@datagrok-libraries/bio 5.53.2 → 5.53.3

package/CHANGELOG.md

@@ -1,5 +1,10 @@
 # bio changelog
 
+## 5.53.3 (2025-06-02)
+
+* MSA header tracks
+* Faster methods for getting regions from ISeqSplitted
+
 ## 5.52.0 (2025-05-12)
 
 Sequence rendering with shift configuration. MSA improvements

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.53.2",
+  "version": "5.53.3",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

package/src/utils/macromolecule/types.d.ts

@@ -9,6 +9,11 @@ export interface ISeqSplitted {
     /** For fasta and Helm must not be enclosed to square brackets [meA].*/
     getOriginal(posIdx: number): string;
     length: number;
+    /** Returns list of canonical monomers in the region specified */
+    getCanonicalRegion(start: number, end: number): string[];
+    /** Returns the list of original monomers in the region specified */
+    getOriginalRegion(start: number, end: number): string[];
+    get gapOriginal(): string;
 }
 export interface INotationProvider {
     get defaultGapOriginal(): string;

package/src/utils/macromolecule/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,oBAAoB,EAAC,MAAM,4BAA4B,CAAC;AAChE,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAE1C,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAKpC,MAAM,EAAE,MAAM,CAAC;IAEf,iEAAiE;IACjE,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAEzD,oEAAoE;IACpE,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAExD,IAAI,WAAW,IAAI,MAAM,CAAC;CAC3B;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,kBAAkB,IAAI,MAAM,CAAC;IAEjC,wGAAwG;IACxG,QAAQ,CAAC,UAAU,EAAE,WAAW,GAAG,IAAI,CAAC;IAExC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,0DAA0D;IAC1D,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,GAAG,MAAM,CAAC;IAE3C,sBAAsB,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAAE,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;CAClH;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}

package/src/utils/macromolecule/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AA0CA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAkDA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}

package/src/utils/macromolecule/utils.d.ts

@@ -11,6 +11,9 @@ export declare class StringListSeqSplitted implements ISeqSplitted {
     /** @param {number} posIdx monomer position 0-based index */
     getCanonical(posIdx: number): string;
     getOriginal(posIdx: number): string;
+    getCanonicalRegion(start: number, end: number): string[];
+    getOriginalRegion(start: number, end: number): string[];
+    get gapOriginal(): string;
     constructor(mList: SeqSplittedBase, gapOriginalMonomer: string);
 }
 export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
@@ -19,6 +22,9 @@ export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
     isGap(posIdx: number): boolean;
     getCanonical(posIdx: number): string;
     getOriginal(posIdx: number): string;
+    getCanonicalRegion(start: number, end: number): string[];
+    getOriginalRegion(start: number, end: number): string[];
+    get gapOriginal(): string;
     constructor(seqS: string);
 }
 /** Stats of sequences with specified splitter func, returns { freq, sameLength }.

package/src/utils/macromolecule/utils.d.ts.map

@@ -1 +1 @@
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package/src/utils/macromolecule/utils.js

@@ -26,6 +26,22 @@ export class StringListSeqSplitted {
             throw new Error('Index out of bounds');
         return this.mList[posIdx];
     }
+    getCanonicalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        const len = actEnd - actStart;
+        const gap = this.gapOriginalMonomer;
+        return new Array(len).fill(null).map((_, i) => { const om = this.mList[i + actStart]; return om === gap ? GAP_SYMBOL : om; });
+    }
+    getOriginalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        const len = actEnd - actStart;
+        return new Array(len).fill(null).map((_, i) => this.mList[i + actStart]);
+    }
+    get gapOriginal() {
+        return this.gapOriginalMonomer;
+    }
     constructor(mList, gapOriginalMonomer) {
         this.mList = mList;
         this.gapOriginalMonomer = gapOriginalMonomer;
@@ -48,6 +64,24 @@ export class FastaSimpleSeqSplitted {
             throw new Error('Index out of bounds');
         return this.seqS[posIdx];
     }
+    getCanonicalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        const len = actEnd - actStart;
+        const gap = GapOriginals[NOTATION.FASTA];
+        return new Array(len).fill(null).map((_, i) => {
+            const om = this.seqS[i + actStart];
+            return om === gap ? GAP_SYMBOL : om;
+        });
+    }
+    getOriginalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        return this.seqS.slice(actStart, actEnd); // hacky way but quite effective
+    }
+    get gapOriginal() {
+        return GapOriginals[NOTATION.FASTA];
+    }
     constructor(seqS) {
         this.seqS = seqS;
     }

package/src/utils/macromolecule/utils.js.map

@@ -1 +1 @@
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package/src/utils/sequence-position-scroller.d.ts

