@jbrowse/plugin-breakpoint-split-view 2.6.3 → 2.7.0

package/dist/BreakpointSplitView/components/Overlay.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
 import { BreakpointViewModel } from '../model';
-declare const _default: (props: {
+declare const Overlay: (props: {
     parentRef: React.RefObject<SVGSVGElement>;
     model: BreakpointViewModel;
     trackId: string;
     getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
 }) => React.JSX.Element | null;
-export default _default;
+export default Overlay;

package/dist/BreakpointSplitView/components/Overlay.js

@@ -8,7 +8,7 @@ const mobx_react_1 = require("mobx-react");
 const AlignmentConnections_1 = __importDefault(require("./AlignmentConnections"));
 const Breakends_1 = __importDefault(require("./Breakends"));
 const Translocations_1 = __importDefault(require("./Translocations"));
-exports.default = (0, mobx_react_1.observer)(function (props) {
+const Overlay = (0, mobx_react_1.observer)(function (props) {
     var _a, _b;
     const { model, trackId } = props;
     const tracks = model.getMatchedTracks(trackId);
@@ -20,3 +20,4 @@ exports.default = (0, mobx_react_1.observer)(function (props) {
     }
     return null;
 });
+exports.default = Overlay;

package/dist/BreakpointSplitView/components/Translocations.js

@@ -60,8 +60,7 @@ const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, pa
         // we follow a path in the list of chunks, not from top to bottom,
         // just in series following x1,y1 -> x2,y2
         const ret = [];
-        for (let i = 0; i < chunk.length; i += 1) {
-            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+        for (const { layout: c1, feature: f1, level: level1 } of chunk) {
             const level2 = level1 === 0 ? 1 : 0;
             const id = f1.id();
             if (!c1) {

package/dist/BreakpointSplitView/model.d.ts

@@ -75,12 +75,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
         draggingTrackId: string | undefined;
-        volatileError: Error | undefined;
+        volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
-        trackRefs: {
-            [key: string]: HTMLDivElement;
-        };
+        trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
@@ -104,7 +102,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: string | Error;
+        readonly error: {};
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -121,7 +119,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
-        setError(error: Error | undefined): void;
+        setError(error: unknown): void;
         toggleHeader(): void;
         toggleHeaderOverview(): void;
         toggleNoTracksActive(): void;
@@ -223,6 +221,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
     width: number;
@@ -234,9 +234,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setMinimized(flag: boolean): void;
 } & {
     width: number;
-    matchedTrackFeatures: {
-        [key: string]: Feature[][];
-    };
+    matchedTrackFeatures: Record<string, Feature[][]>;
 } & {
     /**
      * #method
@@ -262,9 +260,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     toggleInteract(): void;
     toggleIntraviewLinks(): void;
     toggleLinkViews(): void;
-    setMatchedTrackFeatures(obj: {
-        [key: string]: Feature[][];
-    }): void;
+    setMatchedTrackFeatures(obj: Record<string, Feature[][]>): void;
 } & {
     afterAttach(): void;
     menuItems(): ({

package/dist/BreakpointSplitView/model.js

@@ -151,7 +151,7 @@ function stateModelFactory(pluginManager) {
         onSubviewAction(actionName, path, args) {
             self.views.forEach(view => {
                 const ret = (0, mobx_state_tree_1.getPath)(view);
-                if (ret.lastIndexOf(path) !== ret.length - path.length) {
+                if (!ret.endsWith(path)) {
                     // @ts-ignore
                     view[actionName](args === null || args === void 0 ? void 0 : args[0]);
                 }

package/dist/BreakpointSplitView/svgcomponents/SVGBackground.js

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
-const color_1 = __importDefault(require("color"));
+const util_1 = require("@jbrowse/core/util");
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, color_1.default)(theme.palette.background.default).hex() }));
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
 }
 exports.default = SVGBackground;

package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -22,8 +22,7 @@ function getTrackNameMaxLen(views, fontSize, session) {
 function getTrackOffsets(view, textOffset, extra = 0) {
     const offsets = {};
     let curr = textOffset;
-    for (let i = 0; i < view.tracks.length; i++) {
-        const track = view.tracks[i];
+    for (const track of view.tracks) {
         offsets[track.configuration.trackId] = curr + extra;
         curr += track.displays[0].height + textOffset;
     }

package/dist/BreakpointSplitView/util.js

@@ -14,7 +14,8 @@ function heightFromSpecificLevel(views, trackId, level, getYPosOverride) {
         : ((_a = views[level].trackRefs[trackId]) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().top) || 0;
 }
 function getPxFromCoordinate(view, refName, coord) {
-    return ((view.bpToPx({ refName, coord }) || {}).offsetPx || 0) - view.offsetPx;
+    var _a;
+    return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
 }
 exports.getPxFromCoordinate = getPxFromCoordinate;
 // get's the yposition of a layout record in a track

