@jbrowse/plugin-breakpoint-split-view 2.18.0 → 3.0.1

package/esm/BreakpointSplitView/types.d.ts

@@ -0,0 +1,22 @@
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    filename?: string;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
+}
+export interface Breakend {
+    MateDirection: string;
+    Join: string;
+    Replacement: string;
+    MatePosition: string;
+}
+export type LayoutRecord = [number, number, number, number];

package/esm/BreakpointSplitView/types.js

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

package/esm/BreakpointSplitView/util.d.ts

@@ -1,4 +1,6 @@
-import type { LayoutRecord } from './model';
+import type { LayoutRecord } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 type LGV = LinearGenomeViewModel;
 interface Display {
@@ -7,6 +9,7 @@ interface Display {
     SNPCoverageDisplay?: {
         height: number;
     };
+    searchFeatureByID?: (str: string) => LayoutRecord;
 }
 interface Track {
     displays: Display[];
@@ -16,4 +19,11 @@ export declare function getPxFromCoordinate(view: LGV, refName: string, coord: n
 export declare function yPos(trackId: string, level: number, views: LGV[], tracks: Track[], c: LayoutRecord, getYPosOverride?: (trackId: string, level: number) => number): number;
 export declare const useNextFrame: (variable: unknown) => void;
 export declare function intersect<T>(cb: (l: T) => string, a1?: T[], a2?: T[], ...rest: T[][]): T[];
+export declare function getClip(cigar: string, strand: number): number;
+export declare function calc(track: Track, f: Feature): LayoutRecord | undefined;
+export declare function getBlockFeatures(model: {
+    views: LinearGenomeViewModel[];
+}, track: {
+    configuration: AnyConfigurationModel;
+}): Promise<Feature[][] | undefined>;
 export {};

package/esm/BreakpointSplitView/util.js

@@ -1,5 +1,6 @@
 import { useEffect, useState } from 'react';
-import { clamp } from '@jbrowse/core/util';
+import { getConf } from '@jbrowse/core/configuration';
+import { clamp, getSession } from '@jbrowse/core/util';
 const [, TOP, , BOTTOM] = [0, 1, 2, 3];
 function cheight(chunk) {
     return chunk[BOTTOM] - chunk[TOP];
@@ -39,3 +40,33 @@ export function intersect(cb, a1 = [], a2 = [], ...rest) {
     const a12 = a1.filter(value => ids.has(cb(value)));
     return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
 }
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
+export function getClip(cigar, strand) {
+    return strand === -1
+        ? +(startClip.exec(cigar) || [])[1] || 0
+        : +(endClip.exec(cigar) || [])[1] || 0;
+}
+export function calc(track, f) {
+    var _a, _b;
+    return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
+}
+export async function getBlockFeatures(model, track) {
+    var _a;
+    const { views } = model;
+    const { rpcManager, assemblyManager } = getSession(model);
+    const assemblyName = (_a = model.views[0]) === null || _a === void 0 ? void 0 : _a.assemblyNames[0];
+    if (!assemblyName) {
+        return undefined;
+    }
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        return undefined;
+    }
+    const sessionId = track.configuration.trackId;
+    return Promise.all(views.map(async (view) => (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(track, ['adapter']),
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+    })).flat()));
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "2.18.0",
+  "version": "3.0.1",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -37,26 +37,26 @@
   },
   "dependencies": {
     "@gmod/vcf": "^6.0.0",
+    "@jbrowse/core": "^3.0.1",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
     "@mui/icons-material": "^6.0.0",
-    "@types/file-saver": "^2.0.1",
-    "file-saver": "^2.0.0"
-  },
-  "peerDependencies": {
-    "@jbrowse/core": "^2.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^6.0.0",
+    "@types/file-saver": "^2.0.1",
+    "file-saver": "^2.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "react": ">=16.8.4",
-    "react-dom": ">=16.8.4",
     "tss-react": "^4.0.0"
   },
+  "peerDependencies": {
+    "react": ">=16.8.4",
+    "react-dom": ">=16.8.4"
+  },
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
 }