jbrowse-plugin-mafviewer 1.3.1 → 1.3.2

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

@@ -0,0 +1,60 @@
+import type { RenderedBase, RenderingContext } from './types';
+/**
+ * Creates a RenderedBase object for spatial indexing
+ * @param xPos - X coordinate of the base
+ * @param rowTop - Y coordinate of the row top
+ * @param context - Rendering context with dimensions
+ * @param pos - Genomic coordinate
+ * @param chr - Chromosome/sequence name
+ * @param sampleId - Sample identifier
+ * @param base - The base character
+ * @param isMatch - Whether this base matches the reference
+ * @param isMismatch - Whether this base is a mismatch
+ * @param isGap - Whether this is a gap
+ * @param isInsertion - Whether this is an insertion
+ * @param featureId - Feature identifier
+ */
+export declare function createRenderedBase(xPos: number, rowTop: number, context: RenderingContext, pos: number, chr: string, sampleId: string, base: string, isMatch: boolean, isMismatch: boolean, isGap: boolean, isInsertion: boolean, featureId: string): RenderedBase;
+/**
+ * Creates a RenderedBase object for insertions with custom width
+ * Uses the actual rendered width instead of the standard scale-based width
+ * This ensures accurate spatial queries for different insertion rendering types:
+ * - Small insertions: INSERTION_LINE_WIDTH (1px) or INSERTION_BORDER_HEIGHT (5px) with borders
+ * - Large insertions (text): measured text width + padding
+ * - Large insertions (line): INSERTION_BORDER_WIDTH (2px)
+ *
+ * @param xPos - X coordinate of the insertion
+ * @param rowTop - Y coordinate of the row top
+ * @param width - Actual rendered width of the insertion
+ * @param context - Rendering context with dimensions
+ * @param pos - Genomic coordinate
+ * @param chr - Chromosome/sequence name
+ * @param sampleId - Sample identifier
+ * @param insertionSequence - The insertion sequence
+ * @param featureId - Feature identifier
+ */
+export declare function createRenderedInsertion(xPos: number, rowTop: number, width: number, context: RenderingContext, pos: number, chr: string, sampleId: string, insertionSequence: string, featureId: string): RenderedBase;
+/**
+ * Checks if an item should be added to the spatial index based on distance filtering
+ * Only returns true if the X position is >0.5px away from the last inserted item
+ * This reduces spatial index density while maintaining useful spatial queries
+ *
+ * @param xPos - X position to check
+ * @param context - Rendering context with lastInsertedX tracking
+ * @param bypassDistanceFilter - If true, always return true (e.g., for insertions)
+ * @returns Whether the item should be added to spatial index
+ *
+ * @example
+ * // Items at X positions: 100.0, 100.3, 100.8, 101.5
+ * // Only items at 100.0, 100.8, 101.5 would return true (>0.5px apart)
+ * // Unless bypassDistanceFilter=true, then all would return true
+ */
+export declare function shouldAddToSpatialIndex(xPos: number, context: RenderingContext, bypassDistanceFilter?: boolean): boolean;
+/**
+ * Adds a rendered base directly to the RBush spatial index
+ * Updates the lastInsertedX tracking for distance filtering
+ *
+ * @param context - Rendering context with spatial index
+ * @param renderedBase - The base to add to the spatial index
+ */
+export declare function addToSpatialIndex(context: RenderingContext, renderedBase: RenderedBase): void;

