jbrowse-plugin-mafviewer 1.4.3 → 1.4.6

package/dist/LinearMafDisplay/stateModel.js

@@ -1,14 +1,22 @@
 import { lazy } from 'react';
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
-import { getEnv, getSession, max, measureText } from '@jbrowse/core/util';
+import { getContainingTrack, getContainingView, getEnv, getSession, max, measureText, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { addDisposer, isAlive, types } from '@jbrowse/mobx-state-tree';
 import { ascending } from 'd3-array';
 import { cluster, hierarchy } from 'd3-hierarchy';
 import deepEqual from 'fast-deep-equal';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive, types } from 'mobx-state-tree';
-import { maxLength, setBrLength } from './util';
+import { computeNodeDescendantNames, maxLength, setBrLength } from './util';
 import { normalize } from '../util';
+const defaultRowHeight = 15;
+const defaultRowProportion = 0.8;
+const defaultShowAllLetters = false;
+const defaultMismatchRendering = true;
+const defaultShowBranchLen = false;
+const defaultTreeAreaWidth = 80;
+const defaultShowAsUpperCase = true;
+const defaultShowSidebar = true;
 const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog/SetRowHeightDialog'));
 /**
  * #stateModel LinearMafDisplay
@@ -30,31 +38,35 @@ export default function stateModelFactory(configSchema, pluginManager) {
         /**
          * #property
          */
-        rowHeight: 15,
+        rowHeight: defaultRowHeight,
         /**
          * #property
          */
-        rowProportion: 0.8,
+        rowProportion: defaultRowProportion,
         /**
          * #property
          */
-        showAllLetters: false,
+        showAllLetters: defaultShowAllLetters,
         /**
          * #property
          */
-        mismatchRendering: true,
+        mismatchRendering: defaultMismatchRendering,
         /**
          * #property
          */
-        showBranchLen: false,
+        showBranchLen: defaultShowBranchLen,
         /**
          * #property
          */
-        treeAreaWidth: 80,
+        treeAreaWidth: defaultTreeAreaWidth,
         /**
          * #property
          */
-        showAsUpperCase: true,
+        showAsUpperCase: defaultShowAsUpperCase,
+        /**
+         * #property
+         */
+        showSidebar: defaultShowSidebar,
     }))
         .volatile(() => ({
         /**
@@ -73,6 +85,14 @@ export default function stateModelFactory(configSchema, pluginManager) {
          * #volatile
          */
         volatileTree: undefined,
+        /**
+         * #volatile
+         */
+        highlightedRowNames: undefined,
+        /**
+         * #volatile
+         */
+        hoveredTreeNode: undefined,
     }))
         .actions(self => ({
         /**
@@ -108,7 +128,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
         /**
          * #action
          */
-        setSamples({ samples, tree }) {
+        setSamples({ samples, tree, }) {
             if (!deepEqual(samples, self.volatileSamples)) {
                 self.volatileSamples = samples;
             }
@@ -122,6 +142,49 @@ export default function stateModelFactory(configSchema, pluginManager) {
         setShowAsUpperCase(arg) {
             self.showAsUpperCase = arg;
         },
+        /**
+         * #action
+         */
+        setTreeAreaWidth(width) {
+            self.treeAreaWidth = width;
+        },
+        /**
+         * #action
+         */
+        setShowSidebar(arg) {
+            self.showSidebar = arg;
+        },
+        /**
+         * #action
+         */
+        setHighlightedRowNames(names, nodePosition) {
+            self.highlightedRowNames = names;
+            self.hoveredTreeNode = nodePosition;
+        },
+        /**
+         * #action
+         */
+        showInsertionSequenceDialog(insertionData) {
+            const { sequence, sampleLabel, chr, pos } = insertionData;
+            const session = getSession(self);
+            const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
+                featureData: {
+                    uniqueId: `insertion-${chr}-${pos}-${sampleLabel}`,
+                    type: 'insertion',
+                    refName: chr,
+                    start: pos,
+                    end: pos + 1,
+                    sample: sampleLabel,
+                    insertionLength: sequence.length,
+                    sequence: self.showAsUpperCase
+                        ? sequence.toUpperCase()
+                        : sequence.toLowerCase(),
+                },
+                view: getContainingView(self),
+                track: getContainingTrack(self),
+            });
+            session.showWidget(featureWidget);
+        },
     }))
         .views(self => ({
         /**
@@ -149,8 +212,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
         get root() {
             return self.volatileTree
                 ? hierarchy(self.volatileTree, d => d.children)
-                    // todo: investigate whether needed, typescript says children always true
-                    .sum(d => (d.children ? 0 : 1))
+                    .sum(d => (d.children?.length ? 0 : 1))
                     .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1))
                 : undefined;
         },
@@ -164,11 +226,18 @@ export default function stateModelFactory(configSchema, pluginManager) {
             const r = self.root;
             if (r) {
                 const width = self.treeAreaWidth;
+                // Use totalHeight - rowHeight so leaves are centered in rows
+                // (first leaf at rowHeight/2, last at totalHeight - rowHeight/2)
                 const clust = cluster()
-                    .size([this.totalHeight, width])
+                    .size([this.totalHeight - self.rowHeight, width])
                     .separation(() => 1);
                 clust(r);
-                setBrLength(r, (r.data.length = 0), width / maxLength(r));
+                // Offset all nodes by rowHeight/2 to center in rows
+                for (const node of r.descendants()) {
+                    node.x = node.x + self.rowHeight / 2;
+                }
+                r.data.length = 0;
+                setBrLength(r, 0, width / maxLength(r));
                 return r;
             }
             else {
@@ -205,6 +274,22 @@ export default function stateModelFactory(configSchema, pluginManager) {
         get leaves() {
             return self.root?.leaves();
         },
+        /**
+         * #getter
+         */
+        get leafMap() {
+            return new Map(this.leaves?.map(leaf => [leaf.data.name, leaf]));
+        },
+        /**
+         * #getter
+         * Precomputed map from hierarchy node to its descendant leaf names
+         */
+        get nodeDescendantNames() {
+            if (this.hierarchy) {
+                return computeNodeDescendantNames(this.hierarchy);
+            }
+            return new Map();
+        },
         /**
          * #getter
          */
@@ -233,7 +318,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 const s = superRenderProps();
                 return {
                     ...s,
-                    notReady: (!self.volatileSamples && !self.volatileTree) || super.notReady,
+                    notReady: (!self.volatileSamples && !self.volatileTree) || s.notReady,
                     config: rendererConfig,
                     samples,
                     rowHeight,
@@ -305,11 +390,41 @@ export default function stateModelFactory(configSchema, pluginManager) {
                             self.setMismatchRendering(!self.mismatchRendering);
                         },
                     },
+                    {
+                        label: 'Show sidebar',
+                        type: 'checkbox',
+                        checked: self.showSidebar,
+                        onClick: () => {
+                            self.setShowSidebar(!self.showSidebar);
+                        },
+                    },
                 ];
             },
         };
     })
         .views(self => ({
+        /**
+         * #getter
+         * Get highlight regions from connected MSA views
+         */
+        get msaHighlights() {
+            const session = getSession(self);
+            const view = getContainingView(self);
+            const highlights = [];
+            // Find MSA views that are connected to our parent view
+            for (const v of session.views) {
+                if (v.type === 'MsaView' &&
+                    v.connectedViewId === view.id) {
+                    const msaView = v;
+                    if (msaView.connectedHighlights) {
+                        for (const h of msaView.connectedHighlights) {
+                            highlights.push(h);
+                        }
+                    }
+                }
+            }
+            return highlights;
+        },
         /**
          * #getter
          */
@@ -331,6 +446,12 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 ?.map(s => measureText(s.label, this.svgFontSize))
                 .map(width => (this.canDisplayLabel ? width : minWidth)) || [], 0);
         },
+        /**
+         * #getter
+         */
+        get sidebarWidth() {
+            return self.showSidebar ? this.labelWidth + 5 + self.treeWidth : 0;
+        },
     }))
         .actions(self => ({
         afterCreate() {
@@ -343,7 +464,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
                         adapterConfig: self.adapterConfig,
                         statusCallback: (message) => {
                             if (isAlive(self)) {
-                                self.setMessage(message);
+                                self.setStatusMessage(message);
                             }
                         },
                     })));
@@ -367,6 +488,24 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 return renderSvg(self, opts, superRenderSvg);
             },
         };
+    })
+        .postProcessSnapshot(snap => {
+        const { rowHeight, rowProportion, showAllLetters, mismatchRendering, showBranchLen, treeAreaWidth, showAsUpperCase, showSidebar, ...rest } = snap;
+        return {
+            ...rest,
+            ...(rowHeight !== defaultRowHeight ? { rowHeight } : {}),
+            ...(rowProportion !== defaultRowProportion ? { rowProportion } : {}),
+            ...(showAllLetters !== defaultShowAllLetters ? { showAllLetters } : {}),
+            ...(mismatchRendering !== defaultMismatchRendering
+                ? { mismatchRendering }
+                : {}),
+            ...(showBranchLen !== defaultShowBranchLen ? { showBranchLen } : {}),
+            ...(treeAreaWidth !== defaultTreeAreaWidth ? { treeAreaWidth } : {}),
+            ...(showAsUpperCase !== defaultShowAsUpperCase
+                ? { showAsUpperCase }
+                : {}),
+            ...(showSidebar !== defaultShowSidebar ? { showSidebar } : {}),
+        };
     });
 }
 //# sourceMappingURL=stateModel.js.map

package/dist/LinearMafDisplay/stateModel.js.map

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package/dist/LinearMafDisplay/types.d.ts

@@ -1,14 +1,14 @@
 export interface NodeWithIds {
     id: string;
     name: string;
-    children: NodeWithIds[];
+    children?: NodeWithIds[];
     length?: number;
     noTree?: boolean;
 }
 export interface NodeWithIdsAndLength {
     id: string;
     name: string;
-    children: NodeWithIdsAndLength[];
+    children?: NodeWithIdsAndLength[];
     noTree?: boolean;
     length: number;
 }

package/dist/LinearMafDisplay/util.d.ts

@@ -2,9 +2,12 @@ import type { NodeWithIds } from './types';
 import type { HierarchyNode } from 'd3-hierarchy';
 export interface HoveredInfo {
     sampleId: string;
+    sampleLabel: string;
     pos: number;
     base: string;
     chr: string;
+    isInsertion?: boolean;
+    isLargeInsertion?: boolean;
     [key: string]: unknown;
 }
 export interface GenomicPosition {
@@ -22,3 +25,6 @@ export interface GenomicPosition {
 export declare function generateTooltipContent(hoveredInfo: HoveredInfo | undefined, p1: GenomicPosition | undefined, p2: GenomicPosition): string;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
+export declare function computeNodeDescendantNames<T extends {
+    name: string;
+}>(root: HierarchyNode<T>): Map<HierarchyNode<T>, string[]>;

package/dist/LinearMafDisplay/util.js

@@ -18,12 +18,13 @@ export function generateTooltipContent(hoveredInfo, p1, p2) {
         // Single position mode
         contentLines.push(`Ref: ${p2.refName}:${toLocale(p2.coord)}`);
         if (hoveredInfo) {
-            const { base, sampleId, pos, chr } = hoveredInfo;
+            const { base, sampleLabel, pos, chr, isInsertion } = hoveredInfo;
             const thresh = 20;
             const len = base.length;
             const lengthSuffix = len > 1 ? ` ${len}bp` : '';
             const baseDisplay = base.length > thresh ? base.slice(0, thresh) + '...' : base;
-            contentLines.push(`Alt ${sampleId}: ${chr}:${pos.toLocaleString('en-US')} (${baseDisplay}${lengthSuffix})`);
+            const insertionLabel = isInsertion ? ' Insertion' : '';
+            contentLines.push(`Alt ${sampleLabel}: ${chr}:${pos.toLocaleString('en-US')} (${baseDisplay}${lengthSuffix}${insertionLabel})`);
         }
     }
     return contentLines.filter(line => !!line).join('<br/>');
@@ -34,12 +35,33 @@ export function maxLength(d) {
 }
 // basically same as setRadius from https://observablehq.com/@d3/tree-of-life
 export function setBrLength(d, y0, k) {
+    const newY0 = y0 + Math.max(d.data.length || 0, 0);
     // @ts-expect-error
-    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    d.len = newY0 * k;
     if (d.children) {
-        d.children.forEach(d => {
-            setBrLength(d, y0, k);
-        });
+        for (const child of d.children) {
+            setBrLength(child, newY0, k);
+        }
+    }
+}
+export function computeNodeDescendantNames(root) {
+    const map = new Map();
+    function visit(node) {
+        if (!node.children || node.children.length === 0) {
+            const names = [node.data.name];
+            map.set(node, names);
+            return names;
+        }
+        const names = [];
+        for (const child of node.children) {
+            for (const name of visit(child)) {
+                names.push(name);
+            }
+        }
+        map.set(node, names);
+        return names;
     }
+    visit(root);
+    return map;
 }
 //# sourceMappingURL=util.js.map

package/dist/LinearMafDisplay/util.js.map

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package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -1,10 +1,7 @@
 import { FeatureRendererType } from '@jbrowse/core/pluggableElementTypes';
 import { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Region } from '@jbrowse/core/util';
-interface Sample {
-    id: string;
-    color?: string;
-}
+import type { Sample } from '../LinearMafDisplay/types';
 interface RenderArgs extends RenderArgsDeserialized {
     samples: Sample[];
     rowHeight: number;
@@ -27,9 +24,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: import("./rendering").Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
+        samples: Sample[];
         canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
@@ -38,10 +35,10 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: import("./rendering").Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
-        imageData: any;
+        samples: Sample[];
+        imageData: ImageBitmap;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -49,11 +46,47 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: import("./rendering").Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
-        reactElement: React.ReactElement;
-        html?: string;
+        samples: Sample[];
+        html: string;
+        reactElement?: React.ReactElement;
+    } | {
+        features: Map<any, any>;
+        width: number;
+        height: number;
+        containsNoTransferables: boolean;
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
+        samples: Sample[];
+        canvasRecordedData: Record<string, unknown>;
+        __rpcResult: true;
+        value: unknown;
+        transferables: Transferable[];
+    } | {
+        features: Map<any, any>;
+        width: number;
+        height: number;
+        containsNoTransferables: boolean;
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
+        samples: Sample[];
+        imageData: ImageBitmap;
+        __rpcResult: true;
+        value: unknown;
+        transferables: Transferable[];
+    } | {
+        features: Map<any, any>;
+        width: number;
+        height: number;
+        containsNoTransferables: boolean;
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
+        samples: Sample[];
+        html: string;
+        __rpcResult: true;
+        value: unknown;
+        transferables: Transferable[];
     }>;
 }
 export {};

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -6,7 +6,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         const { start, end } = region;
         const bpExpansion = 1;
         return {
-            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            // xref https://github.com/mobxjs/@jbrowse/mobx-state-tree/issues/1524 for Omit
             ...region,
             start: Math.floor(Math.max(start - bpExpansion, 0)),
             end: Math.ceil(end + bpExpansion),

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts

@@ -1,12 +1,21 @@
 import React from 'react';
-import { Sample } from '../../LinearMafDisplay/types';
-import { RenderedBase } from '../rendering';
-type SerializedRBush = any;
+import type { Sample } from '../../LinearMafDisplay/types';
+import type { RenderedBase } from '../rendering';
+interface DisplayModel {
+    setHoveredInfo?: (info: Record<string, unknown> | undefined) => void;
+    setHighlightedRowNames?: (names: string[] | undefined) => void;
+    showInsertionSequenceDialog?: (data: {
+        sequence: string;
+        sampleLabel: string;
+        chr: string;
+        pos: number;
+    }) => void;
+}
 declare const LinearMafRendering: (props: {
     width: number;
     height: number;
-    displayModel: any;
-    flatbush: SerializedRBush;
+    displayModel: DisplayModel;
+    flatbush: ArrayBuffer;
     items: RenderedBase[];
     samples: Sample[];
 }) => React.JSX.Element;