@@ -3,6 +3,7 @@
  * This module provides functionality for an interactive MSA (Multiple Sequence Alignment) header
  * with position markers, slider navigation, and position selection.
  */
+import * as DG from 'datagrok-api/dg';
 interface WindowRange {
     start: number;
     end: number;
@@ -22,27 +23,142 @@ interface MSAHeaderOptions {
     width?: number;
     height?: number;
     onPositionChange?: (position: number, range: WindowRange) => void;
+    onHeaderHeightChange?: (height: number) => void;
 }
 interface Preventable {
     preventDefault: () => void;
 }
+/**
+ * Base class for all MSA header tracks
+ */
+export declare abstract class MSAHeaderTrack {
+    protected ctx: CanvasRenderingContext2D | null;
+    protected visible: boolean;
+    protected height: number;
+    protected minHeight: number;
+    protected defaultHeight: number;
+    protected title: string;
+    protected tooltipEnabled: boolean;
+    protected tooltipContent: ((position: number, data: any) => HTMLElement) | null;
+    constructor(height?: number, minHeight?: number, title?: string);
+    /**
+     * Initialize the track with a canvas context
+     */
+    init(ctx: CanvasRenderingContext2D): void;
+    getMonomerAt(x: number, y: number, position: number): string | null;
+    enableTooltip(enabled: boolean): void;
+    setTooltipContentGenerator(contentGenerator: (position: number, data: any) => HTMLElement): void;
+    getTooltipContent(position: number): HTMLElement | null;
+    /**
+     * Get data for a specific position (to be implemented by subclasses)
+     */
+    protected getPositionData(position: number): any;
+    setVisible(visible: boolean): void;
+    getHeight(): number;
+    getDefaultHeight(): number;
+    getMinHeight(): number;
+    setHeight(height: number): void;
+    resetHeight(): void;
+    isVisible(): boolean;
+    setTitle(title: string): void;
+    getTitle(): string;
+    /**
+     * Draw the track at the specified position
+     */
+    abstract draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, currentPosition: number): void;
+}
+export declare class WebLogoTrack extends MSAHeaderTrack {
+    private data;
+    private monomerLib;
+    private biotype;
+    private hoveredPosition;
+    private hoveredMonomer;
+    constructor(data?: Map<number, Map<string, number>>, height?: number, _colorScheme?: string, title?: string);
+    setHovered(position: number, monomer: string | null): void;
+    protected getPositionData(position: number): Map<string, number> | null;
+    setupDefaultTooltip(): void;
+    private createFrequencyTable;
+    private createTooltipContent;
+    setMonomerLib(monomerLib: any): void;
+    setBiotype(biotype: string): void;
+    /**
+     * Calculate which monomer is at the specified coordinates within a WebLogo column
+     */
+    getMonomerAt(x: number, y: number, position: number): string | null;
+    updateData(data: Map<number, Map<string, number>>): void;
+    /**
+     * Draw the WebLogo track
+     */
+    draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, currentPosition: number): void;
+    private drawWebLogoColumn;
+    private drawLettersInColumn;
+    private drawColumnBorder;
+    private drawLetter;
+    private drawLetterSeparators;
+    private drawLetterText;
+    private getMonomerBackgroundColor;
+    private getMonomerTextColor;
+}
+/**
+ * Track for displaying conservation bars
+ */
+export declare class ConservationTrack extends MSAHeaderTrack {
+    private data;
+    private colorScheme;
+    constructor(data: number[], height?: number, colorScheme?: 'default' | 'rainbow' | 'heatmap', title?: string);
+    updateData(data: number[]): void;
+    /**
+     * Draw the conservation track
+     */
+    draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, currentPosition: number): void;
+    private drawConservationBar;
+}
 export declare class MSAScrollingHeader {
     private config;
     private state;
     private canvas;
     private ctx;
     private eventElement;
+    private tracks;
+    private currentHoverPosition;
+    private currentHoverTrack;
+    private previousHoverPosition;
+    private previousHoverTrack;
