jbrowse-plugin-mafviewer 1.3.1 → 1.4.0

package/dist/LinearMafRenderer/rendering/spatialIndex.js

@@ -0,0 +1,19 @@
+import { GAP_STROKE_OFFSET, MIN_X_DISTANCE } from './types';
+export function createRenderedBaseCoords(xPos, rowTop, context) {
+    return {
+        minX: xPos,
+        minY: rowTop,
+        maxX: xPos + context.scale + GAP_STROKE_OFFSET,
+        maxY: rowTop + context.h,
+    };
+}
+export function shouldAddToSpatialIndex(xPos, context, bypassDistanceFilter = false) {
+    return (bypassDistanceFilter ||
+        Math.abs(xPos - context.lastInsertedX) > MIN_X_DISTANCE);
+}
+export function addToSpatialIndex(context, minX, minY, maxX, maxY, renderedBase) {
+    context.spatialIndex.push(renderedBase);
+    context.spatialIndexCoords.push(minX, minY, maxX, maxY);
+    context.lastInsertedX = 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 +1,55 @@
+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;
+}
+export interface RenderedBase {
+    pos: number;
+    chr: string;
+    base: string;
+    sampleId: number;
+    isInsertion?: boolean;
+}
+/**
+ * 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: RenderedBase[];
+    spatialIndexCoords: number[];
+    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/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -39,24 +39,25 @@ export default function MultiMAFWidget({ model }) {
                     } }, ['BigMafAdapter', 'MafTabixAdapter'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
             fileTypeChoice === 'BigMafAdapter' ? (React.createElement(FileSelector, { location: loc, name: "Path to bigMaf", rootModel: rootModel, setLocation: arg => {
                     setLoc(arg);
-                } })) : fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
-                React.createElement(FormControl, null,
-                    React.createElement(FormLabel, null, "Index type"),
-                    React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
-                            setIndexTypeChoice(event.target.value);
-                        } }, ['TBI', 'CSI'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: indexTypeChoice === r, label: r }))))),
-                React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", rootModel: rootModel, setLocation: arg => {
-                        setLoc(arg);
-                    } }),
-                React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", rootModel: rootModel, setLocation: arg => {
-                        setIndexLoc(arg);
-                    } }))) : (React.createElement(React.Fragment, null,
-                React.createElement(FileSelector, { location: loc, name: "Path to TAF.gz (Bgzipped TAF)", rootModel: rootModel, setLocation: arg => {
-                        setLoc(arg);
-                    } }),
-                React.createElement(FileSelector, { location: indexLoc, name: "Path to TAF.gz.tai (TAF index)", rootModel: rootModel, setLocation: arg => {
-                        setIndexLoc(arg);
-                    } })))),
+                } })) : // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
+                    React.createElement(FormControl, null,
+                        React.createElement(FormLabel, null, "Index type"),
+                        React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
+                                setIndexTypeChoice(event.target.value);
+                            } }, ['TBI', 'CSI'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: indexTypeChoice === r, label: r }))))),
+                    React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", rootModel: rootModel, setLocation: arg => {
+                            setLoc(arg);
+                        } }),
+                    React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", rootModel: rootModel, setLocation: arg => {
+                            setIndexLoc(arg);
+                        } }))) : (React.createElement(React.Fragment, null,
+                    React.createElement(FileSelector, { location: loc, name: "Path to TAF.gz (Bgzipped TAF)", rootModel: rootModel, setLocation: arg => {
+                            setLoc(arg);
+                        } }),
+                    React.createElement(FileSelector, { location: indexLoc, name: "Path to TAF.gz.tai (TAF index)", rootModel: rootModel, setLocation: arg => {
+                            setIndexLoc(arg);
+                        } })))),
         React.createElement("div", null,
             React.createElement(FileSelector, { location: nhLoc, name: "Path to newick tree (.nh)", rootModel: rootModel, setLocation: arg => {
                     setNhLoc(arg);
@@ -94,24 +95,25 @@ export default function MultiMAFWidget({ model }) {
                                     samples: sampleNames,
                                     nhLocation: nhLoc,
                                 }
-                                : fileTypeChoice === 'MafTabixAdapter'
-                                    ? {
-                                        type: fileTypeChoice,
-                                        bedGzLocation: loc,
-                                        nhLocation: nhLoc,
-                                        index: {
-                                            indexType: indexTypeChoice,
-                                            location: indexLoc,
+                                : // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                                    fileTypeChoice === 'MafTabixAdapter'
+                                        ? {
+                                            type: fileTypeChoice,
+                                            bedGzLocation: loc,
+                                            nhLocation: nhLoc,
+                                            index: {
+                                                indexType: indexTypeChoice,
+                                                location: indexLoc,
+                                            },
+                                            samples: sampleNames,
+                                        }
+                                        : {
+                                            type: fileTypeChoice,
+                                            tafGzLocation: loc,
+                                            taiLocation: indexLoc,
+                                            nhLocation: nhLoc,
+                                            samples: sampleNames,
                                         },
-                                        samples: sampleNames,
-                                    }
-                                    : {
-                                        type: fileTypeChoice,
-                                        tafGzLocation: loc,
-                                        taiLocation: indexLoc,
-                                        nhLocation: nhLoc,
-                                        samples: sampleNames,
-                                    },
                         });
                         model.view?.showTrack(trackId);
                     }

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

@@ -1 +1 @@
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D,OAAO,EAAE,WAAW;qCACrB;oCACH,CAAC,CAAC;wCACE,IAAI,EAAE,cAAc;wCACpB,aAAa,EAAE,GAAG;wCAClB,WAAW,EAAE,QAAQ;wCACrB,UAAU,EAAE,KAAK;wCACjB,OAAO,EAAE,WAAW;qCACrB;yBACV,CAAC,CAAA;wBAEF,KAAK,CAAC,IAAI,EAAE,SAAS,CAAC,OAAO,CAAC,CAAA;oBAChC,CAAC;oBACD,KAAK,CAAC,SAAS,EAAE,CAAA;oBACjB,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACvC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;oBAC3B,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,aAGM,CACH,CACT,CAAA;AACH,CAAC"}
+{"version":3,"file":"AddTrackWorkflow.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/AddTrackWorkflow.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAEL,UAAU,EACV,yBAAyB,EACzB,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,MAAM,EACN,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,KAAK,EACL,KAAK,EACL,UAAU,EACV,SAAS,GACV,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,KAAK,EAAE,MAAM;KACd;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,EAAE;QACvB,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE;KACzB;IACD,MAAM,EAAE;QACN,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,GAAG;QACjB,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAKH,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,KAAK,EAA4B;IACxE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAClD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IACvD,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GACvC,QAAQ,CAAqB,eAAe,CAAC,CAAA;IAC/C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GACzC,QAAQ,CAAmB,KAAK,CAAC,CAAA;IAEnC,MAAM,SAAS,GAAG,OAAO,CAAM,KAAK,CAAC,CAAA;IACrC,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,oBAAC,KAAK;YACH,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,WAAW;gBACV,oBAAC,SAAS,oBAAsB;gBAChC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,iBAAiB,CAAC,KAAK,CAAC,MAAM,CAAC,KAA2B,CAAC,CAAA;oBAC7D,CAAC,IAEA,CAAC,eAAe,EAAE,iBAAiB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAC7C,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,cAAc,KAAK,CAAC,EAC7B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;YACb,cAAc,KAAK,eAAe,CAAC,CAAC,CAAC,CACpC,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,gBAAgB,EACrB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,MAAM,CAAC,GAAG,CAAC,CAAA;gBACb,CAAC,GACD,CACH,CAAC,CAAC,CAAC,uEAAuE;gBAC3E,cAAc,KAAK,iBAAiB,CAAC,CAAC,CAAC,CACrC;oBACE,oBAAC,WAAW;wBACV,oBAAC,SAAS,qBAAuB;wBACjC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAyB,CAAC,CAAA;4BAC5D,CAAC,IAEA,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACvB,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,eAAe,KAAK,CAAC,EAC9B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;oBACd,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,mBAAmB,EACxB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,yBAAyB,EAC9B,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,+BAA+B,EACpC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,gCAAgC,EACrC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CACK;QACR;YACE,oBAAC,YAAY,IACX,QAAQ,EAAE,KAAK,EACf,IAAI,EAAC,2BAA2B,EAChC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACf,CAAC,GACD;YACF,oBAAC,SAAS,IACR,SAAS,QACT,IAAI,EAAE,EAAE,EACR,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAChC,CAAC,EACD,UAAU,EAAC,0DAA0D,EACrE,WAAW,EACT,wFAAwF,EAE1F,OAAO,EAAC,UAAU,EAClB,SAAS,SACT,CACE;QAEN,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,YAAY,EACvB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC,GACD;QACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,CAAC;oBACH,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI,WAAW,GAAG,EAAc,CAAA;oBAChC,IAAI,CAAC;wBACH,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;oBACnC,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,WAAW,GAAG,OAAO,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;oBAC3C,CAAC;oBAED,MAAM,OAAO,GAAG;wBACd,GAAG,SAAS,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,GAAG,EAAE,EAAE;wBAC/D,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,eAAe;qBACzC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBAEV,IAAI,sBAAsB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACpC,OAAO,CAAC,YAAY,CAAC;4BACnB,OAAO;4BACP,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,SAAS;4BACf,aAAa,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC;4BAC/B,OAAO,EACL,cAAc,KAAK,eAAe;gCAChC,CAAC,CAAC;oCACE,IAAI,EAAE,cAAc;oCACpB,cAAc,EAAE,GAAG;oCACnB,OAAO,EAAE,WAAW;oCACpB,UAAU,EAAE,KAAK;iCAClB;gCACH,CAAC,CAAC,uEAAuE;oCACvE,cAAc,KAAK,iBAAiB;wCACpC,CAAC,CAAC;4CACE,IAAI,EAAE,cAAc;4CACpB,aAAa,EAAE,GAAG;4CAClB,UAAU,EAAE,KAAK;4CACjB,KAAK,EAAE;gDACL,SAAS,EAAE,eAAe;gDAC1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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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package/dist/index.js

@@ -1,6 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { version } from '../package.json';
-import BgzipTaffyAdapterF from './BgzipTaffyAdapter';
 import BigMafAdapterF from './BigMafAdapter';
 import LinearMafDisplayF from './LinearMafDisplay';
 import LinearMafRendererF from './LinearMafRenderer';
@@ -18,7 +17,6 @@ export default class MafViewerPlugin extends Plugin {
         LinearMafDisplayF(pluginManager);
         LinearMafRendererF(pluginManager);
         MafTabixAdapterF(pluginManager);
-        BgzipTaffyAdapterF(pluginManager);
         MafAddTrackWorkflowF(pluginManager);
         MafGetSequencesF(pluginManager);
         MafGetSamplesF(pluginManager);

package/dist/index.js.map

@@ -1 +1 @@
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