jbrowse-plugin-mafviewer 1.4.3 → 1.4.6

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

@@ -1 +1 @@
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package/dist/LinearMafRenderer/configSchema.d.ts

@@ -1,7 +1,2 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    baseColor: {
-        type: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/LinearMafRenderer/configSchema.js

@@ -3,12 +3,7 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
  * #config LinearMafRenderer
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configSchema = ConfigurationSchema('LinearMafRenderer', {
-    baseColor: {
-        type: 'color',
-        defaultValue: 'lightgrey',
-    },
-}, {
+const configSchema = ConfigurationSchema('LinearMafRenderer', {}, {
     /**
      * #baseConfiguration
      */

package/dist/LinearMafRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB;IACE,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,YAAY,EAAE,WAAW;KAC1B;CACF,EACD;IACE;;OAEG;IACH,eAAe,EAAE,IAAI;CACtB,CACF,CAAA;AAED,eAAe,YAAY,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB,EAAE,EACF;IACE;;OAEG;IACH,eAAe,EAAE,IAAI;CACtB,CACF,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/LinearMafRenderer/makeImageData.js

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/makeImageData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AAErD,OAAO,QAAQ,MAAM,UAAU,CAAA;AAE/B,OAAO,EACL,WAAW,EAGX,uBAAuB,GACxB,MAAM,aAAa,CAAA;AACpB,OAAO,EAAE,kBAAkB,EAAE,eAAe,EAAE,kBAAkB,EAAE,MAAM,QAAQ,CAAA;AAahF,MAAM,UAAU,aAAa,CAAC,EAC5B,GAAG,EACH,UAAU,GAIX;IACC,MAAM,EACJ,OAAO,EACP,OAAO,EACP,SAAS,EACT,cAAc,EACd,KAAK,EAAE,WAAW,EAClB,iBAAiB,EACjB,OAAO,EACP,aAAa,EACb,QAAQ,EACR,eAAe,GAChB,GAAG,UAAU,CAAA;IAEd,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,WAAW,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;IACzD,MAAM,CAAC,GAAG,SAAS,GAAG,aAAa,CAAA;IACnC,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,eAAe,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,eAAe,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAA;IACjD,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,CAAC,GAAG,OAAO,CAAA;IACzB,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;IACjB,MAAM,MAAM,GAAG,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;IAClC,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,kBAAkB,EAAE,CAAA;IAEtD,GAAG,CAAC,IAAI,GAAG,WAAW,CAAA;IAEtB,MAAM,gBAAgB,GAAqB;QACzC,GAAG;QACH,KAAK;QACL,OAAO;QACP,WAAW;QACX,SAAS;QACT,CAAC;QACD,GAAG;QACH,MAAM;QACN,YAAY;QACZ,eAAe;QACf,cAAc;QACd,iBAAiB;QACjB,eAAe;QACf,SAAS;QACT,UAAU;QACV,YAAY,EAAE,EAAE;QAChB,kBAAkB,EAAE,EAAE;QACtB,aAAa,EAAE,CAAC,QAAQ,EAAE,wDAAwD;KACnF,CAAA;IAED,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,uBAAuB,CACrB,OAAO,EACP,MAAM,EACN,OAAO,EACP,cAAc,EACd,gBAAgB,CACjB,CAAA;IACH,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,gBAAgB,CAAC,YAAY,CAAC,MAAM,IAAI,CAAC,CAAC,CAAA;IACxE,IAAI,gBAAgB,CAAC,YAAY,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC/C,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1B,CAAC;SAAM,CAAC;QACN,KACE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,gBAAgB,CAAC,kBAAkB,CAAC,MAAM,EACzD,CAAC,GAAG,CAAC,EACL,CAAC,IAAI,CAAC,EACN,CAAC;YACD,QAAQ,CAAC,GAAG,CACV,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,CAAE,EACvC,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,GAAG,CAAC,CAAE,EAC3C,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,GAAG,CAAC,CAAC,EAC1C,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,GAAG,CAAC,CAAC,CAC3C,CAAA;QACH,CAAC;IACH,CAAC;IACD,QAAQ,CAAC,MAAM,EAAE,CAAA;IACjB,OAAO;QACL,QAAQ,EAAE,QAAQ,CAAC,IAAI;QACvB,KAAK,EAAE,gBAAgB,CAAC,YAAY;QACpC,OAAO;KACR,CAAA;AACH,CAAC"}

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

@@ -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

@@ -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

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/insertions.d.ts

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

package/dist/LinearMafRenderer/rendering/insertions.js

@@ -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();
+export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, rowIndex, alignmentStart, chr) {
+    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] === '-') {
@@ -50,25 +49,28 @@ 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,
                     chr,
                     base: insertionSequence,
-                    sampleId,
+                    rowIndex,
                     isInsertion: true,
+                    isLargeInsertion,
                 });
             }
         }

package/dist/LinearMafRenderer/rendering/insertions.js.map

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

@@ -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

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"matches.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/matches.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAI3C,MAAM,UAAU,aAAa,CAC3B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc;IAEd,IAAI,OAAO,CAAC,cAAc,EAAE,CAAC;QAC3B,OAAM;IACR,CAAC;IAED,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;IAC9C,GAAG,CAAC,SAAS,GAAG,WAAW,CAAA;IAE3B,sDAAsD;IACtD,KACE,IAAI,CAAC,GAAG,CAAC,EAAE,aAAa,GAAG,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC,MAAM,EAC1D,CAAC,GAAG,SAAS,EACb,CAAC,EAAE,EACH,CAAC;QACD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,8CAA8C;YAC9C,MAAM,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;YAChC,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,WAAW,IAAI,WAAW,KAAK,GAAG,EAAE,CAAC;gBAClD,MAAM,IAAI,GAAG,MAAM,GAAG,KAAK,GAAG,aAAa,CAAA;gBAC3C,QAAQ,CAAC,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,GAAG,iBAAiB,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;YACxE,CAAC;YACD,aAAa,EAAE,CAAA;QACjB,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/LinearMafRenderer/rendering/mismatches.d.ts

@@ -10,4 +10,4 @@ import type { RenderingContext } from './types';
  * @param alignmentStart - Start position of the alignment
  * @param chr - Chromosome/sequence name
  */
-export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;
+export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, rowIndex: number, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/mismatches.js

@@ -12,7 +12,7 @@ import { GAP_STROKE_OFFSET } from './types';
  * @param alignmentStart - Start position of the alignment
  * @param chr - Chromosome/sequence name
  */
-export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
+export function renderMismatches(context, alignment, seq, leftPx, rowTop, rowIndex, alignmentStart, chr) {
     const { ctx, scale, h, canvasWidth, showAllLetters, mismatchRendering, colorForBase, } = context;
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
         const currentChar = alignment[i];
@@ -30,7 +30,7 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
                             pos: genomicOffset + alignmentStart,
                             chr,
                             base: currentChar,
-                            sampleId,
+                            rowIndex,
                         });
                     }
                 }
@@ -45,7 +45,7 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
                             pos: genomicOffset + alignmentStart,
                             chr,
                             base: currentChar,
-                            sampleId,
+                            rowIndex,
                         });
                     }
                 }

package/dist/LinearMafRenderer/rendering/spatialIndex.js

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"spatialIndex.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/spatialIndex.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,cAAc,EAAE,MAAM,SAAS,CAAA;AAI3D,MAAM,UAAU,wBAAwB,CACtC,IAAY,EACZ,MAAc,EACd,OAAyB;IAEzB,OAAO;QACL,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,MAAM;QACZ,IAAI,EAAE,IAAI,GAAG,OAAO,CAAC,KAAK,GAAG,iBAAiB;QAC9C,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC;KACzB,CAAA;AACH,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,IAAY,EACZ,OAAyB,EACzB,oBAAoB,GAAG,KAAK;IAE5B,IAAI,oBAAoB,EAAE,CAAC;QACzB,OAAO,IAAI,CAAA;IACb,CAAC;IAED,qEAAqE;IACrE,yEAAyE;IACzE,yEAAyE;IACzE,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC;QACtC,cAAc,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,OAAO,CAAC,OAAO,CAAC,CAC9C,CAAA;AACH,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,OAAyB,EACzB,IAAY,EACZ,IAAY,EACZ,IAAY,EACZ,IAAY,EACZ,YAA0B;IAE1B,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACvC,OAAO,CAAC,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAA;IACvD,OAAO,CAAC,aAAa,GAAG,IAAI,CAAA;AAC9B,CAAC"}

package/dist/LinearMafRenderer/rendering/text.js

@@ -1,4 +1,3 @@
-import { getCharWidthHeight } from '../util';
 import { CHAR_SIZE_WIDTH, VERTICAL_TEXT_OFFSET } from './types';
 function getLetter(a, showAsUpperCase) {
     return showAsUpperCase ? a.toUpperCase() : a;
@@ -14,8 +13,7 @@ function getLetter(a, showAsUpperCase) {
  * @param rowTop - Top pixel position of the row
  */
 export function renderText(context, alignment, origAlignment, seq, leftPx, rowTop) {
-    const { ctx, scale, hp2, rowHeight, showAllLetters, mismatchRendering, contrastForBase, showAsUpperCase, } = context;
-    const { charHeight } = getCharWidthHeight();
+    const { ctx, scale, hp2, rowHeight, showAllLetters, mismatchRendering, contrastForBase, showAsUpperCase, charHeight, } = context;
     // Render text labels when zoomed in enough and row is tall enough
     if (scale >= CHAR_SIZE_WIDTH) {
         for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {

package/dist/LinearMafRenderer/rendering/text.js.map

@@ -1 +1 @@
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+{"version":3,"file":"text.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/text.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,oBAAoB,EAAE,MAAM,SAAS,CAAA;AAI/D,SAAS,SAAS,CAAC,CAAS,EAAE,eAAwB;IACpD,OAAO,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,UAAU,CACxB,OAAyB,EACzB,SAAiB,EACjB,aAAqB,EACrB,GAAW,EACX,MAAc,EACd,MAAc;IAEd,MAAM,EACJ,GAAG,EACH,KAAK,EACL,GAAG,EACH,SAAS,EACT,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,eAAe,EACf,UAAU,GACX,GAAG,OAAO,CAAA;IAEX,kEAAkE;IAClE,IAAI,KAAK,IAAI,eAAe,EAAE,CAAC;QAC7B,KACE,IAAI,CAAC,GAAG,CAAC,EAAE,aAAa,GAAG,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC,MAAM,EAC1D,CAAC,GAAG,SAAS,EACb,CAAC,EAAE,EACH,CAAC;YACD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;gBACnB,8CAA8C;gBAC9C,MAAM,IAAI,GAAG,MAAM,GAAG,KAAK,GAAG,aAAa,CAAA;gBAC3C,MAAM,UAAU,GAAG,CAAC,KAAK,GAAG,eAAe,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA,CAAC,iCAAiC;gBACtF,MAAM,WAAW,GAAG,SAAS,CAAC,CAAC,CAAE,CAAA;gBACjC,iEAAiE;gBACjE,IAAI,CAAC,cAAc,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,WAAW,CAAC,IAAI,WAAW,KAAK,GAAG,EAAE,CAAC;oBACtE,GAAG,CAAC,SAAS,GAAG,iBAAiB;wBAC/B,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,OAAO,CAAC,CAAC,wCAAwC;wBACpF,CAAC,CAAC,OAAO,CAAA;oBACX,IAAI,SAAS,GAAG,UAAU,EAAE,CAAC;wBAC3B,oCAAoC;wBACpC,GAAG,CAAC,QAAQ,CACV,SAAS,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,EAAE,EAAE,eAAe,CAAC,EAClD,IAAI,GAAG,UAAU,EACjB,GAAG,GAAG,MAAM,GAAG,oBAAoB,CACpC,CAAA;oBACH,CAAC;gBACH,CAAC;gBACD,aAAa,EAAE,CAAA;YACjB,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/LinearMafRenderer/rendering/types.d.ts

@@ -11,10 +11,7 @@ export declare const MIN_ROW_HEIGHT_FOR_BORDERS = 5;
 export declare const HIGH_BP_PER_PX_THRESHOLD = 10;
 export declare const INSERTION_BORDER_HEIGHT = 5;
 export declare const MIN_X_DISTANCE = 0.5;
-export interface Sample {
-    id: string;
-    color?: string;
-}
+export type { Sample } from '../../LinearMafDisplay/types';
 export interface GenomicRegion {
     start: number;
     end: number;
@@ -24,8 +21,9 @@ export interface RenderedBase {
     pos: number;
     chr: string;
     base: string;
-    sampleId: number;
+    rowIndex: number;
     isInsertion?: boolean;
+    isLargeInsertion?: boolean;
 }
 /**
  * Shared rendering context containing all necessary parameters for rendering operations
@@ -33,6 +31,7 @@ export interface RenderedBase {
 export interface RenderingContext {
     ctx: CanvasRenderingContext2D;
     scale: number;
+    bpPerPx: number;
     canvasWidth: number;
     rowHeight: number;
     h: number;
@@ -43,6 +42,8 @@ export interface RenderingContext {
     showAllLetters: boolean;
     mismatchRendering: boolean;
     showAsUpperCase: boolean;
+    charWidth: number;
+    charHeight: number;
     spatialIndex: RenderedBase[];
     spatialIndexCoords: number[];
     lastInsertedX: number;

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
 import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { getRoot } from '@jbrowse/mobx-state-tree';
 import { Button, FormControl, FormControlLabel, FormLabel, Paper, Radio, RadioGroup, TextField, } from '@mui/material';
-import { getRoot } from 'mobx-state-tree';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     textbox: {

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

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package/dist/MafAddTrackWorkflow/index.js

@@ -1,5 +1,5 @@
 import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 import MultiMAFWidget from './AddTrackWorkflow';
 export default function MafAddTrackWorkflowF(pluginManager) {
     pluginManager.addAddTrackWorkflowType(() => new AddTrackWorkflowType({

package/dist/MafAddTrackWorkflow/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,qCAAqC,CAAA;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,oBAAoB,CAAC,aAA4B;IACvE,aAAa,CAAC,uBAAuB,CACnC,GAAG,EAAE,CACH,IAAI,oBAAoB,CAAC;QACvB,IAAI,EAAE,WAAW;QACjB,cAAc,EAAE,cAAc;QAC9B,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;KAC5B,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafGetSequences/MafGetSequences.d.ts

@@ -12,5 +12,6 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
         headers?: Record<string, string>;
         regions: Region[];
         showAllLetters: boolean;
+        includeInsertions?: boolean;
     }, rpcDriverClassName: string): Promise<string[]>;
 }

package/dist/MafGetSequences/MafGetSequences.js

@@ -6,7 +6,7 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
     name = 'MafGetSequences';
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { samples, regions, adapterConfig, sessionId, showAllLetters } = deserializedArgs;
+        const { samples, regions, adapterConfig, sessionId, showAllLetters, includeInsertions, } = deserializedArgs;
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
         const features = await firstValueFrom(dataAdapter.getFeatures(regions[0], deserializedArgs).pipe(toArray()));
         return processFeaturesToFasta({
@@ -14,6 +14,7 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
             samples,
             regions,
             showAllLetters,
+            includeInsertions,
         });
     }
 }

package/dist/MafGetSequences/MafGetSequences.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MafGetSequences.js","sourceRoot":"","sources":["../../src/MafGetSequences/MafGetSequences.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,wCAAwC,MAAM,8EAA8E,CAAA;AACnI,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAO3D,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,wCAAwC;IACnF,IAAI,GAAG,iBAAiB,CAAA;IAExB,KAAK,CAAC,OAAO,CACX,IASC,EACD,kBAA0B;QAE1B,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACtD,IAAI,EACJ,kBAAkB,CACnB,CAAA;QACD,MAAM,EACJ,OAAO,EACP,OAAO,EACP,aAAa,EACb,SAAS,EACT,cAAc,EACd,iBAAiB,GAClB,GAAG,gBAAgB,CAAA;QACpB,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,WAAW,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAE,EAAE,gBAAgB,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACvE,CAAA;QACD,OAAO,sBAAsB,CAAC;YAC5B,QAAQ,EAAE,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;YACjD,OAAO;YACP,OAAO;YACP,cAAc;YACd,iBAAiB;SAClB,CAAC,CAAA;IACJ,CAAC;CACF"}

package/dist/MafSequenceWidget/LabelsCanvas.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import type { Sample } from '../LinearMafDisplay/types';
+interface LabelsCanvasProps {
+    samples: Sample[];
+    maxLabelLength: number;
+}
+export default function LabelsCanvas({ samples, maxLabelLength, }: LabelsCanvasProps): React.JSX.Element;
+export {};

package/dist/MafSequenceWidget/LabelsCanvas.js

@@ -0,0 +1,37 @@
+import React, { useEffect, useRef } from 'react';
+import { useTheme } from '@mui/material';
+import { CHAR_WIDTH, FONT, LABEL_PADDING, ROW_HEIGHT } from './constants';
+export default function LabelsCanvas({ samples, maxLabelLength, }) {
+    const theme = useTheme();
+    const canvasRef = useRef(null);
+    const labelWidth = maxLabelLength * CHAR_WIDTH + LABEL_PADDING;
+    const canvasHeight = samples.length * ROW_HEIGHT;
+    useEffect(() => {
+        const canvas = canvasRef.current;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        const dpr = window.devicePixelRatio || 1;
+        canvas.width = labelWidth * dpr;
+        canvas.height = canvasHeight * dpr;
+        canvas.style.width = `${labelWidth}px`;
+        canvas.style.height = `${canvasHeight}px`;
+        ctx.scale(dpr, dpr);
+        ctx.fillStyle = theme.palette.background.paper;
+        ctx.fillRect(0, 0, labelWidth, canvasHeight);
+        ctx.font = FONT;
+        ctx.textBaseline = 'top';
+        for (let rowIdx = 0; rowIdx < samples.length; rowIdx++) {
+            const sample = samples[rowIdx];
+            const y = rowIdx * ROW_HEIGHT;
+            ctx.fillStyle = theme.palette.text.secondary;
+            ctx.fillText(sample.label ?? sample.id, 2, y + 2);
+        }
+    }, [samples, labelWidth, canvasHeight, theme]);
+    return React.createElement("canvas", { ref: canvasRef, style: { display: 'block' } });
+}
+//# sourceMappingURL=LabelsCanvas.js.map

package/dist/MafSequenceWidget/LabelsCanvas.js.map

@@ -0,0 +1 @@
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package/dist/MafSequenceWidget/MafSequenceHoverHighlight.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const MafSequenceHoverHighlight: ({ model, }: {
+    model: LinearGenomeViewModel;
+}) => React.JSX.Element | null;
+export default MafSequenceHoverHighlight;

package/dist/MafSequenceWidget/MafSequenceHoverHighlight.js

@@ -0,0 +1,52 @@
+import React from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { colord } from '@jbrowse/core/util/colord';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    highlight: {
+        height: '100%',
+        position: 'absolute',
+        background: colord(theme.palette.primary.main).alpha(0.4).toRgbString(),
+        borderLeft: `2px solid ${theme.palette.primary.main}`,
+        borderRight: `2px solid ${theme.palette.primary.main}`,
+        pointerEvents: 'none',
+        zIndex: 10,
+    },
+}));
+const MafSequenceHoverHighlight = observer(function MafSequenceHoverHighlight({ model, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { assemblyManager } = session;
+    // Find MafSequenceWidget instances that are connected to this view
+    const widgets = 'widgets' in session ? session.widgets : undefined;
+    if (!widgets) {
+        return null;
+    }
+    const highlights = [];
+    for (const [, widget] of widgets) {
+        const w = widget;
+        if (w.type === 'MafSequenceWidget' && w.connectedViewId === model.id) {
+            const mafWidget = widget;
+            const { hoverHighlight } = mafWidget;
+            if (hoverHighlight) {
+                const { refName, start, end, assemblyName } = hoverHighlight;
+                const assembly = assemblyManager.get(assemblyName);
+                const canonicalRefName = assembly?.getCanonicalRefName(refName) ?? refName;
+                const startPx = model.bpToPx({
+                    refName: canonicalRefName,
+                    coord: start,
+                });
+                const endPx = model.bpToPx({ refName: canonicalRefName, coord: end });
+                if (startPx && endPx) {
+                    const left = Math.min(startPx.offsetPx, endPx.offsetPx) - model.offsetPx;
+                    const width = Math.max(Math.abs(endPx.offsetPx - startPx.offsetPx), 3);
+                    highlights.push(React.createElement("div", { key: `maf-hover-${mafWidget.id}`, className: classes.highlight, style: { left, width } }));
+                }
+            }
+        }
+    }
+    return React.createElement(React.Fragment, null, highlights);
+});
+export default MafSequenceHoverHighlight;
+//# sourceMappingURL=MafSequenceHoverHighlight.js.map