jbrowse-plugin-mafviewer 1.3.1 → 1.3.2

package/dist/LinearMafRenderer/makeImageData.js

@@ -1,9 +1,7 @@
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { featureSpanPx, measureText } from '@jbrowse/core/util';
-import { fillRect, getCharWidthHeight, getColorBaseMap, getContrastBaseMap, } from './util';
-function getLetter(a, showAsUpperCase) {
-    return showAsUpperCase ? a.toUpperCase() : a;
-}
+import RBush from 'rbush';
+import { FONT_CONFIG, processFeatureAlignment, processFeatureInsertions, } from './rendering';
+import { 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];
@@ -12,154 +10,38 @@ export function makeImageData({ ctx, renderArgs, }) {
     const theme = createJBrowseTheme(configTheme);
     const colorForBase = getColorBaseMap(theme);
     const contrastForBase = getContrastBaseMap(theme);
-    const { charHeight } = getCharWidthHeight();
     const sampleToRowMap = new Map(samples.map((s, i) => [s.id, i]));
     const scale = 1 / bpPerPx;
-    const f = 0.4;
-    const h2 = rowHeight / 2;
     const hp2 = h / 2;
     const offset = (rowHeight - h) / 2;
-    // sample as alignments
-    ctx.font = 'bold 10px Courier New,monospace';
+    ctx.font = FONT_CONFIG;
+    const renderingContext = {
+        ctx,
+        scale,
+        canvasWidth,
+        rowHeight,
+        h,
+        hp2,
+        offset,
+        colorForBase,
+        contrastForBase,
+        showAllLetters,
+        mismatchRendering,
+        showAsUpperCase,
+        spatialIndex: new RBush(),
+        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()) {
-        const [leftPx] = featureSpanPx(feature, region, bpPerPx);
-        const vals = feature.get('alignments');
-        const seq = feature.get('seq').toLowerCase();
-        const r = Object.entries(vals);
-        for (const [sample, val] of r) {
-            const origAlignment = val.seq;
-            const alignment = origAlignment.toLowerCase();
-            const row = sampleToRowMap.get(sample);
-            if (row === undefined) {
-                continue;
-            }
-            const t = rowHeight * row;
-            const t2 = offset + t;
-            // gaps
-            ctx.beginPath();
-            ctx.fillStyle = 'black';
-            for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-                if (seq[i] !== '-') {
-                    if (alignment[i] === '-') {
-                        const l = leftPx + scale * o;
-                        ctx.moveTo(l, t + h2);
-                        ctx.lineTo(l + scale + f, t + h2);
-                    }
-                    o++;
-                }
-            }
-            ctx.stroke();
-            if (!showAllLetters) {
-                // matches
-                ctx.fillStyle = 'lightgrey';
-                for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-                    if (seq[i] !== '-') {
-                        const c = alignment[i];
-                        const l = leftPx + scale * o;
-                        if (seq[i] === c && c !== '-' && c !== ' ') {
-                            fillRect(ctx, l, t2, scale + f, h, canvasWidth);
-                        }
-                        o++;
-                    }
-                }
-            }
-            // mismatches
-            for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-                const c = alignment[i];
-                if (seq[i] !== '-') {
-                    if (c !== '-') {
-                        const l = leftPx + scale * o;
-                        if (seq[i] !== c && c !== ' ') {
-                            fillRect(ctx, l, t2, scale + f, h, canvasWidth, mismatchRendering
-                                ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                                    (colorForBase[c] ?? 'black')
-                                : 'orange');
-                        }
-                        else if (showAllLetters) {
-                            fillRect(ctx, l, t2, scale + f, h, canvasWidth, mismatchRendering
-                                ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                                    (colorForBase[c] ?? 'black')
-                                : 'lightblue');
-                        }
-                    }
-                    o++;
-                }
-            }
-            // font
-            const charSizeW = 10;
-            if (scale >= charSizeW) {
-                for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-                    if (seq[i] !== '-') {
-                        const l = leftPx + scale * o;
-                        const offset = (scale - charSizeW) / 2 + 1;
-                        const c = alignment[i];
-                        if ((showAllLetters || seq[i] !== c) && c !== '-') {
-                            ctx.fillStyle = mismatchRendering
-                                ? (contrastForBase[c] ?? 'white')
-                                : 'black';
-                            if (rowHeight > charHeight) {
-                                ctx.fillText(getLetter(origAlignment[i] || '', showAsUpperCase), l + offset, hp2 + t + 3);
-                            }
-                        }
-                        o++;
-                    }
-                }
-            }
-        }
+        processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap, renderingContext);
     }
-    // second pass for insertions, has slightly improved look since the
-    // insertions are always 'on top' of the other features
+    // Second pass: render insertions on top
     for (const feature of features.values()) {
-        const [leftPx] = featureSpanPx(feature, region, bpPerPx);
-        const vals = feature.get('alignments');
-        const seq = feature.get('seq').toLowerCase();
-        for (const [sample, val] of Object.entries(vals)) {
-            const origAlignment = val.seq;
-            const alignment = origAlignment.toLowerCase();
-            const row = sampleToRowMap.get(sample);
-            if (row === undefined) {
-                continue;
-            }
-            const t = rowHeight * row;
-            const t2 = offset + t;
-            for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-                let ins = '';
-                while (seq[i] === '-') {
-                    if (alignment[i] !== '-' && alignment[i] !== ' ') {
-                        ins += alignment[i];
-                    }
-                    i++;
-                }
-                if (ins.length > 0) {
-                    const l = leftPx + scale * o - 1;
-                    if (ins.length > 10) {
-                        const txt = `${ins.length}`;
-                        if (bpPerPx > 10) {
-                            fillRect(ctx, l - 1, t2, 2, h, canvasWidth, 'purple');
-                        }
-                        else if (h > charHeight) {
-                            const rwidth = measureText(txt, 10);
-                            const padding = 2;
-                            fillRect(ctx, l - rwidth / 2 - padding, t2, rwidth + 2 * padding, h, canvasWidth, 'purple');
-                            ctx.fillStyle = 'white';
-                            ctx.fillText(txt, l - rwidth / 2, t + h);
-                        }
-                        else {
-                            const padding = 2;
-                            fillRect(ctx, l - padding, t2, 2 * padding, h, canvasWidth, 'purple');
-                        }
-                    }
-                    else {
-                        fillRect(ctx, l, t2, 1, h, canvasWidth, 'purple');
-                        if (bpPerPx < 0.2 && rowHeight > 5) {
-                            fillRect(ctx, l - 2, t2, 5, 1, canvasWidth);
-                            fillRect(ctx, l - 2, t2 + h - 1, 5, 1, canvasWidth);
-                        }
-                    }
-                }
-                o++;
-            }
-        }
+        processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext);
     }
+    // Return serialized RBush spatial index
+    return {
+        rbush: renderingContext.spatialIndex.toJSON(),
+    };
 }
 //# sourceMappingURL=makeImageData.js.map