package/dist/LinearMafRenderer/rendering/spatialIndex.js

@@ -0,0 +1,99 @@
+import { GAP_STROKE_OFFSET, MIN_X_DISTANCE } from './types';
+/**
+ * Creates a RenderedBase object for spatial indexing
+ * @param xPos - X coordinate of the base
+ * @param rowTop - Y coordinate of the row top
+ * @param context - Rendering context with dimensions
+ * @param pos - Genomic coordinate
+ * @param chr - Chromosome/sequence name
+ * @param sampleId - Sample identifier
+ * @param base - The base character
+ * @param isMatch - Whether this base matches the reference
+ * @param isMismatch - Whether this base is a mismatch
+ * @param isGap - Whether this is a gap
+ * @param isInsertion - Whether this is an insertion
+ * @param featureId - Feature identifier
+ */
+export function createRenderedBase(xPos, rowTop, context, pos, chr, sampleId, base, isMatch, isMismatch, isGap, isInsertion, featureId) {
+    return {
+        minX: xPos,
+        minY: rowTop,
+        maxX: xPos + context.scale + GAP_STROKE_OFFSET,
+        maxY: rowTop + context.h,
+        pos,
+        chr,
+        sampleId,
+        base,
+        isMatch,
+        isMismatch,
+        isGap,
+        isInsertion,
+        featureId,
+    };
+}
+/**
+ * Creates a RenderedBase object for insertions with custom width
+ * Uses the actual rendered width instead of the standard scale-based width
+ * This ensures accurate spatial queries for different insertion rendering types:
+ * - Small insertions: INSERTION_LINE_WIDTH (1px) or INSERTION_BORDER_HEIGHT (5px) with borders
+ * - Large insertions (text): measured text width + padding
+ * - Large insertions (line): INSERTION_BORDER_WIDTH (2px)
+ *
+ * @param xPos - X coordinate of the insertion
+ * @param rowTop - Y coordinate of the row top
+ * @param width - Actual rendered width of the insertion
+ * @param context - Rendering context with dimensions
+ * @param pos - Genomic coordinate
+ * @param chr - Chromosome/sequence name
+ * @param sampleId - Sample identifier
+ * @param insertionSequence - The insertion sequence
+ * @param featureId - Feature identifier
+ */
+export function createRenderedInsertion(xPos, rowTop, width, context, pos, chr, sampleId, insertionSequence, featureId) {
+    return {
+        minX: xPos,
+        minY: rowTop,
+        maxX: xPos + width,
+        maxY: rowTop + context.h,
+        pos,
+        chr,
+        sampleId,
+        base: insertionSequence,
+        isMatch: false,
+        isMismatch: false,
+        isGap: false,
+        isInsertion: true,
+        featureId,
+    };
+}
+/**
+ * Checks if an item should be added to the spatial index based on distance filtering
+ * Only returns true if the X position is >0.5px away from the last inserted item
+ * This reduces spatial index density while maintaining useful spatial queries
+ *
+ * @param xPos - X position to check
+ * @param context - Rendering context with lastInsertedX tracking
+ * @param bypassDistanceFilter - If true, always return true (e.g., for insertions)
+ * @returns Whether the item should be added to spatial index
+ *
+ * @example
+ * // Items at X positions: 100.0, 100.3, 100.8, 101.5
+ * // Only items at 100.0, 100.8, 101.5 would return true (>0.5px apart)
+ * // Unless bypassDistanceFilter=true, then all would return true
+ */
+export function shouldAddToSpatialIndex(xPos, context, bypassDistanceFilter = false) {
+    return (bypassDistanceFilter ||
+        Math.abs(xPos - context.lastInsertedX) > MIN_X_DISTANCE);
+}
+/**
+ * Adds a rendered base directly to the RBush spatial index
+ * Updates the lastInsertedX tracking for distance filtering
+ *
+ * @param context - Rendering context with spatial index
+ * @param renderedBase - The base to add to the spatial index
+ */
+export function addToSpatialIndex(context, renderedBase) {
+    context.spatialIndex.insert(renderedBase);
+    context.lastInsertedX = renderedBase.minX;
+}
+//# sourceMappingURL=spatialIndex.js.map

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

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

@@ -0,0 +1,12 @@
+import type { RenderingContext } from './types';
+/**
+ * Renders text labels for bases when zoom level is sufficient
+ * Only shows text for mismatches (or all letters when showAllLetters is true)
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample (lowercase)
+ * @param origAlignment - Original alignment preserving case
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ */
+export declare function renderText(context: RenderingContext, alignment: string, origAlignment: string, seq: string, leftPx: number, rowTop: number, _sampleId: string, _featureId: string): void;

package/dist/LinearMafRenderer/rendering/text.js

@@ -0,0 +1,42 @@
+import { getCharWidthHeight } from '../util';
+import { CHAR_SIZE_WIDTH, VERTICAL_TEXT_OFFSET } from './types';
+function getLetter(a, showAsUpperCase) {
+    return showAsUpperCase ? a.toUpperCase() : a;
+}
+/**
+ * Renders text labels for bases when zoom level is sufficient
+ * Only shows text for mismatches (or all letters when showAllLetters is true)
+ * @param context - Rendering context with canvas and styling info
+ * @param alignment - The aligned sequence for this sample (lowercase)
+ * @param origAlignment - Original alignment preserving case
+ * @param seq - The reference sequence
+ * @param leftPx - Left pixel position of the feature
+ * @param rowTop - Top pixel position of the row
+ */
+export function renderText(context, alignment, origAlignment, seq, leftPx, rowTop, _sampleId, _featureId) {
+    const { ctx, scale, hp2, rowHeight, showAllLetters, mismatchRendering, contrastForBase, showAsUpperCase, } = context;
+    const { charHeight } = getCharWidthHeight();
+    // 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++) {
+            if (seq[i] !== '-') {
+                // Only process non-gap positions in reference
+                const xPos = leftPx + scale * genomicOffset;
+                const textOffset = (scale - CHAR_SIZE_WIDTH) / 2 + 1; // Center text in available space
+                const currentChar = alignment[i];
+                // Show text for mismatches or all letters (depending on setting)
+                if ((showAllLetters || seq[i] !== currentChar) && currentChar !== '-') {
+                    ctx.fillStyle = mismatchRendering
+                        ? (contrastForBase[currentChar] ?? 'white') // Use contrasting color for readability
+                        : 'black';
+                    if (rowHeight > charHeight) {
+                        // Only render if row is tall enough
+                        ctx.fillText(getLetter(origAlignment[i] || '', showAsUpperCase), xPos + textOffset, hp2 + rowTop + VERTICAL_TEXT_OFFSET);
+                    }
+                }
+                genomicOffset++;
+            }
+        }
+    }
+}
+//# sourceMappingURL=text.js.map

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

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

@@ -0,0 +1,67 @@
+import RBush from 'rbush';
+export declare const FONT_CONFIG = "bold 10px Courier New,monospace";
+export declare const CHAR_SIZE_WIDTH = 10;
+export declare const GAP_STROKE_OFFSET = 0.4;
+export declare const INSERTION_LINE_WIDTH = 1;
+export declare const INSERTION_BORDER_WIDTH = 2;
+export declare const INSERTION_PADDING = 2;
+export declare const VERTICAL_TEXT_OFFSET = 3;
+export declare const LARGE_INSERTION_THRESHOLD = 10;
+export declare const HIGH_ZOOM_THRESHOLD = 0.2;
+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 interface GenomicRegion {
+    start: number;
+    end: number;
+    refName: string;
+}
+/**
+ * Represents a rendered letter/base with its spatial and genomic coordinates
+ * This structure is designed for insertion into an RBush spatial index
+ */
+export interface RenderedBase {
+    minX: number;
+    minY: number;
+    maxX: number;
+    maxY: number;
+    pos: number;
+    chr: string;
+    sampleId: string;
+    base: string;
+    isMatch: boolean;
+    isMismatch: boolean;
+    isGap: boolean;
+    isInsertion: boolean;
+    featureId: string;
+}
+/**
+ * Shared rendering context containing all necessary parameters for rendering operations
+ */
+export interface RenderingContext {
+    ctx: CanvasRenderingContext2D;
+    scale: number;
+    canvasWidth: number;
+    rowHeight: number;
+    h: number;
+    hp2: number;
+    offset: number;
+    colorForBase: Record<string, string>;
+    contrastForBase: Record<string, string>;
+    showAllLetters: boolean;
+    mismatchRendering: boolean;
+    showAsUpperCase: boolean;
+    spatialIndex: RBush<RenderedBase>;
+    lastInsertedX: number;
+}
+export interface AlignmentRecord {
+    seq: string;
+    start: number;
+    strand: number;
+    chr: string;
+}

package/dist/LinearMafRenderer/rendering/types.js

@@ -0,0 +1,15 @@
+// Rendering constants
+export const FONT_CONFIG = 'bold 10px Courier New,monospace';
+export const CHAR_SIZE_WIDTH = 10;
+export const GAP_STROKE_OFFSET = 0.4;
+export const INSERTION_LINE_WIDTH = 1;
+export const INSERTION_BORDER_WIDTH = 2;
+export const INSERTION_PADDING = 2;
+export const VERTICAL_TEXT_OFFSET = 3;
+export const LARGE_INSERTION_THRESHOLD = 10;
+export const HIGH_ZOOM_THRESHOLD = 0.2;
+export const MIN_ROW_HEIGHT_FOR_BORDERS = 5;
+export const HIGH_BP_PER_PX_THRESHOLD = 10;
+export const INSERTION_BORDER_HEIGHT = 5;
+export const MIN_X_DISTANCE = 0.5;
+//# sourceMappingURL=types.js.map

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

@@ -0,0 +1 @@
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package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -51,35 +51,61 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                 for (const feature of features) {
                     const data = feature.get('field5').split(',');
                     const alignments = {};
-                    const len = data.length;
-                    for (let j = 0; j < len; j++) {
+                    const dataLength = data.length;
+                    for (let j = 0; j < dataLength; j++) {
                         const elt = data[j];
-                        const seq = elt.split(':')[5];
-                        const ad = elt.split(':');
-                        const ag = ad[0].split('.');
-                        const [n1, n2 = '', ...rest] = ag;
-                        let assemblyName;
-                        let last = '';
-                        if (ag.length === 2) {
-                            assemblyName = n1;
-                            last = n2;
+                        // Cache split result to avoid redundant operations
+                        const parts = elt.split(':');
+                        // Use destructuring for better performance than multiple array access
+                        const [assemblyAndChr, startStr, srcSizeStr, strandStr, unknownStr, seq,] = parts;
+                        // Skip if we don't have all required parts
+                        if (!assemblyAndChr || !seq) {
+                            continue;
                         }
-                        else if (!Number.isNaN(+n2)) {
-                            assemblyName = `${n1}.${n2}`;
-                            last = rest.join('.');
+                        // Optimized assembly name parsing with simplified logic
+                        let assemblyName;
+                        let chr;
+                        const firstDotIndex = assemblyAndChr.indexOf('.');
+                        if (firstDotIndex === -1) {
+                            // No dot found, entire string is assembly name
+                            assemblyName = assemblyAndChr;
+                            chr = '';
                         }
                         else {
-                            assemblyName = n1;
-                            last = [n2, ...rest].join('.');
+                            const secondDotIndex = assemblyAndChr.indexOf('.', firstDotIndex + 1);
+                            if (secondDotIndex === -1) {
+                                // Only one dot: assembly.chr
+                                assemblyName = assemblyAndChr.slice(0, Math.max(0, firstDotIndex));
+                                chr = assemblyAndChr.slice(Math.max(0, firstDotIndex + 1));
+                            }
+                            else {
+                                // Multiple dots: check if second part is numeric (version number)
+                                const secondPart = assemblyAndChr.slice(firstDotIndex + 1, secondDotIndex);
+                                const isNumeric = secondPart.length > 0 && !Number.isNaN(+secondPart);
+                                if (isNumeric) {
+                                    // assembly.version.chr format
+                                    assemblyName = assemblyAndChr.slice(0, Math.max(0, secondDotIndex));
+                                    chr = assemblyAndChr.slice(Math.max(0, secondDotIndex + 1));
+                                }
+                                else {
+                                    // assembly.chr.more format
+                                    assemblyName = assemblyAndChr.slice(0, Math.max(0, firstDotIndex));
+                                    chr = assemblyAndChr.slice(Math.max(0, firstDotIndex + 1));
+                                }
+                            }
                         }
                         if (assemblyName) {
-                            firstAssemblyNameFound = firstAssemblyNameFound || assemblyName;
+                            // Set first assembly name found (only once)
+                            if (!firstAssemblyNameFound) {
+                                firstAssemblyNameFound = assemblyName;
+                            }
+                            // Create alignment record with optimized number conversion
                             alignments[assemblyName] = {
-                                chr: last,
-                                start: +ad[1],
-                                srcSize: +ad[2],
-                                strand: ad[3] === '-' ? -1 : 1,
-                                unknown: +ad[4],
+                                chr,
+                                start: +startStr,
+                                srcSize: +srcSizeStr,
+                                strand: strandStr === '-' ? -1 : 1,
+                                unknown: +unknownStr,
                                 seq,
                             };
                         }

package/dist/MafTabixAdapter/MafTabixAdapter.js.map

@@ -1 +1 @@
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