@jbrowse/plugin-alignments 2.10.3 → 2.11.0

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Files changed (17) hide show
  1. package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts +1 -1
  2. package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js +3 -3
  3. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +1 -1
  4. package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +1 -1
  5. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -1
  6. package/dist/LinearPileupDisplay/model.d.ts +17 -10
  7. package/dist/LinearPileupDisplay/model.js +11 -2
  8. package/dist/PileupRenderer/components/PileupRendering.d.ts +6 -6
  9. package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts +1 -1
  10. package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js +3 -3
  11. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +1 -1
  12. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +1 -1
  13. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -1
  14. package/esm/LinearPileupDisplay/model.d.ts +17 -10
  15. package/esm/LinearPileupDisplay/model.js +11 -2
  16. package/esm/PileupRenderer/components/PileupRendering.d.ts +6 -6
  17. package/package.json +2 -2
package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts CHANGED
@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
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  model: AlignmentFeatureWidgetModel;
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  feature: SimpleFeatureSerialized;
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  viewType: ViewType;
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- }): React.JSX.Element;
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+ }): React.JSX.Element | null;
package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js CHANGED
@@ -65,7 +65,7 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
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  ret.push([res[i], res[i + 1]]);
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  }
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  }
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- return (react_1.default.createElement(react_1.default.Fragment, null, ret.length ? (react_1.default.createElement("div", null,
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+ return ret.length ? (react_1.default.createElement("div", null,
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  react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
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  error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
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  react_1.default.createElement("ul", null, ret.map((arg, index) => {
@@ -82,11 +82,11 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
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  f1.refName,
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  ":",
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  (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start),
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- " ->",
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  ' ',
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+ "-> ",
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  f2.refName,
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  ":",
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  (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end)))));
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- })))) : null));
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+ })))) : null;
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  }
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  exports.default = LaunchBreakpointSplitViewPanel;
package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -538,7 +538,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
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  }
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  catch (e) {
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  console.error(e);
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- session.notify(`${e}`, 'error');
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+ session.notifyError(`${e}`, e);
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  }
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  }));
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  },
package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
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  modificationTagMap: ObservableMap<string, string>;
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  colorBy?: {
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  type: string;
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- } | undefined;
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+ };
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  };
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  handleClose: () => void;
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  }) => React.JSX.Element;
package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts CHANGED
@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
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  setFeatureHeight: (arg?: number) => void;
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  setNoSpacing: (arg?: boolean) => void;
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  featureHeightSetting: number;
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- noSpacing?: boolean | undefined;
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+ noSpacing?: boolean;
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  };
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  handleClose: () => void;
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  }) => React.JSX.Element;
package/dist/LinearPileupDisplay/model.d.ts CHANGED
@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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  * #stateModel LinearPileupDisplay
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  * #category display
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  * extends
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- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
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+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
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  */
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  declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -96,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  } & {
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  configuration: AnyConfigurationSchemaType;
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  featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- /**
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- * #action
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- */
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  noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
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  type: import("mobx-state-tree").ISimpleType<string>;
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  tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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- extra: import("mobx-state-tree").IType<any, any, any>;
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+ extra: import("mobx-state-tree").IType<any, any, any>; /**
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+ * #action
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+ */
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  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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  filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
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  flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -185,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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  regionCannotBeRendered(): null;
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  } & {
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- setMessage(arg?: string | undefined): void; /**
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- * #getter
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- */
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+ setMessage(arg?: string | undefined): void;
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  setError(error?: unknown): void;
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  setRpcDriverName(rpcDriverName: string): void;
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  reload(): void;
@@ -237,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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  } & {
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
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+ readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
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+ * #getter
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+ */
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  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
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  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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  searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -246,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  deleteBlock(key: string): void;
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  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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  clearFeatureSelection(): void;
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- setFeatureIdUnderMouse(feature?: string | undefined): void;
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+ setFeatureIdUnderMouse(feature?: string | undefined): void; /**