package/esm/BreakpointSplitView/components/Overlay.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
 import { BreakpointViewModel } from '../model';
-declare const _default: (props: {
+declare const Overlay: (props: {
     parentRef: React.RefObject<SVGSVGElement>;
     model: BreakpointViewModel;
     trackId: string;
     getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
 }) => React.JSX.Element | null;
-export default _default;
+export default Overlay;

package/esm/BreakpointSplitView/components/Overlay.js

@@ -3,7 +3,7 @@ import { observer } from 'mobx-react';
 import AlignmentConnections from './AlignmentConnections';
 import Breakends from './Breakends';
 import Translocations from './Translocations';
-export default observer(function (props) {
+const Overlay = observer(function (props) {
     var _a, _b;
     const { model, trackId } = props;
     const tracks = model.getMatchedTracks(trackId);
@@ -15,3 +15,4 @@ export default observer(function (props) {
     }
     return null;
 });
+export default Overlay;

package/esm/BreakpointSplitView/components/Translocations.js

@@ -35,8 +35,7 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
         // we follow a path in the list of chunks, not from top to bottom,
         // just in series following x1,y1 -> x2,y2
         const ret = [];
-        for (let i = 0; i < chunk.length; i += 1) {
-            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+        for (const { layout: c1, feature: f1, level: level1 } of chunk) {
             const level2 = level1 === 0 ? 1 : 0;
             const id = f1.id();
             if (!c1) {

package/esm/BreakpointSplitView/model.d.ts

@@ -75,12 +75,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
         draggingTrackId: string | undefined;
-        volatileError: Error | undefined;
+        volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
-        trackRefs: {
-            [key: string]: HTMLDivElement;
-        };
+        trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
@@ -104,7 +102,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: string | Error;
+        readonly error: {};
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -121,7 +119,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
-        setError(error: Error | undefined): void;
+        setError(error: unknown): void;
         toggleHeader(): void;
         toggleHeaderOverview(): void;
         toggleNoTracksActive(): void;
@@ -223,6 +221,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
     width: number;
@@ -234,9 +234,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setMinimized(flag: boolean): void;
 } & {
     width: number;
-    matchedTrackFeatures: {
-        [key: string]: Feature[][];
-    };
+    matchedTrackFeatures: Record<string, Feature[][]>;
 } & {
     /**
      * #method
@@ -262,9 +260,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     toggleInteract(): void;
     toggleIntraviewLinks(): void;
     toggleLinkViews(): void;
-    setMatchedTrackFeatures(obj: {
-        [key: string]: Feature[][];
-    }): void;
+    setMatchedTrackFeatures(obj: Record<string, Feature[][]>): void;
 } & {
     afterAttach(): void;
     menuItems(): ({

package/esm/BreakpointSplitView/model.js

@@ -123,7 +123,7 @@ export default function stateModelFactory(pluginManager) {
         onSubviewAction(actionName, path, args) {
             self.views.forEach(view => {
                 const ret = getPath(view);
-                if (ret.lastIndexOf(path) !== ret.length - path.length) {
+                if (!ret.endsWith(path)) {
                     // @ts-ignore
                     view[actionName](args === null || args === void 0 ? void 0 : args[0]);
                 }

package/esm/BreakpointSplitView/svgcomponents/SVGBackground.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
-import Color from 'color';
+import { stripAlpha } from '@jbrowse/core/util';
 export default function SVGBackground({ width, height, shift, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: Color(theme.palette.background.default).hex() }));
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -16,8 +16,7 @@ function getTrackNameMaxLen(views, fontSize, session) {
 function getTrackOffsets(view, textOffset, extra = 0) {
     const offsets = {};
     let curr = textOffset;
-    for (let i = 0; i < view.tracks.length; i++) {
-        const track = view.tracks[i];
+    for (const track of view.tracks) {
         offsets[track.configuration.trackId] = curr + extra;
         curr += track.displays[0].height + textOffset;
     }

package/esm/BreakpointSplitView/util.js

@@ -11,7 +11,8 @@ function heightFromSpecificLevel(views, trackId, level, getYPosOverride) {
         : ((_a = views[level].trackRefs[trackId]) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().top) || 0;
 }
 export function getPxFromCoordinate(view, refName, coord) {
-    return ((view.bpToPx({ refName, coord }) || {}).offsetPx || 0) - view.offsetPx;
+    var _a;
+    return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
 }
 // get's the yposition of a layout record in a track
 export function yPos(trackId, level, views, tracks, c, getYPosOverride) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "2.6.3",
+  "version": "2.7.0",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -39,7 +39,6 @@
     "@gmod/vcf": "^5.0.9",
     "@mui/icons-material": "^5.0.1",
     "@types/file-saver": "^2.0.1",
-    "color": "^3.1.3",
     "file-saver": "^2.0.0"
   },
   "peerDependencies": {
@@ -47,7 +46,7 @@
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
-    "mobx-react": "^7.0.0",
+    "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.4",
     "react-dom": ">=16.8.4",
@@ -59,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }