@jbrowse/plugin-linear-genome-view 2.13.0 → 2.13.1

package/dist/LinearGenomeView/components/TrackContainer.js

@@ -49,9 +49,9 @@ const useStyles = (0, mui_1.makeStyles)()({
 const TrackContainer = (0, mobx_react_1.observer)(function ({ model, track, }) {
     const { classes } = useStyles();
     const display = track.displays[0];
-    const { draggingTrackId } = model;
+    const { draggingTrackId, showTrackOutlines } = model;
     const ref = (0, react_1.useRef)(null);
-    return (react_1.default.createElement(material_1.Paper, { ref: ref, className: classes.root, variant: "outlined", onClick: event => {
+    return (react_1.default.createElement(material_1.Paper, { ref: ref, className: classes.root, variant: showTrackOutlines ? 'outlined' : undefined, elevation: showTrackOutlines ? undefined : 0, onClick: event => {
             var _a;
             if (event.detail === 2 && !track.displays[0].featureIdUnderMouse) {
                 const left = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;

package/dist/LinearGenomeView/model.d.ts

@@ -74,6 +74,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     width: number;
 } & {
@@ -95,7 +96,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     leftOffset: undefined | BpOffset;
     rightOffset: undefined | BpOffset;
 } & {
-    scaleBarDisplayPrefix(): "";
     /**
      * #getter
      * this is the effective value of the track labels setting, incorporating
@@ -115,6 +115,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly assemblyNames: string[];
 } & {
+    /**
+     * #method
+     */
+    scaleBarDisplayPrefix(): string;
     /**
      * #method
      */
@@ -217,6 +221,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly trackTypeActions: Map<string, MenuItem[]>;
 } & {
+    /**
+     * #action
+     */
+    setShowTrackOutlines(arg: boolean): void;
     /**
      * #action
      */
@@ -616,6 +624,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }>>, import("mobx-state-tree")._NotCustomized>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;

package/dist/LinearGenomeView/model.js

@@ -177,6 +177,11 @@ function stateModelFactory(pluginManager) {
          * color by CDS
          */
         colorByCDS: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => Boolean(JSON.parse((0, util_1.localStorageGetItem)('lgv-colorByCDS') || 'false'))),
+        /**
+         * #property
+         * color by CDS
+         */
+        showTrackOutlines: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => Boolean(JSON.parse((0, util_1.localStorageGetItem)('lgv-showTrackOutlines') || 'true'))),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -194,9 +199,6 @@ function stateModelFactory(pluginManager) {
         rightOffset: undefined,
     }))
         .views(self => ({
-        scaleBarDisplayPrefix() {
-            return '';
-        },
         /**
          * #getter
          * this is the effective value of the track labels setting, incorporating
@@ -234,6 +236,15 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .views(self => ({
+        /**
+         * #method
+         */
+        scaleBarDisplayPrefix() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return (0, mobx_state_tree_1.getParent)(self, 2).type === 'LinearSyntenyView'
+                ? self.assemblyNames[0]
+                : '';
+        },
         /**
          * #method
          */
@@ -253,8 +264,7 @@ function stateModelFactory(pluginManager) {
          */
         get assemblyErrors() {
             const { assemblyManager } = (0, util_1.getSession)(self);
-            const { assemblyNames } = self;
-            return assemblyNames
+            return self.assemblyNames
                 .map(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.error; })
                 .filter(f => !!f)
                 .join(', ');
@@ -441,6 +451,12 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setShowTrackOutlines(arg) {
+            self.showTrackOutlines = arg;
+        },
         /**
          * #action
          */
@@ -1017,6 +1033,12 @@ function stateModelFactory(pluginManager) {
                             checked: !self.hideHeader,
                             onClick: () => self.setHideHeader(!self.hideHeader),
                         },
+                        {
+                            label: 'Show track outlines',
+                            type: 'checkbox',
+                            checked: self.showTrackOutlines,
+                            onClick: () => self.setShowTrackOutlines(!self.showTrackOutlines),
+                        },
                         {
                             label: 'Show header overview',
                             type: 'checkbox',

package/dist/index.d.ts

@@ -380,6 +380,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showGridlines: boolean;
                 highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
                 colorByCDS: boolean;
+                showTrackOutlines: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -401,12 +402,12 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: undefined | import("./LinearGenomeView").BpOffset;
                 rightOffset: undefined | import("./LinearGenomeView").BpOffset;
             } & {
-                scaleBarDisplayPrefix(): "";
                 readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
             } & {
+                scaleBarDisplayPrefix(): string;
                 MiniControlsComponent(): import("react").FC<any>;
                 HeaderComponent(): import("react").FC<any>;
                 readonly assemblyErrors: string;
@@ -436,6 +437,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setShowTrackOutlines(arg: boolean): void;
                 setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
@@ -576,6 +578,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
                 colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }, {
                 width: number;
             } & {
@@ -597,12 +600,12 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: undefined | import("./LinearGenomeView").BpOffset;
                 rightOffset: undefined | import("./LinearGenomeView").BpOffset;
             } & {
-                scaleBarDisplayPrefix(): "";
                 readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
             } & {
+                scaleBarDisplayPrefix(): string;
                 MiniControlsComponent(): import("react").FC<any>;
                 HeaderComponent(): import("react").FC<any>;
                 readonly assemblyErrors: string;
@@ -632,6 +635,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setShowTrackOutlines(arg: boolean): void;
                 setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
@@ -772,6 +776,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
                 colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }>>, import("mobx-state-tree")._NotCustomized>>;
         }) => import("react").JSX.Element;
     };

package/esm/LinearGenomeView/components/TrackContainer.js

@@ -21,9 +21,9 @@ const useStyles = makeStyles()({
 const TrackContainer = observer(function ({ model, track, }) {
     const { classes } = useStyles();
     const display = track.displays[0];
-    const { draggingTrackId } = model;
+    const { draggingTrackId, showTrackOutlines } = model;
     const ref = useRef(null);
-    return (React.createElement(Paper, { ref: ref, className: classes.root, variant: "outlined", onClick: event => {
+    return (React.createElement(Paper, { ref: ref, className: classes.root, variant: showTrackOutlines ? 'outlined' : undefined, elevation: showTrackOutlines ? undefined : 0, onClick: event => {
             var _a;
             if (event.detail === 2 && !track.displays[0].featureIdUnderMouse) {
                 const left = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;

package/esm/LinearGenomeView/model.d.ts

@@ -74,6 +74,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     width: number;
 } & {
@@ -95,7 +96,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     leftOffset: undefined | BpOffset;
     rightOffset: undefined | BpOffset;
 } & {
-    scaleBarDisplayPrefix(): "";
     /**
      * #getter
      * this is the effective value of the track labels setting, incorporating
@@ -115,6 +115,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly assemblyNames: string[];
 } & {
+    /**
+     * #method
+     */
+    scaleBarDisplayPrefix(): string;
     /**
      * #method
      */
@@ -217,6 +221,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly trackTypeActions: Map<string, MenuItem[]>;
 } & {
+    /**
+     * #action
+     */
+    setShowTrackOutlines(arg: boolean): void;
     /**
      * #action
      */
@@ -616,6 +624,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }>>, import("mobx-state-tree")._NotCustomized>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;

package/esm/LinearGenomeView/model.js

@@ -7,7 +7,7 @@ import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
 import { when, transaction, autorun } from 'mobx';
-import { addDisposer, cast, getSnapshot, getRoot, resolveIdentifier, types, } from 'mobx-state-tree';
+import { addDisposer, cast, getSnapshot, getRoot, resolveIdentifier, types, getParent, } from 'mobx-state-tree';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { moveTo, pxToBp, bpToPx } from '@jbrowse/core/util/Base1DUtils';
 import { saveAs } from 'file-saver';
@@ -147,6 +147,11 @@ export function stateModelFactory(pluginManager) {
          * color by CDS
          */
         colorByCDS: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-colorByCDS') || 'false'))),
+        /**
+         * #property
+         * color by CDS
+         */
+        showTrackOutlines: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showTrackOutlines') || 'true'))),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -164,9 +169,6 @@ export function stateModelFactory(pluginManager) {
         rightOffset: undefined,
     }))
         .views(self => ({
-        scaleBarDisplayPrefix() {
-            return '';
-        },
         /**
          * #getter
          * this is the effective value of the track labels setting, incorporating
@@ -204,6 +206,15 @@ export function stateModelFactory(pluginManager) {
         },
     }))
         .views(self => ({
+        /**
+         * #method
+         */
+        scaleBarDisplayPrefix() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return getParent(self, 2).type === 'LinearSyntenyView'
+                ? self.assemblyNames[0]
+                : '';
+        },
         /**
          * #method
          */
@@ -223,8 +234,7 @@ export function stateModelFactory(pluginManager) {
          */
         get assemblyErrors() {
             const { assemblyManager } = getSession(self);
-            const { assemblyNames } = self;
-            return assemblyNames
+            return self.assemblyNames
                 .map(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.error; })
                 .filter(f => !!f)
                 .join(', ');
@@ -411,6 +421,12 @@ export function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setShowTrackOutlines(arg) {
+            self.showTrackOutlines = arg;
+        },
         /**
          * #action
          */
@@ -987,6 +1003,12 @@ export function stateModelFactory(pluginManager) {
                             checked: !self.hideHeader,
                             onClick: () => self.setHideHeader(!self.hideHeader),
                         },
+                        {
+                            label: 'Show track outlines',
+                            type: 'checkbox',
+                            checked: self.showTrackOutlines,
+                            onClick: () => self.setShowTrackOutlines(!self.showTrackOutlines),
+                        },
                         {
                             label: 'Show header overview',
                             type: 'checkbox',

package/esm/index.d.ts

@@ -380,6 +380,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showGridlines: boolean;
                 highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
                 colorByCDS: boolean;
+                showTrackOutlines: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -401,12 +402,12 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: undefined | import("./LinearGenomeView").BpOffset;
                 rightOffset: undefined | import("./LinearGenomeView").BpOffset;
             } & {
-                scaleBarDisplayPrefix(): "";
                 readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
             } & {
+                scaleBarDisplayPrefix(): string;
                 MiniControlsComponent(): import("react").FC<any>;
                 HeaderComponent(): import("react").FC<any>;
                 readonly assemblyErrors: string;
@@ -436,6 +437,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setShowTrackOutlines(arg: boolean): void;
                 setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
@@ -576,6 +578,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
                 colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }, {
                 width: number;
             } & {
@@ -597,12 +600,12 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: undefined | import("./LinearGenomeView").BpOffset;
                 rightOffset: undefined | import("./LinearGenomeView").BpOffset;
             } & {
-                scaleBarDisplayPrefix(): "";
                 readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
             } & {
+                scaleBarDisplayPrefix(): string;
                 MiniControlsComponent(): import("react").FC<any>;
                 HeaderComponent(): import("react").FC<any>;
                 readonly assemblyErrors: string;
@@ -632,6 +635,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setShowTrackOutlines(arg: boolean): void;
                 setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
@@ -772,6 +776,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
                 colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }>>, import("mobx-state-tree")._NotCustomized>>;
         }) => import("react").JSX.Element;
     };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.13.0",
+  "version": "2.13.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -61,5 +61,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
 }