@jbrowse/plugin-breakpoint-split-view 3.4.0 → 3.5.1

package/dist/BreakpointSplitView/components/BreakpointSplitViewOverlay.js

@@ -21,7 +21,7 @@ const useStyles = (0, mui_1.makeStyles)()({
     base: {
         pointerEvents: 'none',
         width: '100%',
-        zIndex: 1001,
+        zIndex: 100,
     },
 });
 const BreakpointSplitViewOverlay = (0, mobx_react_1.observer)(function ({ model, }) {

package/dist/BreakpointSplitView/getClip.d.ts

@@ -0,0 +1 @@
+export declare function getClip(cigar: string, strand: number): number;

package/dist/BreakpointSplitView/getClip.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getClip = getClip;
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
+function getClip(cigar, strand) {
+    return strand === -1
+        ? +(startClip.exec(cigar) || [])[1] || 0
+        : +(endClip.exec(cigar) || [])[1] || 0;
+}

package/dist/BreakpointSplitView/model.d.ts

@@ -63,7 +63,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly assemblyDisplayNames: string[];
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {

package/dist/BreakpointSplitView/model.js

@@ -45,15 +45,15 @@ const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera")
 const file_saver_1 = require("file-saver");
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
+const getClip_1 = require("./getClip");
 const util_2 = require("./util");
 const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
 function stateModelFactory(pluginManager) {
-    const minHeight = 40;
     const defaultHeight = 400;
     return mobx_state_tree_1.types
         .compose('BreakpointSplitView', models_1.BaseViewModel, mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('BreakpointSplitView'),
-        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.refinement('viewHeight', mobx_state_tree_1.types.number, (n) => n >= minHeight), defaultHeight),
+        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, defaultHeight),
         trackSelectorType: 'hierarchical',
         showIntraviewLinks: true,
         linkViews: false,
@@ -104,7 +104,7 @@ function stateModelFactory(pluginManager) {
                         feature,
                         layout: (0, util_2.calc)(tracks[level], feature),
                         level,
-                        clipPos: (0, util_2.getClip)(feature.get('CIGAR'), feature.get('strand')),
+                        clipPos: (0, getClip_1.getClip)(feature.get('CIGAR'), feature.get('strand')),
                     }
                     : undefined;
             })
@@ -168,6 +168,9 @@ function stateModelFactory(pluginManager) {
                     if (!self.views.every(view => view.initialized)) {
                         return;
                     }
+                    if (self.matchedTracks.some(track => { var _a, _b; return (_b = (_a = track.displays[0]).notReady) === null || _b === void 0 ? void 0 : _b.call(_a); })) {
+                        return;
+                    }
                     self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
                         track.configuration.trackId,
                         await (0, util_2.getBlockFeatures)(self, track),

package/dist/BreakpointSplitView/util.d.ts

@@ -9,21 +9,20 @@ interface Display {
     SNPCoverageDisplay?: {
         height: number;
     };
+    notReady?: () => boolean;
     searchFeatureByID?: (str: string) => LayoutRecord;
 }
 interface Track {
     displays: Display[];
+    configuration: AnyConfigurationModel;
 }
 export declare function heightFromSpecificLevel(views: LGV[], trackId: string, level: number, getYPosOverride?: (trackId: string, level: number) => number): number;
 export declare function getPxFromCoordinate(view: LGV, refName: string, coord: number): number;
 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>;
+}, track: Track): Promise<Feature[][][]>;
 export {};

package/dist/BreakpointSplitView/util.js

@@ -5,12 +5,12 @@ exports.heightFromSpecificLevel = heightFromSpecificLevel;
 exports.getPxFromCoordinate = getPxFromCoordinate;
 exports.yPos = yPos;
 exports.intersect = intersect;
-exports.getClip = getClip;
 exports.calc = calc;
 exports.getBlockFeatures = getBlockFeatures;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
 const [, TOP, , BOTTOM] = [0, 1, 2, 3];
 function cheight(chunk) {
     return chunk[BOTTOM] - chunk[TOP];
@@ -51,33 +51,17 @@ 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])/);
-function getClip(cigar, strand) {
-    return strand === -1
-        ? +(startClip.exec(cigar) || [])[1] || 0
-        : +(endClip.exec(cigar) || [])[1] || 0;
-}
 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());
 }
 async function getBlockFeatures(model, track) {
-    var _a;
     const { views } = model;
-    const { rpcManager, assemblyManager } = (0, util_1.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', {
+    const { rpcManager } = (0, util_1.getSession)(model);
+    const sessionId = (0, tracks_1.getRpcSessionId)(track);
+    return Promise.all(views.flatMap(async (view) => (await rpcManager.call(sessionId, 'CoreGetFeatures', {
         adapterConfig: (0, configuration_1.getConf)(track, ['adapter']),
         sessionId,
         regions: view.staticBlocks.contentBlocks,
-    })).flat()));
+    }))));
 }

package/esm/BreakpointSplitView/components/BreakpointSplitViewOverlay.js

@@ -16,7 +16,7 @@ const useStyles = makeStyles()({
     base: {
         pointerEvents: 'none',
         width: '100%',
-        zIndex: 1001,
+        zIndex: 100,
     },
 });
 const BreakpointSplitViewOverlay = observer(function ({ model, }) {

package/esm/BreakpointSplitView/getClip.d.ts

@@ -0,0 +1 @@
+export declare function getClip(cigar: string, strand: number): number;

package/esm/BreakpointSplitView/getClip.js

@@ -0,0 +1,7 @@
+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;
+}

package/esm/BreakpointSplitView/model.d.ts

@@ -63,7 +63,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
-        readonly stickyViewHeaders: boolean;
+        readonly assemblyDisplayNames: string[];
+        readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+        readonly stickyViewHeaders: boolean | undefined;
         readonly rubberbandTop: number;
         readonly pinnedTracksTop: number;
     } & {

package/esm/BreakpointSplitView/model.js

@@ -6,15 +6,15 @@ import PhotoCamera from '@mui/icons-material/PhotoCamera';
 import { saveAs } from 'file-saver';
 import { autorun } from 'mobx';
 import { addDisposer, getPath, onAction, types } from 'mobx-state-tree';
-import { calc, getBlockFeatures, getClip, intersect } from './util';
+import { getClip } from './getClip';
+import { calc, getBlockFeatures, intersect } from './util';
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
 export default function stateModelFactory(pluginManager) {
-    const minHeight = 40;
     const defaultHeight = 400;
     return types
         .compose('BreakpointSplitView', BaseViewModel, types.model({
         type: types.literal('BreakpointSplitView'),
-        height: types.optional(types.refinement('viewHeight', types.number, (n) => n >= minHeight), defaultHeight),
+        height: types.optional(types.number, defaultHeight),
         trackSelectorType: 'hierarchical',
         showIntraviewLinks: true,
         linkViews: false,
@@ -129,6 +129,9 @@ export default function stateModelFactory(pluginManager) {
                     if (!self.views.every(view => view.initialized)) {
                         return;
                     }
+                    if (self.matchedTracks.some(track => { var _a, _b; return (_b = (_a = track.displays[0]).notReady) === null || _b === void 0 ? void 0 : _b.call(_a); })) {
+                        return;
+                    }
                     self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
                         track.configuration.trackId,
                         await getBlockFeatures(self, track),

package/esm/BreakpointSplitView/util.d.ts

@@ -9,21 +9,20 @@ interface Display {
     SNPCoverageDisplay?: {
         height: number;
     };
+    notReady?: () => boolean;
     searchFeatureByID?: (str: string) => LayoutRecord;
 }
 interface Track {
     displays: Display[];
+    configuration: AnyConfigurationModel;
 }
 export declare function heightFromSpecificLevel(views: LGV[], trackId: string, level: number, getYPosOverride?: (trackId: string, level: number) => number): number;
 export declare function getPxFromCoordinate(view: LGV, refName: string, coord: number): number;
 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>;
+}, track: Track): Promise<Feature[][][]>;
 export {};

package/esm/BreakpointSplitView/util.js

@@ -1,6 +1,7 @@
 import { useEffect, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { clamp, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 const [, TOP, , BOTTOM] = [0, 1, 2, 3];
 function cheight(chunk) {
     return chunk[BOTTOM] - chunk[TOP];
@@ -40,33 +41,17 @@ 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', {
+    const { rpcManager } = getSession(model);
+    const sessionId = getRpcSessionId(track);
+    return Promise.all(views.flatMap(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": "3.4.0",
+  "version": "3.5.1",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -37,8 +37,8 @@
   },
   "dependencies": {
     "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.4.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.4.0",
+    "@jbrowse/core": "^3.5.1",
+    "@jbrowse/plugin-linear-genome-view": "^3.5.1",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@types/file-saver": "^2.0.1",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
+  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
 }