@jbrowse/plugin-alignments 2.10.3 → 2.11.0

package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts

@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
     viewType: ViewType;
-}): React.JSX.Element;
+}): React.JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -65,7 +65,7 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return (react_1.default.createElement(react_1.default.Fragment, null, ret.length ? (react_1.default.createElement("div", null,
+    return ret.length ? (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
         error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
         react_1.default.createElement("ul", null, ret.map((arg, index) => {
@@ -82,11 +82,11 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
                         f1.refName,
                         ":",
                         (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start),
-                        " ->",
                         ' ',
+                        "-> ",
                         f2.refName,
                         ":",
                         (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end)))));
-        })))) : null));
+        })))) : null;
 }
 exports.default = LaunchBreakpointSplitViewPanel;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -538,7 +538,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                 }
                 catch (e) {
                     console.error(e);
-                    session.notify(`${e}`, 'error');
+                    session.notifyError(`${e}`, e);
                 }
             }));
         },

package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
         modificationTagMap: ObservableMap<string, string>;
         colorBy?: {
             type: string;
-        } | undefined;
+        };
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
         setFeatureHeight: (arg?: number) => void;
         setNoSpacing: (arg?: boolean) => void;
         featureHeightSetting: number;
-        noSpacing?: boolean | undefined;
+        noSpacing?: boolean;
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/dist/LinearPileupDisplay/model.d.ts

@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -96,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     configuration: AnyConfigurationSchemaType;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #action
-     */
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>;
+        extra: import("mobx-state-tree").IType<any, any, any>; /**
+         * #action
+         */
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -185,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void; /**
-     * #getter
-     */
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -237,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
+     * #getter
+     */
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -246,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
+     * #method
+     */
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
@@ -375,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
+    /**
+     * #action
+     * overrides base from SharedLinearPileupDisplay to make sortReady false
+     * since changing feature height destroys the sort-induced layout
+     */
+    setFeatureHeight(n?: number): void;
 } & {
     /**
      * #action

package/dist/LinearPileupDisplay/model.js

@@ -39,14 +39,14 @@ const Sort_1 = __importDefault(require("@mui/icons-material/Sort"));
 // locals
 const SharedLinearPileupDisplayMixin_1 = require("./SharedLinearPileupDisplayMixin");
 const mobx_1 = require("mobx");
-// async
+// lzies
 const SortByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTag'))));
 const ModificationsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByModifications'))));
 /**
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
@@ -153,6 +153,15 @@ function stateModelFactory(configSchema) {
                 tag,
             };
         },
+        /**
+         * #action
+         * overrides base from SharedLinearPileupDisplay to make sortReady false
+         * since changing feature height destroys the sort-induced layout
+         */
+        setFeatureHeight(n) {
+            self.sortReady = false;
+            self.featureHeight = n;
+        },
     }))
         .actions(self => {
         // resets the sort object and refresh whole display on reload

package/dist/PileupRenderer/components/PileupRendering.d.ts

@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
         type: string;
         pos: number;
         refName: string;
-    } | undefined;
+    };
     colorBy?: {
         type: string;
-        tag?: string | undefined;
-    } | undefined;
+        tag?: string;
+    };
     filterBy?: {
         tagFilter?: {
             tag: string;
-        } | undefined;
-    } | undefined;
-    onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
+        };
+    };
+    onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
 }) => React.JSX.Element;
 export default PileupRendering;

package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts

@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
     viewType: ViewType;
-}): React.JSX.Element;
+}): React.JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -40,7 +40,7 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return (React.createElement(React.Fragment, null, ret.length ? (React.createElement("div", null,
+    return ret.length ? (React.createElement("div", null,
         React.createElement(Typography, null, "Launch split views with breakend source and target"),
         error ? React.createElement(ErrorMessage, { error: error }) : null,
         React.createElement("ul", null, ret.map((arg, index) => {
@@ -57,10 +57,10 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
                         f1.refName,
                         ":",
                         toLocale(f1.strand === 1 ? f1.end : f1.start),
-                        " ->",
                         ' ',
+                        "-> ",
                         f2.refName,
                         ":",
                         toLocale(f2.strand === 1 ? f2.start : f2.end)))));
-        })))) : null));
+        })))) : null;
 }

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -509,7 +509,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                 }
                 catch (e) {
                     console.error(e);
-                    session.notify(`${e}`, 'error');
+                    session.notifyError(`${e}`, e);
                 }
             }));
         },

package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
         modificationTagMap: ObservableMap<string, string>;
         colorBy?: {
             type: string;
-        } | undefined;
+        };
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
         setFeatureHeight: (arg?: number) => void;
         setNoSpacing: (arg?: boolean) => void;
         featureHeightSetting: number;
-        noSpacing?: boolean | undefined;
+        noSpacing?: boolean;
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/esm/LinearPileupDisplay/model.d.ts

@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -96,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     configuration: AnyConfigurationSchemaType;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #action
-     */
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>;
+        extra: import("mobx-state-tree").IType<any, any, any>; /**
+         * #action
+         */
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -185,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void; /**
-     * #getter
-     */
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -237,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
+     * #getter
+     */
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -246,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
+     * #method
+     */
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
@@ -375,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
+    /**
+     * #action
+     * overrides base from SharedLinearPileupDisplay to make sortReady false
+     * since changing feature height destroys the sort-induced layout
+     */
+    setFeatureHeight(n?: number): void;
 } & {
     /**
      * #action

package/esm/LinearPileupDisplay/model.js

@@ -11,14 +11,14 @@ import SortIcon from '@mui/icons-material/Sort';
 // locals
 import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
 import { observable } from 'mobx';
-// async
+// lzies
 const SortByTagDialog = lazy(() => import('./components/SortByTag'));
 const ModificationsDialog = lazy(() => import('./components/ColorByModifications'));
 /**
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 function stateModelFactory(configSchema) {
     return types
@@ -125,6 +125,15 @@ function stateModelFactory(configSchema) {
                 tag,
             };
         },
+        /**
+         * #action
+         * overrides base from SharedLinearPileupDisplay to make sortReady false
+         * since changing feature height destroys the sort-induced layout
+         */
+        setFeatureHeight(n) {
+            self.sortReady = false;
+            self.featureHeight = n;
+        },
     }))
         .actions(self => {
         // resets the sort object and refresh whole display on reload

package/esm/PileupRenderer/components/PileupRendering.d.ts

@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
         type: string;
         pos: number;
         refName: string;
-    } | undefined;
+    };
     colorBy?: {
         type: string;
-        tag?: string | undefined;
-    } | undefined;
+        tag?: string;
+    };
     filterBy?: {
         tagFilter?: {
             tag: string;
-        } | undefined;
-    } | undefined;
-    onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
+        };
+    };
+    onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
 }) => React.JSX.Element;
 export default PileupRendering;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.10.3",
+  "version": "2.11.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }