@datagrok-libraries/bio 5.62.0 → 5.63.0

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.62.0",
+  "version": "5.63.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",
@@ -17,7 +17,7 @@
     "@datagrok-libraries/utils": "^4.5.7",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "^8.1.5",
-    "datagrok-api": "^1.25.0",
+    "datagrok-api": "^1.26.0",
     "dayjs": "^1.11.13",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",
@@ -36,6 +36,7 @@
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",
     "@typescript-eslint/parser": "^8.8.1",
+    "datagrok-tools": "^4.14.20",
     "eslint": "8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-deprecation": "^3.0.0",

package/src/types/monomer-library.d.ts

@@ -167,11 +167,12 @@ export interface IMonomerLibHelper {
     /** reads single collection and returns monomer symbols in it . name should be extention qualified*/
     readMonomerCollection(collectionName: string): Promise<MonomerCollection>;
     /** add or update monomer collecion */
-    addOrUpdateMonomerCollection(collectionName: string, monomerSymbols: string[], description?: string): Promise<void>;
+    addOrUpdateMonomerCollection(collectionName: string, monomerSymbols: string[], description?: string, tags?: string[]): Promise<void>;
     deleteMonomerCollection(collectionName: string): Promise<void>;
 }
 export type MonomerCollection = {
     description?: string;
+    tags?: string[];
     monomerSymbols: string[];
     updatedBy: string;
     updatedOn: string;

package/src/types/monomer-library.d.ts.map

@@ -1 +1 @@
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package/src/types/monomer-library.js.map

@@ -1 +1 @@
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package/src/utils/annotation-track.d.ts

@@ -0,0 +1,42 @@
+/**
+ * AnnotationTrack — MSA header track displaying colored region bands.
+ *
+ * Shows FR/CDR regions (or any structure annotations) as colored horizontal
+ * rectangles with centered labels. This track is designed to be the primary
+ * (first) track in the MSA header when annotation data exists.
+ */
+import * as DG from 'datagrok-api/dg';
+import { MSAHeaderTrack } from './sequence-position-scroller';
+interface RegionSpan {
+    name: string;
+    color: string;
+    startIdx: number;
+    endIdx: number;
+    /** Scheme position name for start, e.g. "27" in IMGT */
+    startPos: string;
+    /** Scheme position name for end */
+    endPos: string;
+    /** Source numbering scheme, e.g. "IMGT" */
+    sourceScheme?: string;
+    description?: string;
+}
+export declare class AnnotationTrack extends MSAHeaderTrack {
+    private tableCol;
+    private regions;
+    private posList;
+    private _cacheVersion;
+    constructor(tableCol: DG.Column<string>, title?: string);
+    /** Returns true if there are region annotations to display. */
+    hasRegions(): boolean;
+    /** Returns the region covering the given 0-based position index, or null. */
+    getRegionAtPosition(posIdx: number): RegionSpan | null;
+    /** Override: provide tooltip content for the annotation track. */
+    getTooltipContent(position: number, _monomer: string | null): HTMLElement | null;
+    draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, _currentPosition: number): void;
+    private _ensureUpToDate;
+    private _rebuildRegions;
+    private _getPosList;
+    private _defaultColor;
+}
+export {};
+//# sourceMappingURL=annotation-track.d.ts.map

package/src/utils/annotation-track.d.ts.map

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package/src/utils/annotation-track.js

