@weng-lab/genomebrowser 0.0.16 → 0.0.18

package/dist/components/tracks/importance/importance.d.ts

@@ -0,0 +1,32 @@
+import { Domain } from '../../../utils/types';
+import { DisplayMode } from '../types';
+import { ImportanceTrackAnnotation, ImportanceTrackData, ImportanceTrackDataPoint } from './importanceTrack';
+export type ImportanceProps = {
+    data: ImportanceTrackData;
+    width: number;
+    height: number;
+    domain: Domain;
+    id: string;
+    title: string;
+    titleSize: number;
+    trackMargin: number;
+    displayMode: DisplayMode;
+};
+export type ImportanceOptions = {
+    onSequenceLoaded?: (sequence: string) => void;
+    allowSelection?: boolean;
+    onSelectionEnd?: (coordinates: [number, number], values: ImportanceTrackDataPoint[]) => void;
+    onBaseMousedOver?: (x: ImportanceTrackDataPoint, i: number) => void;
+    onBaseClicked?: (x: ImportanceTrackDataPoint, i: number) => void;
+    onBaseMousedOut?: () => void;
+    svgRef?: React.RefObject<SVGSVGElement>;
+    zeroLineProps?: React.SVGProps<SVGLineElement>;
+    annotations?: ImportanceTrackAnnotation[];
+    transform?: string;
+};
+export declare const DefaultImportance: {
+    titleSize: number;
+    trackMargin: number;
+    canDrag: boolean;
+};
+export default function Importance(props: ImportanceProps & ImportanceOptions): import("react/jsx-runtime").JSX.Element;

package/dist/components/tracks/importance/importanceTrack.d.ts

@@ -0,0 +1,62 @@
+import { default as React } from 'react';
+export type ImportanceTrackAnnotation = {
+    coordinates: [number, number];
+    color: string;
+    onMouseOver?: () => void;
+    children?: React.ReactElement[];
+};
+export type ImportanceTrackDataPoint = {
+    base: string;
+    importance: number;
+};
+export type ImportanceTrackSequence = {
+    sequence: string;
+    importance: number[];
+};
+export type ImportanceTrackData = ImportanceTrackDataPoint[] | ImportanceTrackSequence;
+export declare function isImportanceTrackSequence(data: ImportanceTrackData): data is ImportanceTrackSequence;
+/**
+ * Properties of an ImportanceTrack component.
+ * @member width the width of the component in SVG coordinates.
+ * @member height the height of the component in SVG coordinates.
+ * @member transform optional SVG transform to apply to the component.
+ * @member allowSelection if set, allows the user to click and drag to select sequences from the track.
+ * @member onSelectionEnd callback receiving information about a selection when the user releases the mouse.
+ * @member onBaseMousedOver callback receiving information about a moused over base in the sequence.
+ * @member onBaseMousedOut callback triggered when the user mouses out of a previously moused over base.
+ * @member onBaseClicked callback receiving information about a clicked base in the sequence.
+ * @member svgRef optional React reference to the containing SVG component.
+ * @member zeroLineProps optional SVG properties of the horizontal line at importance=0.
+ */
+export type TrackProps = {
+    width: number;
+    height: number;
+    transform?: string;
+    allowSelection?: boolean;
+    onSelectionEnd?: (coordinates: [number, number], values: ImportanceTrackDataPoint[]) => void;
+    onBaseMousedOver?: (x: ImportanceTrackDataPoint, i: number) => void;
+    onBaseClicked?: (x: ImportanceTrackDataPoint, i: number) => void;
+    onBaseMousedOut?: () => void;
+    svgRef?: React.RefObject<SVGSVGElement>;
+    zeroLineProps?: React.SVGProps<SVGLineElement>;
+    annotations?: ImportanceTrackAnnotation[];
+};
+/**
+ * Properties of an ImportanceTrack component.
+ * @member data the sequence/importance data to render.
+ */
+export type ImportanceTrackProps = TrackProps & {
+    data: ImportanceTrackData;
+    onSequenceLoaded?: (sequence: string) => void;
+};
+/**
+ *
+ * A sequence/importance track. Must be rendered within an SVG element. Data may be provided as a sequence string
+ * plus an array of importance values or an array of sequence/importance value pairs.
+ *
+ * @param props component properties; see TrackProps and ImportanceTrackProps.
+ * @returns a rendered ImportanceTrack component instance.
+ *
+ */
+declare const ImportanceTrack: React.FC<ImportanceTrackProps>;
+export default ImportanceTrack;

package/dist/components/tracks/importance/index.d.ts

@@ -0,0 +1,4 @@
+import { default as Importance, ImportanceProps, ImportanceOptions, DefaultImportance } from './importance';
+export { Importance };
+export type { ImportanceProps, ImportanceOptions };
+export { DefaultImportance };

package/dist/components/tracks/importance/letter.d.ts

@@ -0,0 +1,16 @@
+import { default as React } from 'react';
+import { ImportanceTrackDataPoint } from './importanceTrack';
+export type LetterProps = ImportanceTrackDataPoint & {
+    fill?: string;
+    x: number;
+    totalHeight: number;
+    totalWidth: number;
+    transform: (x: number) => [number, number, string];
+    xScale: number;
+    onMouseOver?: () => void;
+    onMouseOut?: () => void;
+    onMouseUp?: () => void;
+    onClick?: () => void;
+};
+declare const Letter: React.FC<LetterProps>;
+export default Letter;

package/dist/components/tracks/importance/utils.d.ts

@@ -0,0 +1,27 @@
+import { ImportanceTrackAnnotation, ImportanceTrackData, ImportanceTrackDataPoint } from './importanceTrack';
+export type Range = {
+    start: number;
+    end: number;
+};
+export declare function linearTransform(initial: Range, final: Range): (value: number) => number;
+type YRange = {
+    start: number;
+    end: number;
+};
+export type GenomicRange = {
+    chromosome: string;
+    start: number;
+    end: number;
+};
+export declare function yRange<T>(values: T[], transform: (v: T) => number): YRange;
+export declare function svgElementTransform(transform: (x: number) => number): (x: number) => [number, number, string];
+export declare function useRenderedImportanceTrackData(data: ImportanceTrackData, height: number): [ImportanceTrackDataPoint[], (x: number) => [number, number, string], (x: number) => number];
+export declare function useRenderedImportanceTrackAnnotations(annotations: ImportanceTrackAnnotation[], data: ImportanceTrackDataPoint[], transform: (x: number) => number): {
+    y: number;
+    height: number;
+    coordinates: [number, number];
+    color: string;
+    onMouseOver?: () => void;
+    children?: React.ReactElement[];
+}[];
+export {};

package/dist/components/tracks/motif/index.d.ts

@@ -1,4 +1,4 @@
-import { default as DenseMotif } from './dense';
-import { DenseMotifProps, SquishMotifProps } from './types';
-import { default as SquishMotif } from './squish';
-export { DenseMotif, SquishMotif, type DenseMotifProps, type SquishMotifProps };
+import { default as Motif, MotifProps, MotifOptions, DefaultMotif } from './motif';
+export { Motif };
+export type { MotifProps, MotifOptions };
+export { DefaultMotif };

package/dist/components/tracks/motif/motif.d.ts

@@ -0,0 +1,33 @@
+import { TrackType, DisplayMode } from '../types';
+import { Rect } from './types';
+import { Domain } from '../../../utils/types';
+export type MotifProps = {
+    displayMode: DisplayMode;
+    width: number;
+    height: number;
+    id: string;
+    domain: Domain;
+    data?: Rect[];
+    title: string;
+    titleSize: number;
+    trackMargin: number;
+};
+export type MotifOptions = {
+    transform?: string;
+    peakColor?: string;
+    color?: string;
+    peaks?: Rect[];
+    svgRef?: React.RefObject<SVGSVGElement>;
+    rowHeight?: number;
+    onHeightChanged?: (height: number) => void;
+    canDrag?: boolean;
+};
+export declare const DefaultMotif: {
+    trackType: TrackType;
+    titleSize: number;
+    trackMargin: number;
+    height: number;
+    displayMode: DisplayMode;
+    canDrag: boolean;
+};
+export default function Motif(props: MotifProps & MotifOptions): import("react/jsx-runtime").JSX.Element | null;

package/dist/components/tracks/motif/types.d.ts

@@ -8,7 +8,6 @@ export type DenseMotifProps = {
     width: number;
     height: number;
     id?: string;
-    transform?: string;
     color?: string;
     peakColor?: string;
     domain: Domain;
@@ -16,6 +15,8 @@ export type DenseMotifProps = {
     peaks?: Rect[];
     svgRef?: React.RefObject<SVGSVGElement>;
     onHeightChanged?: (height: number) => void;
+    canDrag?: boolean;
+    hoverColor?: string;
 };
 export type SquishMotifProps = {
     data?: Rect[];
@@ -23,10 +24,11 @@ export type SquishMotifProps = {
     width: number;
     rowHeight: number;
     id?: string;
-    transform?: string;
     color?: string;
     peakColor?: string;
     domain: Domain;
     svgRef?: React.RefObject<SVGSVGElement>;
     onHeightChanged?: (height: number) => void;
+    canDrag?: boolean;
+    hoverColor?: string;
 };

package/dist/components/tracks/types.d.ts

@@ -2,6 +2,10 @@ import { OperationVariables, LazyQueryExecFunction } from '@apollo/client';
 import { BigBedOptions, BigWigOptions } from '../../lib';
 import { TranscriptOptions } from './transcripts';
 import { Rect } from './bigbed/types';
+import { ImportanceTrackAnnotation, ImportanceTrackDataPoint } from './importance/importanceTrack';
+import { Rect as MotifRect } from './motif/types';
+import { MotifOptions } from './motif/motif';
+import { ImportanceOptions } from './importance/importance';
 /**
  * Display modes for tracks
  */
@@ -21,6 +25,7 @@ export declare enum TrackType {
     RULER = "ruler",
     BIGWIG = "bigwig",
     BIGBED = "bigbed",
+    IMPORTANCE = "importance",
     TRANSCRIPT = "transcript",
     BAM = "bam",
     MOTIF = "motif",
@@ -39,7 +44,8 @@ export type BaseTrack = {
     trackMargin: number;
     displayMode: DisplayMode;
     trackType: TrackType;
-    data?: any[];
+    data?: any;
+    loading?: boolean;
     hoverColor?: string;
     error?: string;
     refetch?: LazyQueryExecFunction<any, OperationVariables>;
@@ -75,4 +81,27 @@ export type TranscriptTrackProps = {
     version: TranscriptHumanVersion | TranscriptMouseVersion;
     props?: TranscriptOptions;
 } & BaseTrack;
-export type TrackProps = BigWigTrackProps | BigBedTrackProps | TranscriptTrackProps;
+export type ImportanceTrackProps = {
+    signalURL: string;
+    onSequenceLoaded?: (sequence: string) => void;
+    transform?: string;
+    allowSelection?: boolean;
+    onSelectionEnd?: (coordinates: [number, number], values: ImportanceTrackDataPoint[]) => void;
+    onBaseMousedOver?: (x: ImportanceTrackDataPoint, i: number) => void;
+    onBaseClicked?: (x: ImportanceTrackDataPoint, i: number) => void;
+    onBaseMousedOut?: () => void;
+    svgRef?: React.RefObject<SVGSVGElement>;
+    zeroLineProps?: React.SVGProps<SVGLineElement>;
+    annotations?: ImportanceTrackAnnotation[];
+    props?: ImportanceOptions;
+} & BaseTrack;
+export type MotifTrackProps = {
+    assembly: string;
+    consensusRegex: string;
+    peaksAccession: string;
+    peaks?: MotifRect[];
+    occurences: boolean;
+    rowHeight?: number;
+    props?: MotifOptions;
+} & BaseTrack;
+export type TrackProps = BigWigTrackProps | BigBedTrackProps | TranscriptTrackProps | MotifTrackProps | ImportanceTrackProps;