@weng-lab/genomebrowser 1.1.0 → 1.2.0

package/dist/api/apiTypes.d.ts

@@ -6,6 +6,7 @@ export interface BigRequest {
     chr1: string;
     start: number;
     end: number;
+    preRenderedWidth?: number;
 }
 export interface BigResponse {
     bigRequests: {
@@ -59,3 +60,22 @@ export interface MotifRect {
     end: number;
     pwm?: number[][];
 }
+export interface MethylCRequest {
+    plusStrand: {
+        cpgPlus: BigRequest;
+        chgPlus: BigRequest;
+        chhPlus: BigRequest;
+        depthPlus: BigRequest;
+    };
+    minusStrand: {
+        cpgMinus: BigRequest;
+        chgMinus: BigRequest;
+        chhMinus: BigRequest;
+        depthMinus: BigRequest;
+    };
+}
+export interface MethylCResponse {
+    bigRequests: {
+        data: any;
+    }[];
+}

package/dist/api/queries.d.ts

@@ -1,7 +1,7 @@
 /**
  * All GraphQL queries for the genome browser
  */
-export declare const BIGDATA_QUERY: import('graphql').DocumentNode;
-export declare const TRANSCRIPT_GENES_QUERY: import('graphql').DocumentNode;
-export declare const MOTIF_QUERY: import('graphql').DocumentNode;
+export declare const BIGDATA_QUERY: import('@apollo/client').DocumentNode;
+export declare const TRANSCRIPT_GENES_QUERY: import('@apollo/client').DocumentNode;
+export declare const MOTIF_QUERY: import('@apollo/client').DocumentNode;
 export declare const VARIANT_QUERY = "\n  query SNP($assembly: String!, $coordinates: [GenomicRangeInput]) {\n    snpQuery(assembly: $assembly, coordinates: $coordinates, common: true) {\n      id\n      coordinates {\n        chromosome\n        start\n        end\n      }\n    }\n  }\n";

package/dist/api/queryExecutor.d.ts

@@ -7,6 +7,7 @@ export interface QueryExecutors {
     fetchImportance: LazyQueryExecFunction<unknown, OperationVariables>;
     fetchBulkBed: LazyQueryExecFunction<unknown, OperationVariables>;
     fetchSnps: LazyQueryExecFunction<unknown, OperationVariables>;
+    fetchMethylC: LazyQueryExecFunction<unknown, OperationVariables>;
 }
 /**
  * Execute all queries concurrently based on built requests

package/dist/api/requestBuilder.d.ts

@@ -8,12 +8,13 @@ export interface AllRequests {
     importanceRequests: BigRequest[];
     bulkBedRequests: BigRequest[];
     ldRequest?: LDRequest;
+    methylCRequest?: BigRequest[];
 }
 /**
  * Build BigWig/BigBed requests for given tracks
  */
-export declare function buildBigRequests(tracks: Track[], domain: Domain): BigRequest[];
-/**
+export declare function buildBigRequests(tracks: Track[], domain: Domain, preRenderedWidth: number): BigRequest[];
+/**`
  * Build BulkBed requests for given tracks
  */
 export declare function buildBulkBedRequests(tracks: Track[], domain: Domain): BigRequest[];
@@ -34,7 +35,8 @@ export declare function buildImportanceRequests(tracks: Track[], currentDomain:
  * Build LD request for given tracks (first LD track found)
  */
 export declare function buildLDRequest(tracks: Track[], domain: Domain): LDRequest | undefined;
+export declare function buildMethylCRequest(tracks: Track[], domain: Domain, preRenderedWidth: number): BigRequest[] | undefined;
 /**
  * Build all requests for all track types in one coordinated call
  */
-export declare function buildAllRequests(tracks: Track[], expandedDomain: Domain, currentDomain: Domain): AllRequests;
+export declare function buildAllRequests(tracks: Track[], expandedDomain: Domain, currentDomain: Domain, preRenderedWidth: number): AllRequests;

package/dist/api/resultsProcessor.d.ts

@@ -14,6 +14,8 @@ export interface QueryResults {
     importanceError?: ApolloError;
     bulkBedError?: ApolloError;
     snpError?: ApolloError;
+    methylCData?: BigResponse;
+    methylCError?: ApolloError;
 }
 export interface ProcessedResult {
     trackId: string;

package/dist/components/cytoband/centromere.d.ts

@@ -0,0 +1,2 @@
+import { CentromereProps } from './types';
+export default function Centromere(props: CentromereProps): import("react/jsx-runtime").JSX.Element;

package/dist/components/cytoband/cytoband.d.ts

@@ -0,0 +1,2 @@
+import { CytobandProps } from './types';
+export default function Cytoband(props: CytobandProps): import("react/jsx-runtime").JSX.Element | null;

package/dist/components/cytoband/cytobands.d.ts

@@ -0,0 +1,5 @@
+import { Domain } from '../../utils/types';
+export default function Cytobands({ assembly, currentDomain, }: {
+    assembly: string;
+    currentDomain: Domain;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/components/cytoband/highlight.d.ts

@@ -0,0 +1,2 @@
+import { CytobandHighlightProps } from './types';
+export default function CytobandHighlight(props: CytobandHighlightProps): import("react/jsx-runtime").JSX.Element;

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

@@ -0,0 +1,61 @@
+import { default as React } from 'react';
+import { Domain } from '../../utils/types';
+export type Highlight = {
+    color: string;
+    start: number;
+    end: number;
+};
+export type ShortHighlightProps = {
+    highlight: Highlight;
+    x: (value: number) => number;
+    height: number;
+};
+export type Cytoband = {
+    stain: string;
+    coordinates: Domain;
+};
+export type CytobandColors = {
+    default: string;
+    centromere: string;
+    stalk: string;
+};
+export type CytobandsProps = {
+    data: Cytoband[];
+    width: number;
+    height: number;
+    id: string;
+    colors?: CytobandColors;
+    transform?: string;
+    highlight?: Highlight;
+    highlights?: Highlight[];
+    onHighlightMouseOver?: (highlight: Highlight, x: number, i: number) => void;
+    onHighlightMouseOut?: () => void;
+    onHighlightClick?: (highlight: Highlight, x: number, i: number) => void;
+    domain?: Domain;
+    children?: React.ReactNode;
+    opacity?: number;
+};
+export type CytobandProps = {
+    colors: CytobandColors;
+    width: number;
+    height: number;
+    type: string;
+    x: number;
+    opacity?: number;
+};
+export type CentromereProps = {
+    color: string;
+    width: number;
+    height: number;
+    x: number;
+    opening: boolean;
+};
+export type CytobandHighlightProps = {
+    x: (value: number) => number;
+    height: number;
+    width: number;
+    highlight: Highlight;
+    onMouseOver?: () => void;
+    onMouseOut?: () => void;
+    onClick?: () => void;
+};

package/dist/components/modal/helpers.d.ts

@@ -0,0 +1,7 @@
+export declare function getTextColor(backgroundColor: string): string;
+export declare function shadeColor(color: string, percent: number): string;
+export declare const isDark: (color: string) => boolean;
+export declare function getButtonColors(trackColor: string, selected: boolean): {
+    backgroundColor: string;
+    color: string;
+};

package/dist/components/modal/modal.d.ts

@@ -1,4 +1 @@
 export default function Modal(): import("react/jsx-runtime").JSX.Element | null;
-export declare function getTextColor(backgroundColor: string): string;
-export declare function shadeColor(color: string, percent: number): string;
-export declare const isDark: (color: string) => boolean;

package/dist/components/tracks/bigwig/full.d.ts

@@ -1,2 +1,6 @@
 import { FullBigWigProps } from './types';
+/**
+ * @deprecated Use ReworkBigWig instead
+ * Keeping this file in case something breaks
+ */
 export default function FullBigWig({ data, range, customRange, id, height, color, dimensions, tooltip, }: FullBigWigProps): import("react/jsx-runtime").JSX.Element;

package/dist/components/tracks/bigwig/rework.d.ts

@@ -0,0 +1,2 @@
+import { FullBigWigProps } from './types';
+export default function ReworkBigWig({ data, customRange, id, height, color, dimensions, tooltip }: FullBigWigProps): import("react/jsx-runtime").JSX.Element;

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

@@ -1,5 +1,5 @@
 import { Config, TrackDimensions, TrackType } from '../types';
-export interface BigWigConfig extends Config<BigWigData> {
+export interface BigWigConfig extends Config<Data> {
     trackType: TrackType.BigWig;
     url: string;
     range?: YRange;
@@ -11,7 +11,7 @@ interface BigWigProps {
     color: string;
     data: Data;
     dimensions: TrackDimensions;
-    tooltip?: React.FC<BigWigData>;
+    tooltip?: React.FC<Data>;
 }
 export interface FullBigWigProps extends BigWigProps {
     range: YRange;
@@ -43,7 +43,7 @@ export interface BigZoomData {
     sumData: number;
     sumSquares: number;
 }
-export type Data = ValuedPoint[] | BigWigData[] | BigZoomData[];
+export type Data = ValuedPoint[];
 export declare enum DataType {
     ValuedPoint = "valuedPoint",
     BigZoomData = "bigZoomData",

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

@@ -6,7 +6,6 @@ export interface BulkBedDataset {
 export interface BulkBedConfig extends Config<BulkBedRect> {
     trackType: TrackType.BulkBed;
     datasets: BulkBedDataset[];
-    urls?: string[];
     gap?: number;
 }
 export interface BulkBedProps {

package/dist/components/tracks/methylC/combined.d.ts

@@ -0,0 +1 @@
+export default function CombinedMethylC(): import("react/jsx-runtime").JSX.Element;

package/dist/components/tracks/methylC/defaultMethylCTooltip.d.ts

@@ -0,0 +1,4 @@
+import { ValuedPoint } from '../bigwig/types';
+export default function DefaultMethylCTooltip({ tooltipValues }: {
+    tooltipValues: ValuedPoint[];
+}): import("react/jsx-runtime").JSX.Element;

package/dist/components/tracks/methylC/helpers.d.ts

@@ -0,0 +1,3 @@
+import { ValuedPoint, YRange } from '../bigwig/types';
+export declare function generateSignal(data: ValuedPoint[], height: number, color: string, inverted?: boolean, customRange?: YRange): import("react/jsx-runtime").JSX.Element | null;
+export declare function generateLineGraph(data: ValuedPoint[], height: number, color: string, inverted?: boolean, customRange?: YRange): import("react/jsx-runtime").JSX.Element | null;

package/dist/components/tracks/methylC/split.d.ts

@@ -0,0 +1,3 @@
+import { MethylCProps } from './types';
+declare function SplitMethylC({ id, height, colors, data, dimensions, range, tooltip }: MethylCProps): import("react/jsx-runtime").JSX.Element;
+export default SplitMethylC;

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

@@ -0,0 +1,58 @@
+import { ValuedPoint, YRange } from '../bigwig/types';
+import { Config, DisplayMode, TrackDimensions, TrackType } from '../types';
+export interface MethylCConfig extends Config<MethylData> {
+    trackType: TrackType.MethylC;
+    displayMode: DisplayMode.Split | DisplayMode.Combined;
+    colors: {
+        cpg: string;
+        chg: string;
+        chh: string;
+        depth: string;
+    };
+    urls: {
+        plusStrand: {
+            cpg: {
+                url: string;
+            };
+            chg: {
+                url: string;
+            };
+            chh: {
+                url: string;
+            };
+            depth: {
+                url: string;
+            };
+        };
+        minusStrand: {
+            cpg: {
+                url: string;
+            };
+            chg: {
+                url: string;
+            };
+            chh: {
+                url: string;
+            };
+            depth: {
+                url: string;
+            };
+        };
+    };
+    range?: YRange;
+}
+export type MethylData = ValuedPoint[];
+export interface MethylCProps {
+    id: string;
+    height: number;
+    colors: {
+        cpg: string;
+        chg: string;
+        chh: string;
+        depth: string;
+    };
+    data: MethylData[];
+    dimensions: TrackDimensions;
+    tooltip?: React.FC<ValuedPoint[]>;
+    range?: YRange;
+}

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

@@ -5,13 +5,16 @@ export declare enum TrackType {
     Motif = "motif",
     Importance = "importance",
     LDTrack = "ldtrack",
-    BulkBed = "bulkbed"
+    BulkBed = "bulkbed",
+    MethylC = "methylc"
 }
 export declare enum DisplayMode {
     Full = "full",
     Dense = "dense",
     Squish = "squish",
-    Pack = "pack"
+    Pack = "pack",
+    Combined = "combined",
+    Split = "split"
 }
 export interface InteractionConfig<Item> {
     onClick?: (item: Item) => void;