@sjcrh/proteinpaint-client 2.225.0 → 2.226.0

package/dist/chunk-ZNHC46CT.js

@@ -1,340 +0,0 @@
-import {
-  summaryInit
-} from "./chunk-ES7XNERS.js";
-import {
-  navInit
-} from "./chunk-PPICALUF.js";
-import {
-  skipPrevActionAbort,
-  storeInit
-} from "./chunk-Z7CCL464.js";
-import {
-  AppBase,
-  downloadSVGsAsPdf,
-  filterRxCompInit,
-  newSandboxDiv,
-  sayerror,
-  vocabInit
-} from "./chunk-OOVVKQSD.js";
-import {
-  importPlot
-} from "./chunk-QRZRAMHA.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  AppApi,
-  getCompInit,
-  multiInit
-} from "./chunk-HBNB5TRH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// mass/plot.js
-var MassPlot = class _MassPlot {
-  static type = "plot";
-  constructor(opts) {
-    this.type = _MassPlot.type;
-    setRenderers(this);
-    this.initUi(opts);
-  }
-  reactsTo(action) {
-    if (action.type.endsWith("_group")) return true;
-    if (action.type.startsWith("plot_")) {
-      return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    if (action.type.endsWith("customTerm")) return true;
-  }
-  // !!! NOTE: This getState() method is reused by the plot-specific recover component.
-  // When logging something within getState, it may have been called by either the plot or recover instance
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      groups: appState.groups,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
-    if (!this.components) await this.setComponents(this.opts);
-  }
-  async setComponents(opts) {
-    const _ = await importPlot(opts.chartType);
-    const promises = {
-      // recover: recoverInit({
-      // 	app: this.app,
-      // 	holder: this.dom.localRecoverDiv,
-      // 	getState: appState => this.getState(appState),
-      // 	reactsTo: action =>
-      // 		action.id == this.id &&
-      // 		(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
-      // 		action._track_ != 'none',
-      // 	plot_id: this.id,
-      // 	maxHistoryLen: 10,
-      // 	hideLabel: true
-      // }),
-      chart: _.componentInit({
-        app: this.app,
-        holder: this.dom.viz,
-        header: this.dom.paneTitleDiv,
-        id: this.id,
-        plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
-        /******* reason for passing plotDiv to chart ********
-        				- this plot instance may allow to launch a new plot as a persistent sandbox
-        				  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
-        				  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
-        				  thus the need to directly access plotDiv
-        				- example: mds3 tk from genome browser can launch disco etc
-        				- having access to plotDiv may offer flexibility for the plot to do stuff
-        
-        				since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
-        				this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
-        				*/
-        getFilterImage: async () => this.components.filter.getFilterImage()
-      })
-    };
-    const plotFilterCfg = this.app.vocabApi.termdbConfig?.plotFilter;
-    if (!this.state.config.hidePlotFilter && !plotFilterCfg?.hide) {
-      const filterDisabledMsg = plotFilterCfg?.disabledMessage;
-      const filterHolder = filterDisabledMsg ? this.dom.filterDiv.append("div").style("pointer-events", "none").style("opacity", 0.5) : this.dom.filterDiv;
-      if (filterDisabledMsg) this.dom.filterDiv.attr("title", filterDisabledMsg).style("cursor", "not-allowed");
-      promises.filter = filterRxCompInit({
-        app: this.app,
-        vocabApi: this.app.vocabApi,
-        parentId: this.id,
-        holder: filterHolder,
-        hideLabel: true,
-        emptyLabel: "+Add new filter",
-        callback: (filter) => {
-          this.app.dispatch({
-            id: this.id,
-            type: "plot_edit",
-            config: { filter }
-          });
-        }
-      });
-    }
-    this.components = await multiInit(promises);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-};
-var plotInit = getCompInit(MassPlot);
-function setRenderers(self) {
-  self.initUi = function(opts) {
-    const holder = opts.holder;
-    opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
