chr !== a.chr || start !== a.start || stop !== a.stop)\n\n\t\tif (a && coordsChanged) {\n\t\t\t// New coordinates \u2014 re-fetch and update tracks in place\n\t\t\tthis.view.showOverlay()\n\n\t\t\ttry {\n\t\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\t\tif ('error' in dmrResult) throw new Error(dmrResult.error)\n\n\t\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\t\tconst blkRegion = this.blockInstance?.rglst?.[0]\n\t\t\t\tconst viewStart = blkRegion?.start ?? start\n\t\t\t\tconst viewStop = blkRegion?.stop ?? stop\n\t\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop)\n\n\t\t\t\tthis.view.updateTracks(vm.viewData, this.blockInstance)\n\t\t\t\tthis.view.updateLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\t\tthis.view.showLoessNote(!vm.viewData.showDots)\n\t\t\t\tthis.view.clearDiagnostics()\n\t\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t\t} catch (e: unknown) {\n\t\t\t\tif (this.app.isAbortError(e)) return\n\t\t\t\tthis.view.hideOverlay()\n\t\t\t\tthrow e\n\t\t\t}\n\t\t\tthis.view.hideOverlay()\n\t\t} else {\n\t\t\t// First render, or same coordinates with changed settings (e.g. backend toggle) \u2014 full build\n\t\t\tthis.dom.holder.selectAll('*').remove()\n\t\t\tthis.dom.loading.style('display', 'block')\n\t\t\tthis.blockInstance = null\n\n\t\t\ttry {\n\t\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\t\tif ('error' in dmrResult) throw new Error(dmrResult.error)\n\n\t\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop)\n\n\t\t\t\tthis.blockInstance = await this.view.renderBlock(\n\t\t\t\t\tvm.viewData,\n\t\t\t\t\tthis.genomeObj,\n\t\t\t\t\tconfig.settings.dmr,\n\t\t\t\t\tchr,\n\t\t\t\t\tstart,\n\t\t\t\t\tstop,\n\t\t\t\t\trglst => this.onBlockCoordinateChange(rglst)\n\t\t\t\t)\n\t\t\t\tthis.view.renderLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\t\tthis.view.showLoessNote(!vm.viewData.showDots)\n\t\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t\t} catch (e: unknown) {\n\t\t\t\tif (this.app.isAbortError(e)) return\n\t\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\t\tthrow e\n\t\t\t}\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t}\n\t}\n\n\tonBlockCoordinateChange(rglst: { chr: string; start: number; stop: number }[]) {\n\t\tif (!this.analyzedRegion || !rglst.length) return\n\t\tconst r = rglst[0]\n\t\tif (r.start >= r.stop || r.start < 0) return\n\t\tconst a = this.analyzedRegion\n\t\tif (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }\n\t\t})\n\t}\n}\n\nexport const componentInit = getCompInit(DmrPlot)\n\nexport function getPlotConfig(opts: Partial<DmrConfig>, app?: any): DmrConfig {\n\tvalidateConfig(opts)\n\n\tconst config = {\n\t\tsettings: {\n\t\t\t// app is passed through so the defaults can tell a CpG-level dataset from an\n\t\t\t// element-level one; opts alone does not carry termdbConfig\n\t\t\tdmr: getDefaultDMRSettings({ ...opts, app })\n\t\t}\n\t}\n\treturn copyMerge(config, opts)\n}\n\n/** Runs in both getPlotConfig and main() because will only run in main()\n * when plot is loaded from a saved state (e.g. mass session file).*/\nfunction validateConfig(opts) {\n\tif (!opts.coordinateOverride) throw new Error('coordinateOverride (chr/start/stop) is required for DMR plot')\n\tif (!opts.group1) throw new Error('group1 is required for DMR plot')\n\tif (!opts.group2) throw new Error('group2 is required for DMR plot')\n}\n\n/** Client-side region size guard (configurable via settings.dmr.maxRegionSize, default 5 Mb).\n *  The server also enforces a hard safety cap (10 Mb) to catch direct API calls or buggy clients. */\nfunction checkRegionSize(span: number, maxRegionSize: number) {\n\tif (span > maxRegionSize) {\n\t\tconst mbLimit = (maxRegionSize / 1_000_000).toFixed(0)\n\t\tconst mbSpan = (span / 1_000_000).toFixed(1)\n\t\tthrow new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`)\n\t}\n}\n"],
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