@@ -0,0 +1,159 @@
+import * as ui from 'datagrok-api/ui';
+import { MSAHeaderTrack } from './sequence-position-scroller';
+import { TAGS as bioTAGS } from './macromolecule/consts';
+import { AnnotationCategory, ANNOTATION_COLORS } from './macromolecule/annotations';
+/** Compact track height for the annotation band. */
+const ANNOTATION_TRACK_HEIGHT = 20;
+const ANNOTATION_TRACK_MIN_HEIGHT = 14;
+const ANNOTATION_FONT = 'bold 9px Roboto, Roboto Local, sans-serif';
+const ANNOTATION_LABEL_COLOR = '#333';
+export class AnnotationTrack extends MSAHeaderTrack {
+    constructor(tableCol, title = 'Annotations') {
+        super(ANNOTATION_TRACK_HEIGHT, ANNOTATION_TRACK_MIN_HEIGHT, title);
+        this.tableCol = tableCol;
+        this.regions = [];
+        this.posList = [];
+        this._cacheVersion = -1;
+        this._rebuildRegions();
+    }
+    /** Returns true if there are region annotations to display. */
+    hasRegions() {
+        this._ensureUpToDate();
+        return this.regions.length > 0;
+    }
+    /** Returns the region covering the given 0-based position index, or null. */
+    getRegionAtPosition(posIdx) {
+        this._ensureUpToDate();
+        for (const region of this.regions) {
+            if (posIdx >= region.startIdx && posIdx <= region.endIdx)
+                return region;
+        }
+        return null;
+    }
+    /** Override: provide tooltip content for the annotation track. */
+    getTooltipContent(position, _monomer) {
+        this._ensureUpToDate();
+        const region = this.getRegionAtPosition(position);
+        if (!region)
+            return null;
+        const scheme = region.sourceScheme ?? '';
+        const posName = position < this.posList.length ? this.posList[position] : '';
+        const lines = [];
+        const nameEl = document.createElement('b');
+        nameEl.textContent = region.name;
+        lines.push(ui.div([nameEl], { style: { fontSize: '13px', marginBottom: '4px' } }));
+        if (scheme)
+            lines.push(ui.divText(`Scheme: ${scheme}`, { style: { fontSize: '12px', color: '#555' } }));
+        lines.push(ui.divText(`Range: ${region.startPos} \u2013 ${region.endPos}`, { style: { fontSize: '12px', color: '#555' } }));
+        if (posName)
+            lines.push(ui.divText(`Position: ${posName}`, { style: { fontSize: '12px', color: '#555' } }));
+        if (region.description)
+            lines.push(ui.divText(region.description, { style: { fontSize: '11px', color: '#888', marginTop: '2px' } }));
+        return ui.divV(lines, { style: { padding: '4px' } });
+    }
+    draw(x, y, width, height, windowStart, positionWidth, totalPositions, _currentPosition) {
+        if (!this.ctx || !this.visible)
+            return;
+        this._ensureUpToDate();
+        if (this.regions.length === 0)
+            return;
+        const g = this.ctx;
+        g.save();
+        // Clip to track bounds
+        g.beginPath();
+        g.rect(x, y, width, height);
+        g.clip();
+        const visibleStart = windowStart - 1; // windowStart is 1-based
+        const visibleEnd = visibleStart + Math.ceil(width / positionWidth) + 2;
+        for (const region of this.regions) {
+            // Skip regions entirely outside the viewport
+            if (region.endIdx < visibleStart || region.startIdx > visibleEnd)
+                continue;
+            const drawStart = Math.max(region.startIdx, visibleStart);
+            const drawEnd = Math.min(region.endIdx, visibleEnd);
+            const rx = x + (drawStart - visibleStart) * positionWidth;
+            const rw = (drawEnd - drawStart + 1) * positionWidth;
+            // Draw background
+            g.fillStyle = region.color;
+            g.globalAlpha = 0.35;
+            g.fillRect(rx, y, rw, height);
+            g.globalAlpha = 1.0;
+            // Draw border
+            g.strokeStyle = region.color;
+            g.globalAlpha = 0.6;
+            g.lineWidth = 1;
+            g.strokeRect(rx + 0.5, y + 0.5, rw - 1, height - 1);
+            g.globalAlpha = 1.0;
+            // Draw label if there's enough room
+            g.font = ANNOTATION_FONT;
+            const labelWidth = g.measureText(region.name).width;
+            if (rw > labelWidth + 4) {
+                g.fillStyle = ANNOTATION_LABEL_COLOR;
+                g.textAlign = 'center';
+                g.textBaseline = 'middle';
+                g.fillText(region.name, rx + rw / 2, y + height / 2);
+            }
+        }
+        g.restore();
+    }
+    _ensureUpToDate() {
+        if (this._cacheVersion !== this.tableCol.version) {
+            this._rebuildRegions();
+            this._cacheVersion = this.tableCol.version;
+        }
+    }
+    _rebuildRegions() {
+        this.regions = [];
+        const annotTag = this.tableCol.getTag(bioTAGS.annotations);
+        if (!annotTag)
+            return;
+        let annotations;
+        try {
+            annotations = JSON.parse(annotTag);
+        }
+        catch {
+            return;
+        }
+        this.posList = this._getPosList();
+        if (this.posList.length === 0)
+            return;
+        for (const annot of annotations) {
+            if (annot.category !== AnnotationCategory.Structure)
+                continue;
+            if (annot.start == null || annot.end == null)
+                continue;
+            const startIdx = this.posList.indexOf(annot.start);
+            const endIdx = this.posList.indexOf(annot.end);
+            if (startIdx < 0 || endIdx < 0)
+                continue;
+            this.regions.push({
+                name: annot.name,
+                color: annot.color ?? this._defaultColor(annot),
+                startIdx,
+                endIdx,
+                startPos: annot.start,
+                endPos: annot.end,
+                sourceScheme: annot.sourceScheme,
+                description: annot.description,
+            });
+        }
+    }
+    _getPosList() {
+        const tag = this.tableCol.getTag(bioTAGS.positionNames);
+        if (!tag)
+            return [];
+        return tag.split(', ');
+    }
+    _defaultColor(annot) {
+        if (annot.name.startsWith('CDR')) {
+            const idx = parseInt(annot.name.replace('CDR', '')) - 1;
+            return ANNOTATION_COLORS.structure.CDR[idx % ANNOTATION_COLORS.structure.CDR.length];
+        }
+        if (annot.name.startsWith('FR')) {
+            const idx = parseInt(annot.name.replace('FR', '')) - 1;
+            return ANNOTATION_COLORS.structure.FR[idx % ANNOTATION_COLORS.structure.FR.length];
+        }
+        return '#90CAF9';
+    }
+}
+//# sourceMappingURL=annotation-track.js.map

package/src/utils/annotation-track.js.map

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package/src/utils/cell-renderer-annotations.d.ts

@@ -0,0 +1,48 @@
+/**
+ * AnnotationRenderer — overlays annotation visuals on top of sequence cells.
+ *
+ * Performance contract:
+ * - When no annotations exist, `hasAnnotations()` returns false and callers skip all drawing.
+ * - Parsed annotation data is cached by column version; re-parsed only on change.
+ * - The companion row-data column (hidden, name starting with ~) is re-looked up when the
+ *   sequence column version changes (so it's found even when created after first render).
+ */
+import * as DG from 'datagrok-api/dg';
+import { SeqAnnotation, SeqAnnotationHit } from './macromolecule/annotations';
+export declare class AnnotationRenderer {
+    private tableCol;
+    private _cache;
+    private _rowCache;
+    private _annotCol;
+    /** Version of tableCol at which _annotCol was last looked up.
+     *  Re-lookup when version changes (setting .annotationColumnName tag bumps it). */
+    private _annotColLookupVersion;
+    constructor(tableCol: DG.Column<string>);
+    /** Fast check — returns false when no annotations exist, so the render loop can skip entirely. */
+    hasAnnotations(): boolean;
+    /** Returns region annotations (column-level). */
+    getAnnotations(): SeqAnnotation[];
+    /** Returns the region name at a given position for a specific row.
+     *  Checks per-row region spans first; falls back to column-level only when
+     *  the row has no per-row region data at all. */
+    getRegionNameAtPosition(posIdx: number, rowIdx?: number): string | null;
+    /** Returns liability hits (non-region) for a specific row and position index. */
+    getHitsAtPosition(rowIdx: number, posIdx: number): SeqAnnotationHit[];
+    /** Draws annotation background + underline for a single position in a cell.
+     *  Called from MonomerPlacer.render() for each visible position.
+     *  @param textBottomY If provided, underline is drawn just below this y-coordinate
+     *    (use in single-line mode so the underline sticks to the letters). */
+    drawPositionBackground(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, posIdx: number, rowIdx: number, textBottomY?: number): void;
+    /** Builds a tooltip HTML snippet for annotations at a given position+row. */
+    getTooltipInfo(posIdx: number, rowIdx: number): string[];
+    /** Finds a per-row region span hit covering the given position, or null. */
+    private _findRowRegionHit;
+    /** Returns true if the row has any per-row region span data (hits with endPositionIndex set).
+     *  When true, column-level region mapping should NOT be used as fallback for this row. */
+    private _rowHasRegionData;
+    private _ensureCache;
+    private _ensureRowCache;
+    private _getPosList;
+    private _getDefaultRegionColor;
+}
+//# sourceMappingURL=cell-renderer-annotations.d.ts.map

package/src/utils/cell-renderer-annotations.d.ts.map

@@ -0,0 +1 @@
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package/src/utils/cell-renderer-annotations.js

@@ -0,0 +1,280 @@
+import { TAGS as bioTAGS } from './macromolecule/consts';
+import { AnnotationCategory, REGION_BG_OPACITY, LIABILITY_UNDERLINE_HEIGHT, ANNOTATION_COLORS, } from './macromolecule/annotations';
+export class AnnotationRenderer {
+    constructor(tableCol) {
+        this.tableCol = tableCol;
+        this._cache = null;
+        this._rowCache = null;
+        this._annotCol = null;
+        /** Version of tableCol at which _annotCol was last looked up.
+         *  Re-lookup when version changes (setting .annotationColumnName tag bumps it). */
+        this._annotColLookupVersion = -1;
+    }
+    /** Fast check — returns false when no annotations exist, so the render loop can skip entirely. */
+    hasAnnotations() {
+        this._ensureCache();
+        return this._cache !== null && this._cache.annotations.length > 0;
+    }
+    /** Returns region annotations (column-level). */
+    getAnnotations() {
+        this._ensureCache();
+        return this._cache?.annotations ?? [];
+    }
+    /** Returns the region name at a given position for a specific row.
+     *  Checks per-row region spans first; falls back to column-level only when
+     *  the row has no per-row region data at all. */
+    getRegionNameAtPosition(posIdx, rowIdx) {
+        // Check per-row region spans first
+        if (rowIdx != null) {
+            const hit = this._findRowRegionHit(rowIdx, posIdx);
+            if (hit) {
+                const annot = this._cache?.annotations.find((a) => a.id === hit.annotationId);
+                return annot?.name ?? null;
+            }
+            // If this row has per-row region data, don't fall back to column-level
+            if (this._rowHasRegionData(rowIdx))
+                return null;
+        }
+        // Fall back to column-level position map
+        this._ensureCache();
+        return this._cache?.positionRegionNames.get(posIdx) ?? null;
+    }
+    /** Returns liability hits (non-region) for a specific row and position index. */
+    getHitsAtPosition(rowIdx, posIdx) {
+        this._ensureRowCache();
+        if (!this._rowCache)
+            return [];
+        const rowData = this._rowCache.data[rowIdx];
+        if (!rowData)
+            return [];
+        return rowData.filter((h) => {
+            if (h.endPositionIndex != null)
+                return false; // Skip region spans
+            return h.positionIndex === posIdx || (h.matchedMonomers.length > 1 && posIdx > h.positionIndex && posIdx < h.positionIndex + h.matchedMonomers.length);
+        });
+    }
+    /** Draws annotation background + underline for a single position in a cell.
+     *  Called from MonomerPlacer.render() for each visible position.
+     *  @param textBottomY If provided, underline is drawn just below this y-coordinate
+     *    (use in single-line mode so the underline sticks to the letters). */
+    drawPositionBackground(g, x, y, w, h, posIdx, rowIdx, textBottomY) {
+        this._ensureCache();
+        if (!this._cache)
+            return;
+        this._ensureRowCache();
+        // Region background — check per-row region spans first, then column-level.
+        // If per-row region data exists for this row, use ONLY that (don't fall back
+        // to column-level, which has generic positions that don't match this row).
+        let regionColor;
+        const rowRegionHit = this._findRowRegionHit(rowIdx, posIdx);
+        if (rowRegionHit) {
+            const annot = this._cache.annotations.find((a) => a.id === rowRegionHit.annotationId);
+            regionColor = annot?.color ?? (annot ? this._getDefaultRegionColor(annot) : undefined);
+        }
+        if (!regionColor && !this._rowHasRegionData(rowIdx))
+            regionColor = this._cache.positionRegionColors.get(posIdx);
+        if (regionColor) {
+            g.save();
+            g.globalAlpha = REGION_BG_OPACITY;
+            g.fillStyle = regionColor;
+            g.fillRect(x, y, w, h);
+            g.restore();
+        }
+        // Liability underline — snapped to text bottom when textBottomY is provided
+        if (this._rowCache) {
+            const rowData = this._rowCache.data[rowIdx];
+            if (rowData) {
+                for (const hit of rowData) {
+                    if (hit.endPositionIndex != null)
+                        continue; // Skip region spans
+                    if (posIdx >= hit.positionIndex && posIdx < hit.positionIndex + hit.matchedMonomers.length) {
+                        const annot = this._cache.annotations.find((a) => a.id === hit.annotationId);
+                        if (annot?.color) {
+                            const underlineY = textBottomY != null
+                                ? textBottomY + 1
+                                : y + h - LIABILITY_UNDERLINE_HEIGHT;
+                            g.fillStyle = annot.color;
+                            g.fillRect(x, underlineY, w, LIABILITY_UNDERLINE_HEIGHT);
+                        }
+                        break; // Only draw one underline
+                    }
+                }
+            }
+        }
+    }
+    /** Builds a tooltip HTML snippet for annotations at a given position+row. */
+    getTooltipInfo(posIdx, rowIdx) {
+        this._ensureCache();
+        const lines = [];
+        if (!this._cache)
+            return lines;
+        this._ensureRowCache();
+        // Region info — check per-row region spans first; fall back to column-level
+        // only when the row has no per-row region data at all.
+        let regionName = null;
+        const rowRegionHit = this._findRowRegionHit(rowIdx, posIdx);
+        if (rowRegionHit) {
+            const annot = this._cache.annotations.find((a) => a.id === rowRegionHit.annotationId);
+            if (annot) {
+                regionName = annot.name;
+                const scheme = annot.sourceScheme ?? '';
+                lines.push(`Region: ${annot.name}${scheme ? ` (${scheme} ${annot.start}-${annot.end})` : ''}`);
+            }
+        }
+        if (!regionName && !this._rowHasRegionData(rowIdx)) {
+            const colRegionName = this._cache.positionRegionNames.get(posIdx);
+            if (colRegionName) {
+                const annot = this._cache.annotations.find((a) => a.name === colRegionName && a.category === AnnotationCategory.Structure);
+                const scheme = annot?.sourceScheme ?? '';
+                lines.push(`Region: ${colRegionName}${scheme ? ` (${scheme} ${annot?.start}-${annot?.end})` : ''}`);
+            }
+        }
+        // Liability hits
+        if (this._rowCache) {
+            const rowData = this._rowCache.data[rowIdx];
+            if (rowData) {
+                for (const hit of rowData) {
+                    if (hit.endPositionIndex != null)
+                        continue; // Skip region spans
+                    if (posIdx >= hit.positionIndex && posIdx < hit.positionIndex + hit.matchedMonomers.length) {
+                        const annot = this._cache.annotations.find((a) => a.id === hit.annotationId);
+                        if (annot) {
+                            const severityLabel = annot.severity ? ` - ${annot.severity.charAt(0).toUpperCase() + annot.severity.slice(1)}` : '';
+                            lines.push(`\u26A0 ${annot.name}${severityLabel}`);
+                        }
+                    }
+                }
+            }
+        }
+        return lines;
+    }
+    /** Finds a per-row region span hit covering the given position, or null. */
+    _findRowRegionHit(rowIdx, posIdx) {
+        this._ensureRowCache();
+        if (!this._rowCache)
+            return null;
+        const rowData = this._rowCache.data[rowIdx];
+        if (!rowData)
+            return null;
+        for (const hit of rowData) {
+            if (hit.endPositionIndex != null && posIdx >= hit.positionIndex && posIdx <= hit.endPositionIndex)
+                return hit;
+        }
+        return null;
+    }
+    /** Returns true if the row has any per-row region span data (hits with endPositionIndex set).
+     *  When true, column-level region mapping should NOT be used as fallback for this row. */
+    _rowHasRegionData(rowIdx) {
+        this._ensureRowCache();
+        if (!this._rowCache)
