npm - jbrowse-plugin-mafviewer - Versions diffs - 1.4.3 → 1.4.5 - Mend

jbrowse-plugin-mafviewer 1.4.3 → 1.4.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (73) hide show

package/dist/LinearMafDisplay/stateModel.js CHANGED Viewed

@@ -10,6 +10,7 @@ import { addDisposer, isAlive, types } from 'mobx-state-tree';
 import { maxLength, setBrLength } from './util';
 import { normalize } from '../util';
 const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog/SetRowHeightDialog'));
+const InsertionSequenceDialog = lazy(() => import('./components/InsertionSequenceDialog/InsertionSequenceDialog'));
 /**
  * #stateModel LinearMafDisplay
  * extends LinearBasicDisplay
@@ -55,6 +56,10 @@ export default function stateModelFactory(configSchema, pluginManager) {
          * #property
          */
         showAsUpperCase: true,
+        /**
+         * #property
+         */
+        showSidebar: true,
     }))
         .volatile(() => ({
         /**
@@ -73,6 +78,14 @@ export default function stateModelFactory(configSchema, pluginManager) {
          * #volatile
          */
         volatileTree: undefined,
+        /**
+         * #volatile
+         */
+        highlightedRowNames: undefined,
+        /**
+         * #volatile
+         */
+        hoveredTreeNode: undefined,
     }))
         .actions(self => ({
         /**
@@ -122,6 +135,38 @@ 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) {
+            getSession(self).queueDialog(handleClose => [
+                InsertionSequenceDialog,
+                {
+                    model: self,
+                    onClose: handleClose,
+                    insertionData,
+                },
+            ]);
+        },
     }))
         .views(self => ({
         /**
@@ -164,10 +209,16 @@ 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);
+                // Offset all nodes by rowHeight/2 to center in rows
+                for (const node of r.descendants()) {
+                    node.x = node.x + self.rowHeight / 2;
+                }
                 setBrLength(r, (r.data.length = 0), width / maxLength(r));
                 return r;
             }
@@ -205,6 +256,36 @@ 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() {
+            const map = new Map();
+            function computeDescendants(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) {
+                    names.push(...computeDescendants(child));
+                }
+                map.set(node, names);
+                return names;
+            }
+            if (this.hierarchy) {
+                computeDescendants(this.hierarchy);
+            }
+            return map;
+        },
         /**
          * #getter
          */
@@ -305,6 +386,14 @@ export default function stateModelFactory(configSchema, pluginManager) {
                             self.setMismatchRendering(!self.mismatchRendering);
                         },
                     },
+                    {
+                        label: 'Show sidebar',
+                        type: 'checkbox',
+                        checked: self.showSidebar,
+                        onClick: () => {
+                            self.setShowSidebar(!self.showSidebar);
+                        },
+                    },
                 ];
             },
         };
@@ -331,6 +420,12 @@ 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() {

package/dist/LinearMafDisplay/stateModel.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/LinearMafDisplay/util.d.ts CHANGED Viewed

@@ -2,6 +2,7 @@ import type { NodeWithIds } from './types';
 import type { HierarchyNode } from 'd3-hierarchy';
 export interface HoveredInfo {
     sampleId: string;
+    sampleLabel: string;
     pos: number;
     base: string;
     chr: string;

package/dist/LinearMafDisplay/util.js CHANGED Viewed

@@ -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/>');

package/dist/LinearMafDisplay/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearMafRenderer/LinearMafRenderer.d.ts CHANGED Viewed

@@ -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;
@@ -27,7 +24,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: import("./rendering").Sample[];
+        samples: Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
         canvasRecordedData: Record<string, unknown>;
@@ -38,7 +35,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: import("./rendering").Sample[];
+        samples: Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
         imageData: any;
@@ -49,7 +46,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        samples: import("./rendering").Sample[];
+        samples: Sample[];
         flatbush: ArrayBufferLike;
         items: import("./rendering").RenderedBase[];
         reactElement: React.ReactElement;

package/dist/LinearMafRenderer/LinearMafRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearMafRenderer/components/LinearMafRendering.js CHANGED Viewed

@@ -1,12 +1,13 @@
-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 [isOverLargeInsertion, setIsOverLargeInsertion] = useState(false);
+    const getFeatureUnderMouse = useCallback((eventClientX, eventClientY) => {
         let offsetX = 0;
         let offsetY = 0;
         if (ref.current) {
@@ -14,28 +15,45 @@ const LinearMafRendering = observer(function (props) {
             offsetX = eventClientX - r.left;
             offsetY = eventClientY - r.top;
         }
-        const x = rbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
+        const x = flatbush2.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',
+                sampleId: s?.id ?? 'unknown',
+                sampleLabel: s?.label || s?.id || 'unknown',
             };
         }
         else {
             return undefined;
         }
-    }
-    return (React.createElement("div", { ref: ref, onMouseMove: e => displayModel.setHoveredInfo?.(getFeatureUnderMouse(e.clientX, e.clientY)), onMouseLeave: () => {
-            displayModel.setHoveredInfo?.(undefined);
-        }, onMouseOut: () => {
+    }, [flatbush2, items, samples]);
+    return (React.createElement("div", { ref: ref, onClick: e => {
+            const feature = getFeatureUnderMouse(e.clientX, e.clientY);
+            if (feature?.isLargeInsertion) {
+                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);
+            setIsOverLargeInsertion(!!feature?.isLargeInsertion);
+        }, onMouseLeave: () => {
             displayModel.setHoveredInfo?.(undefined);
+            displayModel.setHighlightedRowNames?.(undefined);
+            setIsOverLargeInsertion(false);
         }, style: {
             overflow: 'visible',
             position: 'relative',
             height,
+            cursor: isOverLargeInsertion ? 'pointer' : 'default',
         } },
         React.createElement(PrerenderedCanvas, { ...props, style: {
                 position: 'absolute',

package/dist/LinearMafRenderer/components/LinearMafRendering.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearMafRenderer/makeImageData.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import Flatbush from 'flatbush';
-import { FONT_CONFIG, processFeatureAlignment, processFeatureInsertions, } from './rendering';
-import { getColorBaseMap, getContrastBaseMap } from './util';
+import { FONT_CONFIG, processFeatureAlignment, } from './rendering';
+import { getCharWidthHeight, getColorBaseMap, getContrastBaseMap } from './util';
 export function makeImageData({ ctx, renderArgs, }) {
     const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, showAsUpperCase, } = renderArgs;
     const region = regions[0];
@@ -14,10 +14,12 @@ export function makeImageData({ ctx, renderArgs, }) {
     const scale = 1 / bpPerPx;
     const hp2 = h / 2;
     const offset = (rowHeight - h) / 2;
+    const { charWidth, charHeight } = getCharWidthHeight();
     ctx.font = FONT_CONFIG;
     const renderingContext = {
         ctx,
         scale,
+        bpPerPx,
         canvasWidth,
         rowHeight,
         h,
@@ -28,18 +30,15 @@ export function makeImageData({ ctx, renderArgs, }) {
         showAllLetters,
         mismatchRendering,
         showAsUpperCase,
+        charWidth,
+        charHeight,
         spatialIndex: [],
         spatialIndexCoords: [],
         lastInsertedX: -Infinity, // Start with -Infinity so first item is always inserted
     };
-    // First pass: render alignments (gaps, matches, mismatches, text)
     for (const feature of features.values()) {
         processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap, renderingContext);
     }
-    // Second pass: render insertions on top
-    for (const feature of features.values()) {
-        processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext);
-    }
     const flatbush = new Flatbush(renderingContext.spatialIndex.length || 1);
     if (renderingContext.spatialIndex.length === 0) {
         flatbush.add(0, 0, 1, 1);

package/dist/LinearMafRenderer/makeImageData.js.map CHANGED Viewed

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package/dist/LinearMafRenderer/rendering/features.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
 import { Feature } from '@jbrowse/core/util';
 import type { GenomicRegion, RenderingContext } from './types';
 export declare function processFeatureAlignment(feature: Feature, region: GenomicRegion, bpPerPx: number, sampleToRowMap: Map<string, number>, renderingContext: RenderingContext): void;
-export declare function processFeatureInsertions(feature: Feature, region: GenomicRegion, bpPerPx: number, sampleToRowMap: Map<string, number>, renderingContext: RenderingContext): void;

package/dist/LinearMafRenderer/rendering/features.js CHANGED Viewed

@@ -17,22 +17,9 @@ export function processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap
         const alignment = originalAlignment.toLowerCase();
         const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
         renderGaps(renderingContext, alignment, referenceSeq, leftPx, rowTop);
-        renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row, alignmentData.start, alignmentData.chr);
+        renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop);
         renderMismatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row, alignmentData.start, alignmentData.chr);
         renderText(renderingContext, alignment, originalAlignment, referenceSeq, leftPx, rowTop);
-    }
-}
-export function processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext) {
-    const [leftPx] = featureSpanPx(feature, region, bpPerPx);
-    const alignments = feature.get('alignments');
-    const referenceSeq = feature.get('seq').toLowerCase();
-    for (const [sampleId, alignmentData] of Object.entries(alignments)) {
-        const row = sampleToRowMap.get(sampleId);
-        if (row === undefined) {
-            continue;
-        }
-        const alignment = alignmentData.seq.toLowerCase();
-        const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
         renderInsertions(renderingContext, alignment, referenceSeq, leftPx, rowTop, bpPerPx, row, alignmentData.start, alignmentData.chr);
     }
 }

package/dist/LinearMafRenderer/rendering/features.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/insertions.js CHANGED Viewed

@@ -1,10 +1,9 @@
 import { measureText } from '@jbrowse/core/util';
-import { fillRect, getCharWidthHeight } from '../util';
+import { fillRect } from '../util';
 import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
 import { CHAR_SIZE_WIDTH, HIGH_BP_PER_PX_THRESHOLD, HIGH_ZOOM_THRESHOLD, INSERTION_BORDER_HEIGHT, INSERTION_BORDER_WIDTH, INSERTION_LINE_WIDTH, INSERTION_PADDING, LARGE_INSERTION_THRESHOLD, MIN_ROW_HEIGHT_FOR_BORDERS, } from './types';
 export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, alignmentStart, chr) {
-    const { ctx, scale, h, canvasWidth, rowHeight } = context;
-    const { charHeight } = getCharWidthHeight();
+    const { ctx, scale, h, canvasWidth, rowHeight, charHeight } = context;
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
         let insertionSequence = '';
         while (seq[i] === '-') {
@@ -50,18 +49,20 @@ export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerP
                 actualXPos = xPos;
                 actualWidth = INSERTION_LINE_WIDTH;
                 fillRect(ctx, actualXPos, rowTop, actualWidth, h, canvasWidth, 'purple');
+                // Always use a wider hit box for spatial index, even if visual is 1px
+                const hitBoxPadding = 2;
+                actualXPos = xPos - hitBoxPadding;
+                actualWidth = INSERTION_LINE_WIDTH + 2 * hitBoxPadding;
                 if (bpPerPx < HIGH_ZOOM_THRESHOLD &&
                     rowHeight > MIN_ROW_HEIGHT_FOR_BORDERS) {
                     // Add horizontal borders for visibility at high zoom
-                    // Note: borders extend the effective clickable area
-                    actualXPos = xPos - INSERTION_BORDER_WIDTH;
-                    actualWidth = INSERTION_BORDER_HEIGHT;
                     fillRect(ctx, xPos - INSERTION_BORDER_WIDTH, rowTop, INSERTION_BORDER_HEIGHT, INSERTION_LINE_WIDTH, canvasWidth);
                     fillRect(ctx, xPos - INSERTION_BORDER_WIDTH, rowTop + h - INSERTION_LINE_WIDTH, INSERTION_BORDER_HEIGHT, INSERTION_LINE_WIDTH, canvasWidth);
                 }
             }
             // Add insertion to spatial index with actual rendered dimensions
             // Insertions always bypass distance filter
+            const isLargeInsertion = insertionSequence.length > LARGE_INSERTION_THRESHOLD;
             if (shouldAddToSpatialIndex(actualXPos, context, true)) {
                 addToSpatialIndex(context, actualXPos, rowTop, actualXPos + actualWidth, rowTop + context.h, {
                     pos: genomicOffset + alignmentStart,
@@ -69,6 +70,7 @@ export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerP
                     base: insertionSequence,
                     sampleId,
                     isInsertion: true,
+                    isLargeInsertion,
                 });
             }
         }

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package/dist/LinearMafRenderer/rendering/matches.d.ts CHANGED Viewed

@@ -1,2 +1,2 @@
 import type { RenderingContext } from './types';
-export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;
+export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number): void;

package/dist/LinearMafRenderer/rendering/matches.js CHANGED Viewed

@@ -1,7 +1,6 @@
 import { fillRect } from '../util';
-import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
 import { GAP_STROKE_OFFSET } from './types';
-export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
+export function renderMatches(context, alignment, seq, leftPx, rowTop) {
     if (context.showAllLetters) {
         return;
     }
@@ -12,20 +11,9 @@ export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId,
         if (seq[i] !== '-') {
             // Only process non-gap positions in reference
             const currentChar = alignment[i];
-            const xPos = leftPx + scale * genomicOffset;
-            if (seq[i] === currentChar &&
-                currentChar !== '-' &&
-                currentChar !== ' ') {
+            if (seq[i] === currentChar && currentChar !== ' ') {
+                const xPos = leftPx + scale * genomicOffset;
                 fillRect(ctx, xPos, rowTop, scale + GAP_STROKE_OFFSET, h, canvasWidth);
-                // Add to spatial index if distance filter allows
-                if (shouldAddToSpatialIndex(xPos, context)) {
-                    addToSpatialIndex(context, xPos, rowTop, xPos + context.scale + GAP_STROKE_OFFSET, rowTop + context.h, {
-                        pos: genomicOffset + alignmentStart,
-                        chr,
-                        base: currentChar || '',
-                        sampleId,
-                    });
-                }
             }
             genomicOffset++;
         }

package/dist/LinearMafRenderer/rendering/matches.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/spatialIndex.js CHANGED Viewed

@@ -8,8 +8,14 @@ export function createRenderedBaseCoords(xPos, rowTop, context) {
     };
 }
 export function shouldAddToSpatialIndex(xPos, context, bypassDistanceFilter = false) {
-    return (bypassDistanceFilter ||
-        Math.abs(xPos - context.lastInsertedX) > MIN_X_DISTANCE);
+    if (bypassDistanceFilter) {
+        return true;
+    }
+    // Zoom-aware distance threshold: scale threshold based on zoom level
+    // At high zoom (small bpPerPx), use smaller threshold for more precision
+    // At low zoom (large bpPerPx), use larger threshold to reduce index size
+    return (Math.abs(xPos - context.lastInsertedX) >
+        MIN_X_DISTANCE * Math.max(1, context.bpPerPx));
 }
 export function addToSpatialIndex(context, minX, minY, maxX, maxY, renderedBase) {
     context.spatialIndex.push(renderedBase);

package/dist/LinearMafRenderer/rendering/spatialIndex.js.map CHANGED Viewed

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