package/dist/LinearMafRenderer/components/LinearMafRendering.js

@@ -1,41 +1,61 @@
-import React, { useMemo, useRef } from 'react';
+import React, { useCallback, useMemo, useRef, useState } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import Flatbush from 'flatbush';
 import { observer } from 'mobx-react';
 const LinearMafRendering = observer(function (props) {
     const { items, displayModel, height, samples, flatbush } = props;
     const ref = useRef(null);
-    const rbush2 = useMemo(() => Flatbush.from(flatbush), [flatbush]);
-    function getFeatureUnderMouse(eventClientX, eventClientY) {
+    const flatbush2 = useMemo(() => Flatbush.from(flatbush), [flatbush]);
+    const [isOverInsertion, setIsOverInsertion] = useState(false);
+    const getFeatureUnderMouse = useCallback((eventClientX, eventClientY) => {
         let offsetX = 0;
         let offsetY = 0;
         if (ref.current) {
-            const r = ref.current.getBoundingClientRect();
-            offsetX = eventClientX - r.left;
-            offsetY = eventClientY - r.top;
+            const rect = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - rect.left;
+            offsetY = eventClientY - rect.top;
         }
-        const x = rbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
-        if (x.length) {
-            const elt = x.find(idx => items[idx]?.isInsertion);
-            const r = elt !== undefined ? items[elt] : items[x[0]];
-            const s = samples[r.sampleId];
-            return {
-                ...r,
-                sampleId: s?.label || s?.id || 'unknown',
-            };
+        const hits = flatbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
+        if (hits.length === 0) {
+            return undefined;
         }
-        else {
+        const insertionHit = hits.find(idx => items[idx]?.isInsertion);
+        const hitIdx = insertionHit ?? hits[0];
+        const item = hitIdx !== undefined ? items[hitIdx] : undefined;
+        if (!item) {
             return undefined;
         }
-    }
-    return (React.createElement("div", { ref: ref, onMouseMove: e => displayModel.setHoveredInfo?.(getFeatureUnderMouse(e.clientX, e.clientY)), onMouseLeave: () => {
-            displayModel.setHoveredInfo?.(undefined);
-        }, onMouseOut: () => {
+        const sample = samples[item.rowIndex];
+        return {
+            ...item,
+            sampleId: sample?.id ?? 'unknown',
+            sampleLabel: sample?.label || sample?.id || 'unknown',
+        };
+    }, [flatbush2, items, samples]);
+    return (React.createElement("div", { ref: ref, onClick: e => {
+            const feature = getFeatureUnderMouse(e.clientX, e.clientY);
+            if (feature?.isInsertion) {
+                displayModel.showInsertionSequenceDialog?.({
+                    sequence: feature.base,
+                    sampleLabel: feature.sampleLabel,
+                    chr: feature.chr,
+                    pos: feature.pos,
+                });
+            }
+        }, onMouseMove: e => {
+            const feature = getFeatureUnderMouse(e.clientX, e.clientY);
+            displayModel.setHoveredInfo?.(feature);
+            displayModel.setHighlightedRowNames?.(feature?.sampleId ? [feature.sampleId] : undefined);
+            setIsOverInsertion(!!feature?.isInsertion);
+        }, onMouseLeave: () => {
             displayModel.setHoveredInfo?.(undefined);
+            displayModel.setHighlightedRowNames?.(undefined);
+            setIsOverInsertion(false);
         }, style: {
             overflow: 'visible',
             position: 'relative',
             height,
+            cursor: isOverInsertion ? 'pointer' : 'default',
         } },
         React.createElement(PrerenderedCanvas, { ...props, style: {
                 position: 'absolute',