+            return false;
+        const rowData = this._rowCache.data[rowIdx];
+        if (!rowData)
+            return false;
+        return rowData.some((h) => h.endPositionIndex != null);
+    }
+    // --- Internal caching ---
+    _ensureCache() {
+        const currentVersion = this.tableCol.version;
+        if (this._cache && this._cache.colVersion === currentVersion)
+            return;
+        const annotTag = this.tableCol.getTag(bioTAGS.annotations);
+        if (!annotTag) {
+            this._cache = null;
+            return;
+        }
+        let annotations;
+        try {
+            annotations = JSON.parse(annotTag);
+        }
+        catch {
+            this._cache = null;
+            return;
+        }
+        if (!annotations || annotations.length === 0) {
+            this._cache = null;
+            return;
+        }
+        // Build position maps for structure annotations
+        const positionRegionColors = new Map();
+        const positionRegionNames = new Map();
+        const posList = this._getPosList();
+        for (const annot of annotations) {
+            if (annot.category !== AnnotationCategory.Structure)
+                continue;
+            if (annot.start == null || annot.end == null)
+                continue;
+            const startIdx = posList.indexOf(annot.start);
+            const endIdx = posList.indexOf(annot.end);
+            if (startIdx < 0 || endIdx < 0)
+                continue;
+            const color = annot.color ?? this._getDefaultRegionColor(annot);
+            for (let i = startIdx; i <= endIdx; i++) {
+                positionRegionColors.set(i, color);
+                positionRegionNames.set(i, annot.name);
+            }
+        }
+        this._cache = { colVersion: currentVersion, annotations, positionRegionColors, positionRegionNames };
+    }
+    _ensureRowCache() {
+        // Re-lookup companion column when the sequence column version changes.
+        // This ensures we pick up the companion column if it was created after
+        // the first render (e.g., liability scan creates it later).
+        const seqVersion = this.tableCol.version;
+        if (this._annotColLookupVersion !== seqVersion) {
+            this._annotColLookupVersion = seqVersion;
+            const annotColName = this.tableCol.getTag(bioTAGS.annotationColumnName);
+            if (annotColName) {
+                try {
+                    this._annotCol = this.tableCol.dataFrame.columns.byName(annotColName);
+                }
+                catch {
+                    this._annotCol = null;
+                }
+            }
+            else {
+                this._annotCol = null;
+            }
+        }
+        if (!this._annotCol) {
+            this._rowCache = null;
+            return;
+        }
+        const currentVersion = this._annotCol.version;
+        if (this._rowCache && this._rowCache.colVersion === currentVersion)
+            return;
+        const data = new Array(this._annotCol.length);
+        for (let i = 0; i < this._annotCol.length; i++) {
+            const raw = this._annotCol.get(i);
+            if (!raw) {
+                data[i] = null;
+                continue;
+            }
+            try {
+                data[i] = JSON.parse(raw);
+            }
+            catch {
+                data[i] = null;
+            }
+        }
+        this._rowCache = { colVersion: currentVersion, data };
+    }
+    _getPosList() {
+        const posNamesTag = this.tableCol.getTag(bioTAGS.positionNames);
+        if (!posNamesTag)
+            return [];
+        return posNamesTag.split(', ');
+    }
+    _getDefaultRegionColor(annot) {
+        if (annot.name.startsWith('CDR')) {
+            const idx = parseInt(annot.name.replace('CDR', '')) - 1;
+            return ANNOTATION_COLORS.structure.CDR[idx % ANNOTATION_COLORS.structure.CDR.length];
+        }
+        if (annot.name.startsWith('FR')) {
+            const idx = parseInt(annot.name.replace('FR', '')) - 1;
+            return ANNOTATION_COLORS.structure.FR[idx % ANNOTATION_COLORS.structure.FR.length];
+        }
+        return '#90CAF9';
+    }
+}
+//# sourceMappingURL=cell-renderer-annotations.js.map