@jbrowse/plugin-linear-genome-view 2.10.1 → 2.10.3

package/esm/LinearGenomeView/model.d.ts

@@ -81,6 +81,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>;
 }, {
     width: number;
 } & {
@@ -238,19 +239,23 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    toggleHeader(): void;
+    setHideHeader(b: boolean): void;
     /**
      * #action
      */
-    toggleHeaderOverview(): void;
+    setHideHeaderOverview(b: boolean): void;
     /**
      * #action
      */
-    toggleNoTracksActive(): void;
+    setHideNoTracksActive(b: boolean): void;
     /**
      * #action
      */
-    toggleShowGridlines(): void;
+    setShowGridlines(b: boolean): void;
+    /**
+     * #action
+     */
+    setHighlight(highlight: Required<ParsedLocString> | undefined): void;
     /**
      * #action
      */
@@ -306,7 +311,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    toggleCenterLine(): void;
+    setShowCenterLine(b: boolean): void;
     /**
      * #action
      */

package/esm/LinearGenomeView/model.js

@@ -136,6 +136,11 @@ export function stateModelFactory(pluginManager) {
          * show the "gridlines" in the track area
          */
         showGridlines: true,
+        /**
+         * #property
+         * highlights on the LGV from the URL parameters
+         */
+        highlight: types.maybe(types.frozen()),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -418,26 +423,32 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        toggleHeader() {
-            self.hideHeader = !self.hideHeader;
+        setHideHeader(b) {
+            self.hideHeader = b;
+        },
+        /**
+         * #action
+         */
+        setHideHeaderOverview(b) {
+            self.hideHeaderOverview = b;
         },
         /**
          * #action
          */
-        toggleHeaderOverview() {
-            self.hideHeaderOverview = !self.hideHeaderOverview;
+        setHideNoTracksActive(b) {
+            self.hideNoTracksActive = b;
         },
         /**
          * #action
          */
-        toggleNoTracksActive() {
-            self.hideNoTracksActive = !self.hideNoTracksActive;
+        setShowGridlines(b) {
+            self.showGridlines = b;
         },
         /**
          * #action
          */
-        toggleShowGridlines() {
-            self.showGridlines = !self.showGridlines;
+        setHighlight(highlight) {
+            self.highlight = highlight;
         },
         /**
          * #action
@@ -613,8 +624,8 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        toggleCenterLine() {
-            self.showCenterLine = !self.showCenterLine;
+        setShowCenterLine(b) {
+            self.showCenterLine = b;
         },
         /**
          * #action
@@ -891,32 +902,32 @@ export function stateModelFactory(pluginManager) {
                             label: 'Show center line',
                             type: 'checkbox',
                             checked: self.showCenterLine,
-                            onClick: self.toggleCenterLine,
+                            onClick: () => self.setShowCenterLine(!self.showCenterLine),
                         },
                         {
                             label: 'Show header',
                             type: 'checkbox',
                             checked: !self.hideHeader,
-                            onClick: self.toggleHeader,
+                            onClick: () => self.setHideHeader(!self.hideHeader),
                         },
                         {
                             label: 'Show header overview',
                             type: 'checkbox',
                             checked: !self.hideHeaderOverview,
-                            onClick: self.toggleHeaderOverview,
+                            onClick: () => self.setHideHeaderOverview(!self.hideHeaderOverview),
                             disabled: self.hideHeader,
                         },
                         {
                             label: 'Show no tracks active button',
                             type: 'checkbox',
                             checked: !self.hideNoTracksActive,
-                            onClick: self.toggleNoTracksActive,
+                            onClick: () => self.setHideNoTracksActive(!self.hideNoTracksActive),
                         },
                         {
                             label: 'Show guidelines',
                             type: 'checkbox',
                             checked: self.showGridlines,
-                            onClick: self.toggleShowGridlines,
+                            onClick: () => self.setShowGridlines(!self.showGridlines),
                         },
                         ...(canShowCytobands
                             ? [

package/esm/LinearGenomeView/util.d.ts

@@ -24,8 +24,8 @@ export declare function generateLocations(regions: ParsedLocString[] | undefined
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;
-    reversed?: boolean | undefined;
     start?: number | undefined;
+    reversed?: boolean | undefined;
     refName: string;
 }[]>;
 /**

package/esm/index.d.ts

@@ -38,8 +38,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -83,8 +90,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -292,8 +306,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -497,8 +518,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -587,8 +615,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string | undefined;
                 maxHeightReached: boolean;
                 ReactComponent: ({ model, }: {
-                    model: any;
-                }) => any;
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message: import("react").ReactNode;
+                        filled?: boolean | undefined;
+                        status?: string | undefined;
+                        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                    };
+                }) => import("react").JSX.Element | undefined;
                 renderProps: any;
             } & {
                 doReload(): void;
@@ -792,8 +827,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string | undefined;
                 maxHeightReached: boolean;
                 ReactComponent: ({ model, }: {
-                    model: any;
-                }) => any;
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message: import("react").ReactNode;
+                        filled?: boolean | undefined;
+                        status?: string | undefined;
+                        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                    };
+                }) => import("react").JSX.Element | undefined;
                 renderProps: any;
             } & {
                 doReload(): void;
@@ -904,6 +946,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -964,10 +1007,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                setHideHeaderOverview(b: boolean): void;
+                setHideNoTracksActive(b: boolean): void;
+                setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -981,7 +1025,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -1223,6 +1267,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
                 trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
             }, {
                 width: number;
             } & {
@@ -1283,10 +1328,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                setHideHeaderOverview(b: boolean): void;
+                setHideNoTracksActive(b: boolean): void;
+                setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1300,7 +1346,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -1552,6 +1598,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -1612,10 +1659,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                setHideHeaderOverview(b: boolean): void;
+                setHideNoTracksActive(b: boolean): void;
+                setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1629,7 +1677,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -1871,6 +1919,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
                 trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
             }, {
                 width: number;
             } & {
@@ -1931,10 +1980,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                setHideHeaderOverview(b: boolean): void;
+                setHideNoTracksActive(b: boolean): void;
+                setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1948,7 +1998,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -2200,6 +2250,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -2260,10 +2311,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                setHideHeaderOverview(b: boolean): void;
+                setHideNoTracksActive(b: boolean): void;
+                setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -2277,7 +2329,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -2519,6 +2571,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
                 trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
             }, {
                 width: number;
             } & {
@@ -2579,10 +2632,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                setHideHeaderOverview(b: boolean): void;
+                setHideNoTracksActive(b: boolean): void;
+                setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -2596,7 +2650,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.10.1",
+  "version": "2.10.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
+  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
 }