+    private previousHoverMonomer;
+    private dataFrame;
+    private seqHandler;
+    private seqColumn;
+    private onSelectionCallback;
+    private trackButtons;
+    private userSelectedTracks;
+    constructor(options: MSAHeaderOptions);
+    private determineVisibleTracks;
+    private drawTrackButtons;
+    private drawTrackButton;
+    private handleTrackButtonClick;
+    private snapToTrackHeight;
+    private resetToAutoMode;
     /**
-     * Constructor for the MSA Header
-     * @param {MSAHeaderOptions} options - Configuration options
+     * Draw the column title (shown when above threshold)
      */
-    constructor(options: MSAHeaderOptions);
+    private drawColumnTitle;
+    private clearHoverStates;
+    private redraw;
+    setSelectionData(dataFrame: DG.DataFrame, seqColumn: DG.Column<string>, seqHandler: any, callback?: (position: number, monomer: string) => void): void;
+    setupTooltipHandling(): void;
+    private handleTooltipMouseMove;
+    private handleTooltipMouseLeave;
+    private hideTooltip;
+    draw(x: number, y: number, w: number, h: number, currentPos: number, scrollerStart: number, preventable: Preventable, columnName?: string): void;
     /**
-     * Initialize the component
+     * Draw the dotted cells area with position markers
      */
-    private init;
-    get isValid(): boolean;
-    draw(x: number, y: number, w: number, h: number, currentPos: number, scrollerStart: number, preventable: Preventable): void;
+    private drawDottedCells;
+    /**
+     * Draw the position slider
+     */
+    private drawSlider;
+    private setupEventElement;
     getCoords(e: MouseEvent): {
         x: number;
         y: number;
@@ -53,57 +169,37 @@ export declare class MSAScrollingHeader {
     isInSliderArea(e: MouseEvent): boolean;
     get sliderWidth(): number;
     isInSliderDraggableArea(e: MouseEvent): boolean;
-    /**
-     * Handle mouse down (start dragging)
-     * @param {MouseEvent} e - Mouse event
-     */
+    private setupEventListeners;
+    private handleSelectionClick;
+    private selectRowsWithMonomerAtPosition;
+    private init;
+    addTrack(id: string, track: MSAHeaderTrack): void;
+    removeTrack(id: string): void;
+    getTrack<T extends MSAHeaderTrack>(id: string): T | undefined;
+    updateTrack<T extends MSAHeaderTrack>(id: string, updater: (track: T) => void): void;
+    get isValid(): boolean;
     private handleMouseDown;
     private handleMouseWheel;
-    /**
-     * Handle mouse move (dragging)
-     * @param {MouseEvent} e - Mouse event
-     */
     private handleMouseMove;
     private handleKeyDown;
-    /**
-     * Handle mouse up (end dragging)
-     */
     private handleMouseUp;
-    /**
-     * Handle slider drag
-     * @param {number} x - X position of mouse
-     */
     private handleSliderDrag;
     get headerHeight(): number;
-    /** Soft setting of header hight, without redrawing or update event
-     * @param {number} value - New header height
-     */
     set headerHeight(value: number);
-    /**
-     * Handle click on positions
-     * @param {MouseEvent} e - Mouse event
-     */
     private handleClick;
-    /**
-     * Get the current window range
-     * @return {WindowRange} Object with start and end properties
-     */
     getWindowRange(): WindowRange;
-    /**
-     * Update configuration
-     * @param {MSAHeaderOptions} newConfig - New configuration options
-     */
     updateConfig(newConfig: Partial<MSAHeaderOptions>): void;
-    /**
-     * Get current position
-     * @return {number} Current position
-     */
     getCurrentPosition(): number;
+    setCurrentPosition(position: number): void;
     /**
-     * Set current position
-     * @param {number} position - New position
+     * ADDED: Public methods for external control
      */
-    setCurrentPosition(position: number): void;
+    getHeightThresholds(): {
+        BASE: number;
+        WITH_TITLE: number;
+        WITH_WEBLOGO: number;
+        WITH_BOTH: number;
+    };
 }
 export {};
 //# sourceMappingURL=sequence-position-scroller.d.ts.map

package/src/utils/sequence-position-scroller.d.ts.map

@@ -1 +1 @@
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