-    holder.header.style("padding", 0);
-    try {
-      self.dom = {
-        tip: new Menu({ padding: "0px" }),
-        holder,
-        paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
-        localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
-        filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
-        body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-        // will hold no data notice or the page title in multichart views
-        errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
-        // dom.viz will hold the rendered view
-        viz: holder.body.append("div")
-      };
-    } catch (e) {
-      self.dom.errdiv.style("display", "none").text(e);
-    }
-  };
-}
-
-// mass/app.ts
-var MassApp = class extends AppBase {
-  // expected class-specific props
-  constructor(opts, api) {
-    super(opts);
-    this.components = {};
-    this.wasDestroyed = false;
-    this.api = api;
-    if (opts.addLoginCallback) {
-      opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
-    }
-    this.type = "app";
-    this.dom = {
-      holder: opts.holder,
-      // do not modify holder style
-      topbar: opts.holder.append("div"),
-      errdiv: opts.holder.append("div"),
-      plotDiv: opts.holder.append("div")
-    };
-    if (opts.getPlotConfig_mutateSummary) {
-      if (typeof opts.getPlotConfig_mutateSummary != "function")
-        throw new Error("opts.getPlotConfig_mutateSummary is not function");
-    }
-    this.plotIdToSandboxId = {};
-  }
-  static {
-    this.type = "app";
-  }
-  async preApiFreeze(api) {
-    try {
-      api.tip = new Menu({ padding: "5px" });
-      api.tip.d.on("keyup", (event) => {
-        if (event.key == "Escape") api.tip.hide();
-      });
-      api.printError = (e) => this.printError(e);
-      api.vocabApi = await vocabInit({
-        app: api,
-        state: { vocab: this.opts.state.vocab },
-        fetchOpts: this.opts.fetchOpts,
-        getDatasetAccessToken: this.opts.getDatasetAccessToken
-      });
-      api.hasWebGL = function() {
-        try {
-          const canvas = document.createElement("canvas");
-          return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
-        } catch (_) {
-          return false;
-        }
-      };
-      this.opts.state.vocab = api.vocabApi.vocab;
-    } catch (e) {
-      console.log(`preApiFreeze error`, e);
-      throw e;
-    }
-  }
-  async init() {
-    try {
-      const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
-      const embeddedSessionState = this.opts.embeddedSessionState;
-      if (embeddedSessionState) {
-        Object.assign(this.opts.state, embeddedSessionState);
-      }
-      this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
-      this.state = await this.store.copyState();
-      this.components = {};
-      if (this.state.nav.header_mode != "hidden") {
-        this.components.nav = await navInit({
-          app: this.api,
-          holder: this.dom.topbar,
-          header_mode: this.state && this.state.nav && this.state.nav.header_mode,
-          vocab: this.state.vocab,
-          massSessionDuration: this.state.termdbConfig.massSessionDuration,
-          // this.opts.massSessionDuration
-          pkgver: this.opts.pkgver,
-          downloadPlots: () => {
-            this.downloadPlots();
-          }
-        });
-      }
-      this.components.plots = {};
-      if (this.opts.app?.doNotAwaitInitRender) {
-        this.api.dispatch();
-      } else {
-        await this.api.dispatch();
-      }
-    } catch (e) {
-      this.printError(e);
-      throw e;
-    }
-  }
-  async main() {
-    await this.api.vocabApi.main();
-    this.dom.plotDiv?.style(
-      "display",
-      this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
-    );
-    const newPlots = {};
-    let sandbox;
-    for (const plot of this.state.plots) {
-      if (plot.parentId) continue;
-      if (this.components.plots && !(plot.id in this.components.plots)) {
-        sandbox = newSandboxDiv(this.dom.plotDiv, {
-          close: () => {
-            this.api.dispatch({
-              type: "plot_delete",
-              id: plot.id
-            });
-          },
-          plotId: plot.id,
-          beforePlotId: plot.insertBefore || null,
-          style: {
-            width: "98.5%"
-          }
-        });
-        if (plot.chartType == "summary")
-          newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-        else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-      }
-    }
-    const numNewPlots = Object.keys(newPlots).length;
-    if (numNewPlots) {
-      await Promise.all(Object.values(newPlots));
-      for (const plotId in newPlots) {
-        this.components.plots[plotId] = await newPlots[plotId];
-      }
-    }
-    for (const plotId in this.components.plots) {
-      if (!this.state.plots.find((p) => p.id === plotId)) {
-        this.components.plots[plotId].destroy();
-        delete this.components.plots[plotId];
-      }
-    }
-  }
-  printError(e) {
-    const errdiv = e.errdiv || this.dom.errdiv;
-    if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
-    sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
-    if (e.stack) console.log(e.stack);
-    this.bus.emit("error");
-    if (this.opts?.debug) {
-      console.groupCollapsed("Stack trace from MassApp.printError() call.");
-      console.trace();
-      console.groupEnd();
-    }
-  }
-  skipPrevActionAbort(action) {
-    return skipPrevActionAbort(action);
-  }
-  async downloadPlots() {
-    const chartImagesAll = [];
-    let i = 1;
-    const values = Object.values(this.components.plots);
-    for (const plot of values) {
-      const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
-      const chartImages = chart.getChartImages ? chart.getChartImages() : null;
-      if (!chartImages) {
-        console.log(`The ${chart.type} does not support downloading images yet`);
-        continue;
-      }
-      for (const chartImage of chartImages) {
-        if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
-        chartImagesAll.push(chartImage);
-      }
-      i++;
-    }
-    if (chartImagesAll.length > 0) {
-      const filters = [];
-      const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
-      if (globalFilterImg) filters.push(globalFilterImg);
-      downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
-    } else alert("No chart images available for download");
-  }
-};
-var appInit = AppApi.getInitFxn(MassApp);
-
-export {
-  appInit
-};
-//# sourceMappingURL=chunk-ZNHC46CT.js.map

package/dist/chunk-ZSTD6Y3K.js

@@ -1,255 +0,0 @@
-import {
-  DataPointInteractions,
-  axisstyle,
-  createLollipopFromGene,
-  drawHoverShapes,
-  showResultsTable,
-  table2col,
-  to_svg
-} from "./chunk-OOVVKQSD.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  icons
-} from "./chunk-3CIL7KH7.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-2N345NXD.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// plots/manhattan/manhattan.ts
-var manhattanLayoutDefaults = {
-  plotWidth: 1e3,
-  plotHeight: 400,
-  pngDotRadius: 2,
-  yAxisX: 70,
-  yAxisY: 40,
-  yAxisSpace: 20,
-  xAxisLabelPad: 30,
-  yAxisPad: 5,
-  axisColor: "#545454",
-  showYAxisLine: true,
-  fontSize: 12,
-  showLegend: true,
-  legendItemWidth: 80,
-  legendDotRadius: 3,
-  legendRightOffset: 15,
-  legendTextOffset: 12,
-  legendVerticalOffset: 4,
-  legendFontSize: 12,
-  showInteractiveDots: true,
-  interactiveDotRadius: 2,
-  interactiveDotStrokeWidth: 1,
-  showDownload: true,
-  interactiveDotsCap: 5e3,
-  maxTooltipGenes: 5
-};
-function plotManhattan(div, data, settings, app, custom = {}) {
-  const handle = { points: [], highlight: () => {
-  } };
-  settings = {
-    ...settings
-  };
-  let interactivePoints = data.plotData.points;
-  if (data.plotData.points.length > settings.interactiveDotsCap) {
-    interactivePoints = data.plotData.points.sort((a, b) => Math.abs(b.y) - Math.abs(a.y)).slice(0, settings.interactiveDotsCap);
-  }
-  const signed = data.plotData.y_min < 0;
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
-  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
-  const yPad = data.plotData.y_pad ?? settings.pngDotRadius;
-  const yAxisLow = signed ? data.plotData.y_min + yPad : 0;
-  const yAxisScale = linear().domain([yAxisLow, data.plotData.y_max - yPad]).range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)]);
-  const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
-  axisG.call(
-    axisLeft(yAxisScale).tickSizeOuter(0)
-    // removes top/bottom cap lines for clean look
-  );
-  axisstyle({
-    axis: axisG,
-    color: settings.axisColor,
-    fontsize: settings.fontSize + 2,
-    showline: settings.showYAxisLine
-  });
-  svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text((custom.yAxisLabel ?? "-log\u2081\u2080(q-value)") + (data.plotData.has_capped_points ? " [capped]" : ""));
-  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
-  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
-  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
-    const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
-    const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
-    const linkedLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    handle.points = interactivePoints;
-    handle.highlight = (dots) => drawHoverShapes(
-      linkedLayer,
-      dots.map((d) => ({
-        path: circlePath(settings.pngDotRadius + 2),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        stroke: "black",
-        strokeWidth: 2
-      }))
-    );
-    const grin2Hover = (d, container) => {
-      const table = table2col({ holder: container.append("div"), margin: "10px" });
-      table.addRow("Gene", d.gene);
-      table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
-      const [t1, t2] = table.addRow();
-      t1.text("Type");
-      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-      table.addRow("Q-value", d.q_value.toPrecision(3));
-      table.addRow("Subject count", d.nsubj);
-    };
-    const grin2Table = (dots) => ({
-      columns: [
-        { label: "Gene" },
-        { label: "Position" },
-        { label: "Type" },
-        { label: "Q-value", sortable: true },
-        { label: "Subject count", sortable: true }
-      ],
-      rows: dots.map((d) => [
-        { value: d.gene },
-        { value: `${d.chrom}:${d.start}-${d.end}` },
-        {
-          html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
-        },
-        { value: d.q_value.toPrecision(3) },
-        { value: d.nsubj }
-      ])
-    });
-    const interactions = new DataPointInteractions({
-      cover,
-      hoverLayer,
-      hoverTip: geneTip,
-      points: interactivePoints,
-      getX: (d) => d.pixel_x,
-      getY: (d) => d.pixel_y,
-      hitRadius: settings.pngDotRadius + 3,
-      toHoverSpec: (d) => ({
-        path: circlePath(settings.pngDotRadius),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        fill: "none",
-        stroke: "black",
-        strokeWidth: settings.interactiveDotStrokeWidth
-      }),
-      maxTooltipRows: settings.maxTooltipGenes,
-      onHover: custom.onHover,
-      itemNoun: custom.itemNoun ?? "gene",
-      renderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,
-      buildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,
-      // A caller with actions gets the module's standard click flow: an action menu for one
-      // dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.
-      ...custom.getActions ? {
-        getActions: custom.getActions,
-        renderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,
-        getRowKey: custom.getRowKey
-      } : {
-        // Manhattan single-click goes straight to a lollipop launch — no menu.
-        // Release hover-suppression immediately so the cursor's next move re-engages.
-        onSingleClick: (d, _event, ctx) => {
-          ctx.dismiss();
-          if (app && d.gene) createLollipopFromGene(d.gene, app);
-        },
-        // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
-        // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
-        // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
-        // Content is built BEFORE show2 so Menu can measure the populated rect for
-        // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
-        // and extends off the right edge of the viewport.
-        onMultiClick: (dots, event, ctx) => {
-          if (!app) {
-            ctx.dismiss();
-            return;
-          }
-          ctx.clickMenu.clear();
-          const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
-          showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
-          ctx.clickMenu.show2(event.clientX, event.clientY);
-        }
-      }
-    });
-    interactions.attach();
-  }
-  const chroms = Object.entries(data.plotData.chrom_data || {});
-  const oneChrom = chroms.length == 1 ? chroms[0] : void 0;
-  if (oneChrom) {
-    const [, chromData] = oneChrom;
-    const xAxisG = svg.append("g").attr(
-      "transform",
-      `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY + settings.plotHeight + 2 * settings.pngDotRadius})`
-    ).call(
-      axisBottom(xScale.copy().domain(xScale.domain().map((v) => (v - chromData.start) / 1e6))).ticks(8).tickSizeOuter(0)
-    );
-    axisstyle({ axis: xAxisG, color: settings.axisColor, fontsize: settings.fontSize + 2 });
-  } else if (data.plotData.chrom_data) {
-    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
-    chroms.forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
-    });
-  }
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr(
-    "y",
-    // below the Mb tick labels, which the chromosome names it replaces did not have
-    settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad + (oneChrom ? 14 : 0)
-  ).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text(oneChrom ? `${oneChrom[0]} position (Mb)` : "Chromosomes");
-  const title = svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text(custom.title ?? "Manhattan Plot");
-  const titleWidth = title.node().getBBox?.().width || 100;
-  if (settings.showDownload) {
-    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + titleWidth + 8}px`);
-    icons["download"](downloadDiv, {
-      width: 16,
-      height: 16,
-      title: "Download Manhattan plot",
-      handler: () => downloadManhattanSvg(
-        svg.node(),
-        `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`
-      )
-    });
-  }
-  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type).filter(Boolean))];
-  const legendData = custom.legend?.map((l) => ({ type: l.label, color: l.color, hollow: l.hollow })) ?? mutationTypes.map((type) => {
-    const point = data.plotData.points.find((p) => p.type === type);
-    return {
-      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
-      color: point?.color
-    };
-  });
-  if (settings.showLegend && legendData.length > 0) {
-    const legendY = settings.yAxisY / 2;
-    const totalWidth = legendData.length * settings.legendItemWidth;
-    const legendX = settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) - totalWidth - settings.legendRightOffset;
-    legendData.forEach((item, i) => {
-      const x = legendX + i * settings.legendItemWidth;
-      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.hollow ? "none" : item.color).attr("stroke", item.hollow ? item.color : "none");
-      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
-    });
-  }
-  return handle;
-}
-function downloadManhattanSvg(svgNode, fileName) {
-  const clone = svgNode.cloneNode(true);
-  const bbox = svgNode.getBBox();
-  clone.setAttribute("width", bbox.width.toString());
-  clone.setAttribute("height", bbox.height.toString());
-  clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
-  to_svg(clone, fileName, { apply_dom_styles: true });
-}
-
-export {
-  manhattanLayoutDefaults,
-  plotManhattan,
-  downloadManhattanSvg
-};
-//# sourceMappingURL=chunk-ZSTD6Y3K.js.map

package/dist/cohort-ZFGFEEBD.js

@@ -1,66 +0,0 @@
-import {
-  appInit,
-  vocabInit
-} from "./chunk-OOVVKQSD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-QRZRAMHA.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-DOC3HBOV.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-KLJM7HE5.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-HGC4EON3.js";
-import "./chunk-QFQJO7LD.js";
-import {
-  TermTypes
-} from "./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";
-
-// termdb/handlers/cohort.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const cohorts = this.app.vocabApi.app?.opts?.opts?.cohorts0;
-    if (!cohorts?.length) return;
-    const terms = cohorts.map((cohort) => {
-      const term = {
-        id: cohort.id,
-        name: cohort.name,
-        type: TermTypes.COHORT,
-        filter0: cohort.filter,
-        isleaf: true,
-        parent_id: null
-      };
-      return term;
-    });
-    const vocabApi = vocabInit({ vocab: { terms } });
-    appInit({
-      holder,
-      vocabApi,
-      state: {
-        nav: { header_mode: "hide_search" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback(term);
-        }
-      }
-    });
-  }
-};
-export {
-  SearchHandler
-};
-//# sourceMappingURL=cohort-ZFGFEEBD.js.map