@jbrowse/bandage-core 0.1.19 → 4.0.24

package/dist/types/cli/figure.d.ts

@@ -0,0 +1,20 @@
+import type { BubbleSpread } from '../bubbleSpreads.js';
+import type { FigureOptions } from '../figure.js';
+import type { LayoutModeValue } from '../layoutModes.js';
+import type { WalkLayer } from '../walkEncoding.js';
+export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region'> {
+    gfa?: string;
+    gbz?: {
+        db: string;
+        index?: string;
+        region: string;
+        haplotypes?: string[];
+        referenceSample?: string;
+    };
+    region?: string;
+    referencePath?: string;
+    layout?: LayoutModeValue;
+    quality?: number;
+    bubbleSpread?: BubbleSpread;
+    walks?: (string | WalkLayer)[];
+}

package/dist/types/facetGrid.d.ts

@@ -19,3 +19,13 @@ export declare function facetGrid({ count, bounds, pixelRows, width, room, colum
     room: number;
     columns?: number;
 }): FacetGrid;
+export type FacetBy = 'walk' | 'sample';
+export declare function facetCells(names: string[], by: FacetBy): {
+    columns: undefined;
+    count: number;
+    cells: number[];
+} | {
+    columns: number;
+    count: number;
+    cells: number[];
+};

package/dist/types/figure.d.ts

@@ -0,0 +1,24 @@
+import type { ColorScheme } from './colorSchemes.js';
+import type { FacetBy } from './facetGrid.js';
+import type { NodeWidth } from './nodeWidths.js';
+import type { Graph, LayoutResult } from './types.js';
+import type { WalkLayer } from './walkEncoding.js';
+export interface FigureOptions {
+    width?: number;
+    height?: number;
+    walks?: WalkLayer[];
+    facet?: 'none' | FacetBy;
+    columns?: number;
+    colorScheme?: ColorScheme;
+    nodeWidth?: NodeWidth;
+    showDeletionEdges?: boolean;
+    contigThickness?: number;
+    connectorThickness?: number;
+    region?: {
+        refName: string;
+        start: number;
+        end: number;
+    };
+    metadata?: string;
+}
+export declare function figureSvg(graph: Graph, layout: LayoutResult, o?: FigureOptions): string;

package/dist/types/genes/genePins.d.ts

@@ -13,6 +13,10 @@ export interface GeneModel {
 export interface GenePin {
     gene: GeneModel;
     exons: string;
+    exonsByNode: {
+        nodeId: string;
+        d: string;
+    }[];
     at: NodeSegment;
     covered: number;
 }

package/dist/types/index.d.ts

@@ -33,11 +33,14 @@ export type { TubeMapColumn, TubeMapDrawing } from './layout/tubeMapLayout.js';
 export { deletionEdges } from './deletionEdges.js';
 export type { DeletionEdge } from './deletionEdges.js';
 export { facetLifts, walkHighlight, walkLift } from './walkHighlight.js';
-export { walkKey } from './walkKey.js';
-export { FACET_GAP_PX, FACET_PAD_PX, FACET_TITLE_PX, facetGrid, } from './facetGrid.js';
-export type { FacetGrid } from './facetGrid.js';
+export { rangeText, walkKey } from './walkKey.js';
+export { figureSvg } from './figure.js';
+export type { FigureOptions } from './figure.js';
+export { svgCanvas } from './renderer/svgCanvas.js';
+export { FACET_GAP_PX, FACET_PAD_PX, FACET_TITLE_PX, facetCells, facetGrid, } from './facetGrid.js';
+export type { FacetBy, FacetGrid } from './facetGrid.js';
 export type { LiftedWalk, WalkLift } from './walkHighlight.js';
-export { WALK_FIELDS, WALK_SCHEMES, encodingSwatchCss, resolveEncoding, schemeCss, } from './walkEncoding.js';
+export { WALK_FIELDS, WALK_SCHEMES, encodingStops, encodingSwatchCss, resolveEncoding, schemeCss, } from './walkEncoding.js';
 export type { WalkEncoding, WalkField, WalkLayer, WalkScheme, } from './walkEncoding.js';
 export { pathColorsLegible, pathLegend } from './pathColors.js';
 export { bubblesFromGraph } from './bubbles/bubblesFromGraph.js';
@@ -50,7 +53,7 @@ export { walkRows } from './layout/walkRows.js';
 export type { WalkRows } from './layout/walkRows.js';
 export { walkRowsExtent } from './layout/walkRowLayout.js';
 export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
-export { HALO_FACTOR, LEGEND_INSET_PX, layoutLabels } from './labelLayout.js';
+export { HALO_FACTOR, LEGEND_INSET_PX, geneCoverageNote, layoutLabels, } from './labelLayout.js';
 export type { LabelLayout, LabelLayoutSource } from './labelLayout.js';
 export { formatBp } from './graphLabels.js';
 export { genePins } from './genes/genePins.js';

package/dist/types/labelLayout.d.ts

@@ -45,4 +45,5 @@ export interface LabelLayout {
     }>[];
     sizes: GraphLabel[];
 }
+export declare function geneCoverageNote(pin: GenePin): string | undefined;
 export declare function layoutLabels(m: LabelLayoutSource): LabelLayout;

package/dist/types/overlayLabels.d.ts

@@ -13,6 +13,7 @@ export interface LabelCandidate<T> {
     y: number;
     text: string;
     stack?: number;
+    fallback?: string;
 }
 export interface PlacedLabel<T> extends LabelCandidate<T> {
     w: number;

package/dist/types/referenceStrip.d.ts

@@ -1,19 +1,21 @@
 import type { ResolvedColorScheme } from './colorSchemes.js';
 import type { ReferenceRamp } from './renderer/GeometryBuilder.js';
 import type { Graph, NodeSegment } from './types.js';
-export declare const REFERENCE_STRIP_PX = 10;
+export declare const REFERENCE_STRIP_PX = 12;
 export declare const REFERENCE_STRIP_ZONE_PX: number;
 export interface StripBlock {
     node: string;
     bp0: number;
     bp1: number;
-    color: string;
+    colors: string[];
+    faded: boolean;
 }
-export declare function referenceStripBlocks(graph: Graph, { colorScheme, referenceRamp, walkNodes, walkColors, }: {
+export declare function referenceStripBlocks(graph: Graph, { colorScheme, referenceRamp, walks, }: {
     colorScheme: ResolvedColorScheme;
     referenceRamp?: ReferenceRamp;
-    walkNodes?: ReadonlySet<string>;
-    walkColors?: ReadonlyMap<string, number>;
+    walks?: readonly {
+        colors: ReadonlyMap<string, number>;
+    }[];
 }): StripBlock[];
 export interface BpFrame {
     scale: number;
@@ -39,8 +41,15 @@ export interface StripLit {
         y: number;
     };
 }
-export declare function drawReferenceStrip(ctx: CanvasRenderingContext2D, blocks: readonly StripBlock[], frame: BpFrame, { width, lit, darkMode, }: {
+export declare function stripPixels(blocks: readonly StripBlock[], frame: BpFrame, width: number, dpr: number): {
+    colors: string[];
+    x0: number;
+    x1: number;
+    tier: number;
+}[];
+export declare function drawReferenceStrip(ctx: CanvasRenderingContext2D, blocks: readonly StripBlock[], frame: BpFrame, { width, lit, darkMode, dpr, }: {
     width: number;
     lit?: StripLit;
     darkMode?: boolean;
+    dpr?: number;
 }): void;

package/dist/types/renderer/svgCanvas.d.ts

@@ -0,0 +1,4 @@
+export declare function svgCanvas(width: number, height: number): {
+    canvas: HTMLCanvasElement;
+    markup: () => string;
+};

package/dist/types/walkEncoding.d.ts

@@ -48,4 +48,8 @@ export declare function schemeCss(scheme: WalkScheme, t: number): string;
 export declare function schemeColor(scheme: WalkScheme, t: number): number;
 export declare function encodedColor({ field, scheme }: WalkEncoding, t?: number): number;
 export declare const NO_VALUE_COLOR: number;
-export declare function encodingSwatchCss({ field, scheme }: WalkEncoding): string;
+export declare function encodingStops({ field, scheme }: WalkEncoding): {
+    offset: number;
+    color: string;
+}[];
+export declare function encodingSwatchCss(encoding: WalkEncoding): string;

package/dist/types/walkKey.d.ts

@@ -1,4 +1,5 @@
 import type { LiftedWalk } from './walkHighlight.js';
+export declare function rangeText(contig: string | undefined, start: number, end: number): string;
 export declare function walkKey(walk: LiftedWalk, reference?: {
     name?: string;
     start: number;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "0.1.19",
+  "version": "4.0.24",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -24,6 +24,9 @@
   "publishConfig": {
     "access": "public"
   },
+  "bin": {
+    "bandage-figure": "dist/cli/figure.js"
+  },
   "files": [
     "dist"
   ],