@weng-lab/genomebrowser 0.0.1 → 0.0.3

package/dist/hooks/useBrowserState.d.ts

@@ -0,0 +1,2 @@
+import { BrowserState } from '../components/context/browserContext';
+export declare const useBrowserState: (state: BrowserState) => [BrowserState, import('react').Dispatch<import('../components/context/browserContext').BrowserAction>];

package/dist/hooks/useInput.d.ts

@@ -0,0 +1,5 @@
+export declare function useInput(initialValue: string, defaultValue: string, validate: (value: string) => boolean): {
+    value: string;
+    valid: boolean;
+    onChange: (e: React.ChangeEvent<HTMLInputElement>) => void;
+};

package/dist/hooks/useModal.d.ts

@@ -0,0 +1,10 @@
+export interface TrackModalInfo {
+    trackId: string;
+    mouseX: number;
+    mouseY: number;
+}
+export declare function useModal(): {
+    openModal: TrackModalInfo | null;
+    showModal: (trackId: string, mouseX: number, mouseY: number) => void;
+    closeModal: () => void;
+};

package/dist/hooks/useTooltip.d.ts

@@ -0,0 +1,6 @@
+import { default as React } from 'react';
+type MouseOverEvent<T> = (event: React.MouseEvent<SVGRectElement>, v: T) => void;
+type MouseOutEvent = () => void;
+type TooltipCallbacks<T> = [MouseOverEvent<T>, MouseOutEvent];
+export declare function useTooltip<T extends object>(Tooltip: React.FC<T>, width: number, svgRef?: React.RefObject<SVGSVGElement>, onMouseOver?: MouseOverEvent<T>, onMouseOut?: MouseOutEvent): TooltipCallbacks<T>;
+export {};

package/dist/lib.d.ts

@@ -0,0 +1,14 @@
+export { BigWig, DefaultBigWig } from './components/tracks/bigwig';
+export type { BigWigProps, BigWigOptions } from './components/tracks/bigwig';
+export { BigBed, DefaultBigBed } from './components/tracks/bigbed';
+export type { BigBedProps, BigBedOptions } from './components/tracks/bigbed';
+export { Transcript, DefaultTranscript } from './components/tracks/transcripts';
+export type { TranscriptProps, TranscriptOptions } from './components/tracks/transcripts';
+export { Bam, DefaultBam } from './components/tracks/bam';
+export type { BamProps, BamOptions } from './components/tracks/bam';
+export { useBrowserState } from './hooks/useBrowserState';
+export { GenomeBrowser } from './components/browser';
+export { type BrowserState, BrowserActionType } from './components/context/browserContext';
+export { BigWigTrack, BigBedTrack, TranscriptTrack } from './components/tracks/types';
+export type { TrackProps, BigBedTrackProps, BigWigTrackProps, TranscriptTrackProps } from './components/tracks/types';
+export { DisplayMode } from './components/tracks/types';

package/dist/pages/main.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/pages/trackExamples.d.ts

@@ -0,0 +1,4 @@
+import { BigBedTrackProps, BigWigTrackProps, TranscriptTrackProps } from '../components/tracks/types';
+export declare const bigWigExample: BigWigTrackProps;
+export declare const bigBedExample: BigBedTrackProps;
+export declare const transcriptExample: TranscriptTrackProps;

package/dist/utils/colors.d.ts

@@ -0,0 +1,14 @@
+export declare const BLACK = 0;
+export declare const WHITE = 255;
+/**
+ * Convert a color to a ligher shade.
+ * @param color the original color as a hex string (e.g. #fff or ABCDEF)
+ * @param luminosity the fraction by which to change the brightness, from 0 to 1
+ */
+export declare function lighten(color: string, luminosity: number): string;
+/**
+ * Validates a hex color and parses it to an integer.
+ * @param color the color as a hex string (e.g. #fff or ABCDEF)
+ */
+export declare function parseHex(color: string): number;
+export declare function zeroPadHex(h: number): string;

package/dist/utils/coordinates.d.ts

@@ -0,0 +1,39 @@
+import { Domain, YRange, Feature } from './types';
+export declare function m(x: number, y: number): string;
+export declare function l(x: number, y: number): string;
+/**
+ * Creates a closure for mapping values into an X coordinate space.
+ * @param domain object with the start and end coordinates of the original values.
+ * @param width the maximum value of the output space.
+ */
+export declare function xtransform(domain: Domain, width: number): (i: number) => number;
+/**
+ * Creates a linear scale for mapping values into a Y coordinate space.
+ * @param range object with the max and min coordinates of the original values.
+ * @param height the maximum value of the output space.
+ */
+export declare function ytransform(range: YRange, height: number): (i: number) => number;
+/**
+ * Creates a linear scale for mapping values from one coordinate space to another.
+ * @param indomain the original domain.
+ * @param outdomain the output domain.
+ */
+export declare function linearTransform(inDomain: Domain, outDomain: Domain): (value: number) => number;
+/**
+ * Creates a linear scale for mapping track input coordinates to an output x coordinate range. If the
+ * domain is not explicitly given it will be computed from the minima and maxima of the passed track data.
+ * @param domain object with the start and end coordinates to set, or null.
+ * @param data optional array of objects with start and end coordinates to compute the domain.
+ * @param width the maximum value of the output space.
+ */
+export declare function trackXTransform(domain: Domain, data: Domain[], width: number): (i: number) => number;
+/**
+ * Creates a linear scale for mapping track input coordinates to an output x coordinate range. If the
+ * domain is not explicitly given it will be computed from the minima and maxima of the passed track data.
+ * @param domain object with the start and end coordinates to set, or null.
+ * @param data optional array of objects with start and end coordinates to compute the domain.
+ * @param width the maximum value of the output space.
+ */
+export declare function trackYTransform(range: YRange, data: YRange[], height: number): (i: number) => number;
+export declare function groupFeatures<T extends Feature>(features: T[], x: (value: number) => number, fontSize: number, margin?: number | undefined): T[][];
+export declare function formatPoint(point?: number): string;

package/dist/utils/index.d.ts

@@ -0,0 +1,2 @@
+export { isReactElement } from './react';
+export { zeroPadHex } from './colors';

package/dist/utils/react.d.ts

@@ -0,0 +1,2 @@
+import { default as React } from 'react';
+export declare function isReactElement(child: React.ReactNode): child is React.ReactElement;

package/dist/utils/svg.d.ts

@@ -0,0 +1,2 @@
+export declare const svgPoint: (svg: SVGSVGElement, event: React.MouseEvent<SVGElement>) => number[];
+export declare const downloadSVG: (_svg: SVGSVGElement, _scale: SVGSVGElement, filename: string) => void;

package/dist/utils/types.d.ts

@@ -0,0 +1,19 @@
+export interface Domain {
+    chromosome?: string;
+    start: number;
+    end: number;
+}
+export type YRange = {
+    min: number;
+    max: number;
+};
+export interface Feature {
+    coordinates: Domain;
+    name: string;
+    color?: string;
+}
+export type ValuedPoint = {
+    x: number;
+    min: number;
+    max: number;
+};

package/package.json

@@ -1,14 +1,13 @@
 {
   "name": "@weng-lab/genomebrowser",
   "private": false,
-  "version": "0.0.1",
+  "version": "0.0.3",
   "repository": {
     "type": "git",
     "url": "git+https://github.com/weng-lab/genomebrowser.git"
   },
   "description": "UMMS Genome Browser",
   "type": "module",
-  "types": "dist/index.d.ts",
   "files": [
     "dist"
   ],
@@ -18,9 +17,10 @@
     ".": {
       "import": "./dist/gbc.es.js",
       "require": "./dist/gbc.umd.js",
-      "types": "./dist/index.d.ts"
+      "types": "./dist/lib.d.ts"
     }
   },
+  "types": "dist/lib.d.ts",
   "scripts": {
     "dev": "vite",
     "build": "vite build",
@@ -28,15 +28,19 @@
     "preview": "vite preview",
     "storybook": "storybook dev -p 6006",
     "build-storybook": "storybook build",
-    "chromatic": "npx chromatic --project-token=chpt_9f387bfb601552a"
+    "chromatic": "npx chromatic --exit-zero-on-changes --project-token chpt_5e23c1d501d3b2b",
+    "verify": "yarn build && yarn build-storybook"
   },
   "peerDependencies": {
     "react": "^18.3.1",
     "react-dom": "^18.3.1"
   },
   "dependencies": {
+    "@apollo/client": "^3.11.10",
     "bigwig-reader": "^1.3.1",
+    "graphql": "^16.9.0",
     "logots-react": "^0.2.0",
+    "react-colorful": "^5.6.1",
     "react-draggable": "^4.4.6",
     "use-deep-compare-effect": "^1.8.1"
   },
@@ -55,7 +59,7 @@
     "@types/react": "^18.3.3",
     "@types/react-dom": "^18.3.0",
     "@vitejs/plugin-react": "^4.3.1",
-    "chromatic": "^11.12.5",
+    "chromatic": "^11.15.0",
     "eslint": "^9.9.0",
     "eslint-plugin-react-hooks": "^5.1.0-rc.0",
     "eslint-plugin-react-refresh": "^0.4.9",
@@ -85,4 +89,4 @@
     "url": "https://github.com/weng-lab/genomebrowser/issues"
   },
   "homepage": "https://github.com/weng-lab/genomebrowser#readme"
-}
+}