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,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EACL,WAAW,EAIX,uBAAuB,EACvB,wBAAwB,GACzB,MAAM,aAAa,CAAA;AACpB,OAAO,EAAE,eAAe,EAAE,kBAAkB,EAAE,MAAM,QAAQ,CAAA;AAa5D,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;IAElC,GAAG,CAAC,IAAI,GAAG,WAAW,CAAA;IAEtB,MAAM,gBAAgB,GAAqB;QACzC,GAAG;QACH,KAAK;QACL,WAAW;QACX,SAAS;QACT,CAAC;QACD,GAAG;QACH,MAAM;QACN,YAAY;QACZ,eAAe;QACf,cAAc;QACd,iBAAiB;QACjB,eAAe;QACf,YAAY,EAAE,IAAI,KAAK,EAAgB;QACvC,aAAa,EAAE,CAAC,QAAQ,EAAE,wDAAwD;KACnF,CAAA;IAED,kEAAkE;IAClE,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;IAED,wCAAwC;IACxC,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,wBAAwB,CACtB,OAAO,EACP,MAAM,EACN,OAAO,EACP,cAAc,EACd,gBAAgB,CACjB,CAAA;IACH,CAAC;IAED,wCAAwC;IACxC,OAAO;QACL,KAAK,EAAE,gBAAgB,CAAC,YAAY,CAAC,MAAM,EAAE;KAC9C,CAAA;AACH,CAAC"}

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

@@ -0,0 +1,21 @@
+import { Feature } from '@jbrowse/core/util';
+import type { GenomicRegion, RenderingContext } from './types';
+/**
+ * Processes alignment data for a single feature, rendering gaps, matches, mismatches, and text
+ * @param feature - JBrowse feature containing alignment data
+ * @param region - Genomic region being rendered
+ * @param bpPerPx - Base pairs per pixel (zoom level)
+ * @param sampleToRowMap - Maps sample IDs to row indices
+ * @param renderingContext - Shared rendering parameters
+ */
+export declare function processFeatureAlignment(feature: Feature, region: GenomicRegion, bpPerPx: number, sampleToRowMap: Map<string, number>, renderingContext: RenderingContext): void;
+/**
+ * Processes insertion data for a single feature in a separate pass
+ * Insertions are rendered on top to ensure visibility
+ * @param feature - JBrowse feature containing alignment data
+ * @param region - Genomic region being rendered
+ * @param bpPerPx - Base pairs per pixel (zoom level)
+ * @param sampleToRowMap - Maps sample IDs to row indices
+ * @param renderingContext - Shared rendering parameters
+ */
+export declare function processFeatureInsertions(feature: Feature, region: GenomicRegion, bpPerPx: number, sampleToRowMap: Map<string, number>, renderingContext: RenderingContext): void;

package/dist/LinearMafRenderer/rendering/features.js

@@ -0,0 +1,58 @@
+import { featureSpanPx } from '@jbrowse/core/util';
+import { renderGaps } from './gaps';
+import { renderInsertions } from './insertions';
+import { renderMatches } from './matches';
+import { renderMismatches } from './mismatches';
+import { renderText } from './text';
+/**
+ * Processes alignment data for a single feature, rendering gaps, matches, mismatches, and text
+ * @param feature - JBrowse feature containing alignment data
+ * @param region - Genomic region being rendered
+ * @param bpPerPx - Base pairs per pixel (zoom level)
+ * @param sampleToRowMap - Maps sample IDs to row indices
+ * @param renderingContext - Shared rendering parameters
+ */
+export function processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap, renderingContext) {
+    const [leftPx] = featureSpanPx(feature, region, bpPerPx);
+    const alignments = feature.get('alignments');
+    const referenceSeq = feature.get('seq').toLowerCase();
+    const featureId = feature.id() || `feature_${feature.get('start')}_${feature.get('end')}`;
+    for (const [sampleId, alignmentData] of Object.entries(alignments)) {
+        const row = sampleToRowMap.get(sampleId);
+        if (row === undefined) {
+            continue;
+        }
+        const originalAlignment = alignmentData.seq;
+        const alignment = originalAlignment.toLowerCase();
+        const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
+        renderGaps(renderingContext, alignment, referenceSeq, leftPx, rowTop, sampleId, featureId, alignmentData.start, alignmentData.chr);
+        renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, sampleId, featureId, alignmentData.start, alignmentData.chr);
+        renderMismatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, sampleId, featureId, alignmentData.start, alignmentData.chr);
+        renderText(renderingContext, alignment, originalAlignment, referenceSeq, leftPx, rowTop, sampleId, featureId);
+    }
+}
+/**
+ * Processes insertion data for a single feature in a separate pass
+ * Insertions are rendered on top to ensure visibility
+ * @param feature - JBrowse feature containing alignment data
+ * @param region - Genomic region being rendered
+ * @param bpPerPx - Base pairs per pixel (zoom level)
+ * @param sampleToRowMap - Maps sample IDs to row indices
+ * @param renderingContext - Shared rendering parameters
+ */
+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();
+    const featureId = feature.id() || `feature_${feature.get('start')}_${feature.get('end')}`;
+    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, sampleId, featureId, alignmentData.start, alignmentData.chr);
+    }
+}
+//# sourceMappingURL=features.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/rendering/gaps.d.ts

@@ -0,0 +1,12 @@
+import type { RenderingContext } from './types';
+/**
+ * Renders gap indicators (horizontal lines) where the alignment has deletions relative to reference
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export declare function renderGaps(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/gaps.js

@@ -0,0 +1,35 @@
+import { addToSpatialIndex, createRenderedBase, shouldAddToSpatialIndex, } from './spatialIndex';
+import { GAP_STROKE_OFFSET } from './types';
+/**
+ * Renders gap indicators (horizontal lines) where the alignment has deletions relative to reference
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export function renderGaps(context, alignment, seq, leftPx, rowTop, sampleId, featureId, alignmentStart, chr) {
+    const { ctx, scale } = context;
+    const h2 = context.rowHeight / 2;
+    ctx.beginPath();
+    ctx.fillStyle = 'black';
+    for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
+        if (seq[i] !== '-') {
+            if (alignment[i] === '-') {
+                const xPos = leftPx + scale * genomicOffset;
+                ctx.moveTo(xPos, rowTop + h2);
+                ctx.lineTo(xPos + scale + GAP_STROKE_OFFSET, rowTop + h2);
+                // Add to spatial index if distance filter allows
+                if (shouldAddToSpatialIndex(xPos, context)) {
+                    const renderedBase = createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, '-', false, false, true, false, featureId);
+                    addToSpatialIndex(context, renderedBase);
+                }
+            }
+            genomicOffset++;
+        }
+    }
+    ctx.stroke();
+}
+//# sourceMappingURL=gaps.js.map

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

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

@@ -0,0 +1,8 @@
+export * from './types';
+export * from './spatialIndex';
+export * from './gaps';
+export * from './matches';
+export * from './mismatches';
+export * from './text';
+export * from './insertions';
+export * from './features';

package/dist/LinearMafRenderer/rendering/index.js

@@ -0,0 +1,10 @@
+// Re-export all rendering modules
+export * from './types';
+export * from './spatialIndex';
+export * from './gaps';
+export * from './matches';
+export * from './mismatches';
+export * from './text';
+export * from './insertions';
+export * from './features';
+//# sourceMappingURL=index.js.map

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

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

@@ -0,0 +1,14 @@
+import type { RenderingContext } from './types';
+/**
+ * Renders insertion markers where the alignment has bases not present in reference
+ * Large insertions show count, small ones show as colored bars with optional borders
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param bpPerPx - Base pairs per pixel (zoom level)
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/insertions.js

@@ -0,0 +1,84 @@
+import { measureText } from '@jbrowse/core/util';
+import { fillRect, getCharWidthHeight } from '../util';
+import { addToSpatialIndex, createRenderedInsertion, 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';
+/**
+ * Renders insertion markers where the alignment has bases not present in reference
+ * Large insertions show count, small ones show as colored bars with optional borders
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param bpPerPx - Base pairs per pixel (zoom level)
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, featureId, alignmentStart, chr) {
+    const { ctx, scale, h, canvasWidth, rowHeight } = context;
+    const { charHeight } = getCharWidthHeight();
+    for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
+        let insertionSequence = '';
+        while (seq[i] === '-') {
+            if (alignment[i] !== '-' && alignment[i] !== ' ') {
+                insertionSequence += alignment[i];
+            }
+            i++;
+        }
+        if (insertionSequence.length > 0) {
+            // Found an insertion
+            const xPos = leftPx + scale * genomicOffset - INSERTION_LINE_WIDTH;
+            // Determine actual rendered width and position for spatial index
+            let actualXPos;
+            let actualWidth;
+            // Large insertions: show count instead of individual bases
+            if (insertionSequence.length > LARGE_INSERTION_THRESHOLD) {
+                const lengthText = `${insertionSequence.length}`;
+                if (bpPerPx > HIGH_BP_PER_PX_THRESHOLD) {
+                    // Very zoomed out: simple line
+                    actualXPos = xPos - INSERTION_LINE_WIDTH;
+                    actualWidth = INSERTION_BORDER_WIDTH;
+                    fillRect(ctx, actualXPos, rowTop, actualWidth, h, canvasWidth, 'purple');
+                }
+                else if (h > charHeight) {
+                    // Medium zoom: show count in colored box
+                    const textWidth = measureText(lengthText, CHAR_SIZE_WIDTH);
+                    const padding = INSERTION_PADDING;
+                    actualXPos = xPos - textWidth / 2 - padding;
+                    actualWidth = textWidth + 2 * padding;
+                    fillRect(ctx, actualXPos, rowTop, actualWidth, h, canvasWidth, 'purple');
+                    ctx.fillStyle = 'white';
+                    ctx.fillText(lengthText, xPos - textWidth / 2, rowTop + (h * 7) / 8);
+                }
+                else {
+                    const padding = INSERTION_PADDING;
+                    actualXPos = xPos - padding;
+                    actualWidth = 2 * padding;
+                    fillRect(ctx, actualXPos, rowTop, actualWidth, h, canvasWidth, 'purple');
+                }
+            }
+            else {
+                // Small insertions: vertical line with optional border at high zoom
+                actualXPos = xPos;
+                actualWidth = INSERTION_LINE_WIDTH;
+                fillRect(ctx, actualXPos, rowTop, actualWidth, h, canvasWidth, 'purple');
+                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
+            if (shouldAddToSpatialIndex(actualXPos, context, true)) {
+                addToSpatialIndex(context, createRenderedInsertion(actualXPos, rowTop, actualWidth, context, genomicOffset + alignmentStart, chr, sampleId, insertionSequence, featureId));
+            }
+        }
+        genomicOffset++;
+    }
+}
+//# sourceMappingURL=insertions.js.map

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

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

@@ -0,0 +1,13 @@
+import type { RenderingContext } from './types';
+/**
+ * Renders background rectangles for positions where alignment matches reference
+ * Only renders when showAllLetters is false
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/matches.js

@@ -0,0 +1,41 @@
+import { fillRect } from '../util';
+import { addToSpatialIndex, createRenderedBase, shouldAddToSpatialIndex, } from './spatialIndex';
+import { GAP_STROKE_OFFSET } from './types';
+/**
+ * Renders background rectangles for positions where alignment matches reference
+ * Only renders when showAllLetters is false
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId, featureId, alignmentStart, chr) {
+    if (context.showAllLetters) {
+        return;
+    }
+    const { ctx, scale, h, canvasWidth } = context;
+    ctx.fillStyle = 'lightgrey';
+    // Highlight matching bases with light grey background
+    for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
+        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 !== ' ') {
+                fillRect(ctx, xPos, rowTop, scale + GAP_STROKE_OFFSET, h, canvasWidth);
+                // Add to spatial index if distance filter allows
+                if (shouldAddToSpatialIndex(xPos, context)) {
+                    const renderedBase = createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, currentChar || '', true, false, false, false, featureId);
+                    addToSpatialIndex(context, renderedBase);
+                }
+            }
+            genomicOffset++;
+        }
+    }
+}
+//# sourceMappingURL=matches.js.map

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

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

@@ -0,0 +1,13 @@
+import type { RenderingContext } from './types';
+/**
+ * Renders colored rectangles for mismatches and matches (when showAllLetters is true)
+ * Colors are determined by base type when mismatchRendering is enabled
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @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: string, featureId: string, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/mismatches.js

@@ -0,0 +1,47 @@
+import { fillRect } from '../util';
+import { addToSpatialIndex, createRenderedBase, shouldAddToSpatialIndex, } from './spatialIndex';
+import { GAP_STROKE_OFFSET } from './types';
+/**
+ * Renders colored rectangles for mismatches and matches (when showAllLetters is true)
+ * Colors are determined by base type when mismatchRendering is enabled
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ * @param alignmentStart - Start position of the alignment
+ * @param chr - Chromosome/sequence name
+ */
+export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId, featureId, 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];
+        if (seq[i] !== '-') {
+            if (currentChar !== '-') {
+                const xPos = leftPx + scale * genomicOffset;
+                if (seq[i] !== currentChar && currentChar !== ' ') {
+                    // Mismatch: use base-specific color or orange
+                    fillRect(ctx, xPos, rowTop, scale + GAP_STROKE_OFFSET, h, canvasWidth, mismatchRendering
+                        ? (colorForBase[currentChar] ?? 'black')
+                        : 'orange');
+                    // Add to spatial index if distance filter allows
+                    if (shouldAddToSpatialIndex(xPos, context)) {
+                        addToSpatialIndex(context, createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, currentChar, false, true, false, false, featureId));
+                    }
+                }
+                else if (showAllLetters) {
+                    // Match (when showing all letters): use base-specific color or light blue
+                    fillRect(ctx, xPos, rowTop, scale + GAP_STROKE_OFFSET, h, canvasWidth, mismatchRendering
+                        ? (colorForBase[currentChar] ?? 'black')
+                        : 'lightblue');
+                    // Add to spatial index if distance filter allows
+                    if (shouldAddToSpatialIndex(xPos, context)) {
+                        addToSpatialIndex(context, createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, currentChar, true, false, false, false, featureId));
+                    }
+                }
+            }
+            genomicOffset++;
+        }
+    }
+}
+//# sourceMappingURL=mismatches.js.map

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

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