@jbrowse/plugin-linear-comparative-view 2.6.2 → 2.7.0

package/esm/LinearSyntenyView/model.d.ts

@@ -73,12 +73,10 @@ 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;
@@ -102,7 +100,7 @@ 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;
@@ -119,7 +117,7 @@ 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;
@@ -221,6 +219,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
@@ -323,12 +323,10 @@ 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;
@@ -352,7 +350,7 @@ 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;
@@ -369,7 +367,7 @@ 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;
@@ -471,6 +469,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -511,12 +511,10 @@ 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;
@@ -540,7 +538,7 @@ 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;
@@ -557,7 +555,7 @@ 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;
@@ -659,6 +657,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
     closeView(): void;
     setMiddleComparativeHeight(n: number): number;

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -1,6 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
+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: theme.palette.background.default }));
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

package/esm/SyntenyTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function registerSyntenyTrack(pluginManager: PluginManager): void;

package/esm/SyntenyTrack/index.js

@@ -1,13 +1,13 @@
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import configSchemaF from './configSchema';
-export default (pm) => {
-    pm.addTrackType(() => {
-        const configSchema = configSchemaF(pm);
+export default function registerSyntenyTrack(pluginManager) {
+    pluginManager.addTrackType(() => {
+        const configSchema = configSchemaF(pluginManager);
         return new TrackType({
             name: 'SyntenyTrack',
             configSchema,
-            stateModel: createBaseTrackModel(pm, 'SyntenyTrack', configSchema),
+            stateModel: createBaseTrackModel(pluginManager, 'SyntenyTrack', configSchema),
         });
     });
-};
+}

package/esm/util.js

@@ -25,7 +25,8 @@ export function getTrackPos(view, trackConfigId) {
 // Uses bpToPx to get the screen pixel coordinates but ignores some conditions
 // where bpToPx could return undefined
 export function getPxFromCoordinate(view, refName, coord) {
-    return (((bpToPx(view, { refName, coord }) || {}).offsetPx || 0) - view.offsetPx);
+    var _a;
+    return (((_a = bpToPx(view, { refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
 }
 // Retrieves the y-position of a layout record in a track
 // If track not found returns 0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -49,7 +49,7 @@
     "@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": ">=16.8.0",
     "react-dom": ">=16.8.0",
@@ -62,5 +62,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }