@jbrowse/plugin-wiggle 4.1.3 → 4.1.5

package/esm/MultiLinearWiggleDisplay/model.js

@@ -1,12 +1,15 @@
 import { lazy } from 'react';
+import { fromNewick } from '@gmod/hclust';
 import { getConf } from '@jbrowse/core/configuration';
 import { set1 as colors } from '@jbrowse/core/ui/colors';
 import { getContainingView, getSession, max, measureText, } from '@jbrowse/core/util';
 import { stopStopToken } from '@jbrowse/core/util/stopToken';
-import { isAlive, types } from '@jbrowse/mobx-state-tree';
+import { cast, isAlive, types } from '@jbrowse/mobx-state-tree';
 import EqualizerIcon from '@mui/icons-material/Equalizer';
 import VisibilityIcon from '@mui/icons-material/Visibility';
+import { ascending } from '@mui/x-charts-vendor/d3-array';
 import deepEqual from 'fast-deep-equal';
+import { cluster, hierarchy } from "../d3-hierarchy2/index.js";
 import SharedWiggleMixin from "../shared/SharedWiggleMixin.js";
 import axisPropsFromTickScale from "../shared/axisPropsFromTickScale.js";
 import { YSCALEBAR_LABEL_OFFSET, getScale } from "../util.js";
@@ -27,11 +30,18 @@ export function stateModelFactory(_pluginManager, configSchema) {
         type: types.literal('MultiLinearWiggleDisplay'),
         layout: types.optional(types.frozen(), []),
         showSidebar: true,
+        clusterTree: types.maybe(types.string),
+        treeAreaWidth: types.optional(types.number, 80),
+        showTreeSetting: types.maybe(types.boolean),
+        subtreeFilter: types.maybe(types.array(types.string)),
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
         featureUnderMouseVolatile: undefined,
         sourcesVolatile: undefined,
+        hoveredTreeNode: undefined,
+        treeCanvas: undefined,
+        mouseoverCanvas: undefined,
     }))
         .actions(self => ({
         setShowSidebar(arg) {
@@ -43,11 +53,40 @@ export function stateModelFactory(_pluginManager, configSchema) {
             }
             self.sourcesLoadingStopToken = str;
         },
-        setLayout(layout) {
+        setLayout(layout, clearTree = true) {
+            const orderChanged = clearTree &&
+                self.clusterTree &&
+                self.layout.length === layout.length &&
+                self.layout.some((source, idx) => source.name !== layout[idx]?.name);
             self.layout = layout;
+            if (orderChanged) {
+                self.clusterTree = undefined;
+            }
         },
         clearLayout() {
             self.layout = [];
+            self.clusterTree = undefined;
+        },
+        setClusterTree(tree) {
+            self.clusterTree = tree;
+        },
+        setTreeAreaWidth(width) {
+            self.treeAreaWidth = width;
+        },
+        setShowTree(arg) {
+            self.showTreeSetting = arg;
+        },
+        setSubtreeFilter(names) {
+            self.subtreeFilter = names ? cast(names) : undefined;
+        },
+        setHoveredTreeNode(node) {
+            self.hoveredTreeNode = node;
+        },
+        setTreeCanvasRef(ref) {
+            self.treeCanvas = ref || undefined;
+        },
+        setMouseoverCanvasRef(ref) {
+            self.mouseoverCanvas = ref || undefined;
         },
         setSources(sources) {
             if (!deepEqual(sources, self.sourcesVolatile)) {
@@ -121,7 +160,7 @@ export function stateModelFactory(_pluginManager, configSchema) {
         get sources() {
             const sources = Object.fromEntries(self.sourcesVolatile?.map(s => [s.name, s]) || []);
             const iter = self.layout.length ? self.layout : self.sourcesVolatile;
-            return iter
+            let result = iter
                 ?.map(s => ({
                 ...sources[s.name],
                 ...s,
@@ -131,6 +170,11 @@ export function stateModelFactory(_pluginManager, configSchema) {
                 color: s.color ||
                     (!this.isMultiRow ? colors[i] || randomColor() : 'blue'),
             }));
+            if (result && self.subtreeFilter?.length) {
+                const filterSet = new Set(self.subtreeFilter);
+                result = result.filter(s => filterSet.has(s.name));
+            }
+            return result;
         },
         get quantitativeStatsReady() {
             const view = getContainingView(self);
@@ -140,6 +184,9 @@ export function stateModelFactory(_pluginManager, configSchema) {
         },
     }))
         .views(self => ({
+        get showTree() {
+            return self.showTreeSetting ?? true;
+        },
         get rowHeight() {
             const { sources, height, isMultiRow } = self;
             return isMultiRow ? height / (sources?.length || 1) : height;
@@ -151,6 +198,62 @@ export function stateModelFactory(_pluginManager, configSchema) {
             return (getConf(self, 'minimalTicks') ||
                 this.rowHeightTooSmallForScalebar);
         },
+        get root() {
+            const newick = self.clusterTree;
+            if (!newick) {
+                return undefined;
+            }
+            const tree = fromNewick(newick);
+            let root = hierarchy(tree, (d) => d.children)
+                .sum((d) => (d.children ? 0 : 1))
+                .sort((a, b) => ascending(a.data.height || 1, b.data.height || 1));
+            if (self.subtreeFilter?.length) {
+                const filterSet = new Set(self.subtreeFilter);
+                const getLeafNames = (node) => {
+                    if (!node.children?.length) {
+                        return [node.data.name];
+                    }
+                    return node.children.flatMap(child => getLeafNames(child));
+                };
+                const findSubtree = (node) => {
+                    const leafNames = getLeafNames(node);
+                    if (leafNames.length === filterSet.size &&
+                        leafNames.every(name => filterSet.has(name))) {
+                        return node;
+                    }
+                    if (node.children) {
+                        for (const child of node.children) {
+                            const found = findSubtree(child);
+                            if (found) {
+                                return found;
+                            }
+                        }
+                    }
+                    return undefined;
+                };
+                const subtree = findSubtree(root);
+                if (subtree) {
+                    root = subtree;
+                }
+            }
+            return root;
+        },
+    }))
+        .views(self => ({
+        get totalHeight() {
+            return self.rowHeight * (self.sources?.length || 1);
+        },
+        get hierarchy() {
+            const r = self.root;
+            if (!r || !self.sources?.length) {
+                return undefined;
+            }
+            const clust = cluster();
+            clust.size([self.rowHeight * self.sources.length, self.treeAreaWidth]);
+            clust.separation(() => 1);
+            clust(r);
+            return r;
+        },
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
@@ -276,6 +379,29 @@ export function stateModelFactory(_pluginManager, configSchema) {
                                     self.setShowSidebar(!self.showSidebar);
                                 },
                             },
+                            ...(self.isMultiRow
+                                ? [
+                                    {
+                                        label: `Show tree${!self.clusterTree ? ' (run clustering first)' : ''}`,
+                                        type: 'checkbox',
+                                        checked: self.showTree,
+                                        disabled: !self.clusterTree,
+                                        onClick: () => {
+                                            self.setShowTree(!self.showTree);
+                                        },
+                                    },
+                                    ...(self.subtreeFilter?.length
+                                        ? [
+                                            {
+                                                label: 'Clear subtree filter',
+                                                onClick: () => {
+                                                    self.setSubtreeFilter(undefined);
+                                                },
+                                            },
+                                        ]
+                                        : []),
+                                ]
+                                : []),
                             ...(self.graphType
                                 ? [
                                     {
@@ -370,12 +496,14 @@ export function stateModelFactory(_pluginManager, configSchema) {
                 ;
                 (async () => {
                     try {
-                        const [{ getMultiWiggleSourcesAutorun }, { getQuantitativeStatsAutorun },] = await Promise.all([
+                        const [{ getMultiWiggleSourcesAutorun }, { getQuantitativeStatsAutorun }, { setupTreeDrawingAutorun },] = await Promise.all([
                             import("../getMultiWiggleSourcesAutorun.js"),
                             import("../getQuantitativeStatsAutorun.js"),
+                            import("./treeDrawingAutorun.js"),
                         ]);
                         getQuantitativeStatsAutorun(self);
                         getMultiWiggleSourcesAutorun(self);
+                        setupTreeDrawingAutorun(self);
                     }
                     catch (e) {
                         if (isAlive(self)) {
@@ -395,11 +523,15 @@ export function stateModelFactory(_pluginManager, configSchema) {
         if (!snap) {
             return snap;
         }
-        const { layout, showSidebar, ...rest } = snap;
+        const { layout, showSidebar, clusterTree, treeAreaWidth, showTreeSetting, subtreeFilter, ...rest } = snap;
         return {
             ...rest,
             ...(layout?.length ? { layout } : {}),
             ...(!showSidebar ? { showSidebar } : {}),
+            ...(clusterTree !== undefined ? { clusterTree } : {}),
+            ...(treeAreaWidth !== 80 ? { treeAreaWidth } : {}),
+            ...(showTreeSetting !== undefined ? { showTreeSetting } : {}),
+            ...(subtreeFilter?.length ? { subtreeFilter } : {}),
         };
     });
 }

package/esm/MultiLinearWiggleDisplay/renderSvg.js

@@ -3,8 +3,10 @@ import { getContainingView } from '@jbrowse/core/util';
 import { when } from 'mobx';
 import { isReadyOrHasError } from "../svgExportUtil.js";
 import YScaleBars from "./components/YScaleBars.js";
+import { makeSidebarSvg } from "./makeSidebarSvg.js";
 export async function renderSvg(self, opts, superRenderSvg) {
     await when(() => isReadyOrHasError(self));
     const { offsetPx } = getContainingView(self);
-    return (_jsxs(_Fragment, { children: [_jsx("g", { children: await superRenderSvg(opts) }), _jsx("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: _jsx(YScaleBars, { model: self, orientation: "left", exportSVG: true }) })] }));
+    const sidebarSvg = await makeSidebarSvg(self);
+    return (_jsxs(_Fragment, { children: [_jsx("g", { id: "data-layer", children: await superRenderSvg(opts) }), _jsx("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: _jsx(YScaleBars, { model: self, orientation: "left", exportSVG: true }) }), sidebarSvg] }));
 }

package/esm/MultiLinearWiggleDisplay/treeDrawingAutorun.d.ts

@@ -0,0 +1,17 @@
+import type { Source } from '../util.ts';
+import type { ClusterHierarchyNode, HoveredTreeNode } from './components/treeTypes.ts';
+interface TreeDrawingModel {
+    treeCanvas?: HTMLCanvasElement;
+    mouseoverCanvas?: HTMLCanvasElement;
+    hierarchy?: ClusterHierarchyNode;
+    treeAreaWidth: number;
+    height: number;
+    scrollTop: number;
+    rowHeight: number;
+    totalHeight: number;
+    hoveredTreeNode?: HoveredTreeNode;
+    sources?: Source[];
+    isMinimized: boolean;
+}
+export declare function setupTreeDrawingAutorun(self: TreeDrawingModel): void;
+export {};

package/esm/MultiLinearWiggleDisplay/treeDrawingAutorun.js

@@ -0,0 +1,77 @@
+import { getContainingView } from '@jbrowse/core/util';
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
+import { autorun } from 'mobx';
+export function setupTreeDrawingAutorun(self) {
+    addDisposer(self, autorun(function treeDrawAutorun() {
+        if (!isAlive(self) || self.isMinimized) {
+            return;
+        }
+        const { treeCanvas, hierarchy, treeAreaWidth, height, scrollTop, totalHeight: _totalHeight, } = self;
+        if (!treeCanvas || !hierarchy) {
+            return;
+        }
+        const ctx = treeCanvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.resetTransform();
+        ctx.scale(2, 2);
+        ctx.clearRect(0, 0, treeAreaWidth, height);
+        ctx.translate(0, -scrollTop);
+        ctx.strokeStyle = '#0008';
+        ctx.lineWidth = 1;
+        ctx.beginPath();
+        for (const link of hierarchy.links()) {
+            const { source, target } = link;
+            const sy = source.x;
+            const ty = target.x;
+            const tx = target.y;
+            const sx = source.y;
+            ctx.moveTo(sx, sy);
+            ctx.lineTo(sx, ty);
+            ctx.moveTo(sx, ty);
+            ctx.lineTo(tx, ty);
+        }
+        ctx.stroke();
+    }, {
+        name: 'TreeDraw',
+    }));
+    addDisposer(self, autorun(function treeHoverAutorun() {
+        if (!isAlive(self) || self.isMinimized) {
+            return;
+        }
+        const { mouseoverCanvas, hierarchy, rowHeight, hoveredTreeNode, height, scrollTop, sources, totalHeight, } = self;
+        if (!mouseoverCanvas) {
+            return;
+        }
+        const ctx = mouseoverCanvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        const view = getContainingView(self);
+        const viewWidth = view.width;
+        ctx.clearRect(0, 0, viewWidth, height);
+        if (hierarchy && hoveredTreeNode && sources) {
+            ctx.save();
+            ctx.translate(0, -scrollTop);
+            ctx.fillStyle = 'rgba(255,165,0,0.2)';
+            const descendantSet = new Set(hoveredTreeNode.descendantNames);
+            for (let i = 0, l = sources.length; i < l; i++) {
+                const source = sources[i];
+                if (descendantSet.has(source.name)) {
+                    const y = (i + 0.5) * rowHeight;
+                    ctx.fillRect(0, y - rowHeight / 2, viewWidth, rowHeight);
+                }
+            }
+            const { node } = hoveredTreeNode;
+            ctx.fillStyle = 'rgba(255,165,0,0.8)';
+            ctx.beginPath();
+            ctx.arc(node.y, node.x, 4, 0, 2 * Math.PI);
+            ctx.fill();
+            ctx.strokeStyle = 'rgba(255,140,0,1)';
+            ctx.lineWidth = 1;
+            ctx.stroke();
+            ctx.restore();
+        }
+    }, { name: 'TreeHover' }));
+}

package/esm/MultiQuantitativeTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -31,7 +31,7 @@ declare const configSchema: (pluginManager: PluginManager) => import("node_modul
         defaultValue: string;
     };
     adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -43,9 +43,9 @@ declare const configSchema: (pluginManager: PluginManager) => import("node_modul
             defaultValue: string[];
         };
         textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -68,8 +68,8 @@ declare const configSchema: (pluginManager: PluginManager) => import("node_modul
             defaultValue: number;
             description: string;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -80,6 +80,6 @@ declare const configSchema: (pluginManager: PluginManager) => import("node_modul
             type: string;
             defaultValue: boolean;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/esm/MultiRowLineRenderer/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     displayCrossHatches: {
         type: string;
         description: string;
@@ -10,7 +10,7 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         description: string;
         defaultValue: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     color: {
         type: string;
         description: string;
@@ -45,5 +45,5 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         defaultValue: number;
         description: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/esm/MultiRowXYPlotRenderer/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     filled: {
         type: string;
         defaultValue: boolean;
@@ -18,7 +18,7 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         type: string;
         defaultValue: number;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     color: {
         type: string;
         description: string;
@@ -53,5 +53,5 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         defaultValue: number;
         description: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -5,6 +5,9 @@ import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 interface WiggleOptions extends BaseOptions {
     resolution?: number;
     staticBlocks?: Region[];
+    sources?: {
+        name: string;
+    }[];
 }
 interface AdapterEntry {
     dataAdapter: BaseFeatureDataAdapter;

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -87,7 +87,11 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
-            const adapters = await this.getAdapters();
+            let adapters = await this.getAdapters();
+            if (opts.sources?.length) {
+                const sourceNames = new Set(opts.sources.map(s => s.name));
+                adapters = adapters.filter(adp => sourceNames.has(adp.source));
+            }
             merge(...adapters.map(adp => {
                 const { source, dataAdapter } = adp;
                 return dataAdapter.getFeatures(region, opts).pipe(map(f => {

package/esm/MultiWiggleAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const MultiWiggleAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const MultiWiggleAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     subadapters: {
         type: string;
         defaultValue: never[];
@@ -9,5 +9,5 @@ declare const MultiWiggleAdapter: import("node_modules/@jbrowse/core/src/configu
         description: string;
         defaultValue: never[];
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default MultiWiggleAdapter;

package/esm/MultiXYPlotRenderer/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     filled: {
         type: string;
         defaultValue: boolean;
@@ -18,7 +18,7 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         type: string;
         defaultValue: number;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     color: {
         type: string;
         description: string;
@@ -53,5 +53,5 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         defaultValue: number;
         description: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/esm/QuantitativeTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaFactory(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -31,7 +31,7 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("node
         defaultValue: string;
     };
     adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -43,9 +43,9 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("node
             defaultValue: string[];
         };
         textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -68,8 +68,8 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("node
             defaultValue: number;
             description: string;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -80,6 +80,6 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("node
             type: string;
             defaultValue: boolean;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchemaFactory;

package/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.d.ts

@@ -2,5 +2,8 @@ import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableEle
 import type { GetScoreMatrixArgs } from './types.ts';
 export declare class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: GetScoreMatrixArgs, rpcDriverClassName: string): Promise<import("@gmod/hclust").ClusterResult>;
+    execute(args: GetScoreMatrixArgs, rpcDriverClassName: string): Promise<{
+        order: number[];
+        tree: string;
+    }>;
 }

package/esm/WiggleRPC/executeClusterScoreMatrix.d.ts

@@ -3,4 +3,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function executeClusterScoreMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: GetScoreMatrixArgs;
-}): Promise<import("@gmod/hclust").ClusterResult>;
+}): Promise<{
+    order: number[];
+    tree: string;
+}>;

package/esm/WiggleRPC/executeClusterScoreMatrix.js

@@ -1,15 +1,21 @@
-import { clusterData } from '@gmod/hclust';
+import { clusterData, toNewick } from '@gmod/hclust';
 import { getScoreMatrix } from "./getScoreMatrix.js";
 export async function executeClusterScoreMatrix({ pluginManager, args, }) {
     const matrix = await getScoreMatrix({
         pluginManager,
         args,
     });
-    return clusterData({
+    const sampleLabels = Object.keys(matrix);
+    const result = await clusterData({
         data: Object.values(matrix),
+        sampleLabels,
         stopToken: args.stopToken,
         onProgress: a => {
             args.statusCallback?.(a);
         },
     });
+    return {
+        order: result.order,
+        tree: toNewick(result.tree),
+    };
 }

package/esm/XYPlotRenderer/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     filled: {
         type: string;
         defaultValue: boolean;
@@ -18,7 +18,7 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         type: string;
         defaultValue: number;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     color: {
         type: string;
         description: string;
@@ -53,5 +53,5 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         defaultValue: number;
         description: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/esm/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const WiggleRenderer: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const WiggleRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     color: {
         type: string;
         description: string;
@@ -33,5 +33,5 @@ declare const WiggleRenderer: import("node_modules/@jbrowse/core/src/configurati
         defaultValue: number;
         description: string;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default WiggleRenderer;

package/esm/d3-hierarchy2/accessors.d.ts

@@ -0,0 +1,2 @@
+export declare function optional(f: any): any;
+export declare function required(f: any): any;

package/esm/d3-hierarchy2/accessors.js

@@ -0,0 +1,8 @@
+export function optional(f) {
+    return f == null ? null : required(f);
+}
+export function required(f) {
+    if (typeof f !== "function")
+        throw new Error;
+    return f;
+}

package/esm/d3-hierarchy2/array.d.ts

@@ -0,0 +1,2 @@
+export default function (x: any): any;
+export declare function shuffle(array: any, random: any): any;