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+ * #method
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+ */
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  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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  } & {
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  reload(): Promise<void>;
@@ -375,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  * #action
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  */
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  setSortedBy(type: string, tag?: string): void;
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+ /**
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+ * #action
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+ * overrides base from SharedLinearPileupDisplay to make sortReady false
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+ * since changing feature height destroys the sort-induced layout
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+ */
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+ setFeatureHeight(n?: number): void;
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  } & {
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  /**
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  * #action
package/dist/LinearPileupDisplay/model.js CHANGED
@@ -39,14 +39,14 @@ const Sort_1 = __importDefault(require("@mui/icons-material/Sort"));
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  // locals
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  const SharedLinearPileupDisplayMixin_1 = require("./SharedLinearPileupDisplayMixin");
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  const mobx_1 = require("mobx");
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- // async
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+ // lzies
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  const SortByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTag'))));
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  const ModificationsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByModifications'))));
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  /**
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  * #stateModel LinearPileupDisplay
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  * #category display
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  * extends
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- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
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+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
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  */
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  function stateModelFactory(configSchema) {
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  return mobx_state_tree_1.types
@@ -153,6 +153,15 @@ function stateModelFactory(configSchema) {
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  tag,
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  };
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  },
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+ /**
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+ * #action
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+ * overrides base from SharedLinearPileupDisplay to make sortReady false
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+ * since changing feature height destroys the sort-induced layout
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+ */
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+ setFeatureHeight(n) {
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+ self.sortReady = false;
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+ self.featureHeight = n;
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+ },
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  }))
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  .actions(self => {
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  // resets the sort object and refresh whole display on reload
package/dist/PileupRenderer/components/PileupRendering.d.ts CHANGED
@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
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  type: string;
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  pos: number;
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  refName: string;
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- } | undefined;
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+ };
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  colorBy?: {
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  type: string;
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- tag?: string | undefined;
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- } | undefined;
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+ tag?: string;
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+ };
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  filterBy?: {
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  tagFilter?: {
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  tag: string;
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- } | undefined;
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- } | undefined;
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- onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
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+ };
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+ };
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+ onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
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  }) => React.JSX.Element;
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  export default PileupRendering;
package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts CHANGED
@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
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  model: AlignmentFeatureWidgetModel;
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7
  feature: SimpleFeatureSerialized;
8
8
  viewType: ViewType;
9
- }): React.JSX.Element;
9
+ }): React.JSX.Element | null;
package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js CHANGED
@@ -40,7 +40,7 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
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  ret.push([res[i], res[i + 1]]);
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  }
42
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  }
43
- return (React.createElement(React.Fragment, null, ret.length ? (React.createElement("div", null,
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+ return ret.length ? (React.createElement("div", null,
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  React.createElement(Typography, null, "Launch split views with breakend source and target"),
45
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  error ? React.createElement(ErrorMessage, { error: error }) : null,
46
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  React.createElement("ul", null, ret.map((arg, index) => {
@@ -57,10 +57,10 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
57
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  f1.refName,
58
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  ":",
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  toLocale(f1.strand === 1 ? f1.end : f1.start),
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- " ->",
61
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  ' ',
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+ "-> ",
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  f2.refName,
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  ":",
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  toLocale(f2.strand === 1 ? f2.start : f2.end)))));
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- })))) : null));
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+ })))) : null;
66
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  }
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -509,7 +509,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
509
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  }
510
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  catch (e) {
511
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  console.error(e);
512
- session.notify(`${e}`, 'error');
512
+ session.notifyError(`${e}`, e);
513
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  }
514
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  }));
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  },
package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
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  modificationTagMap: ObservableMap<string, string>;
9
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  colorBy?: {
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  type: string;
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- } | undefined;
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+ };
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  };
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  handleClose: () => void;
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  }) => React.JSX.Element;
package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts CHANGED
@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
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  setFeatureHeight: (arg?: number) => void;
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  setNoSpacing: (arg?: boolean) => void;
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  featureHeightSetting: number;
7
- noSpacing?: boolean | undefined;
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+ noSpacing?: boolean;
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  };
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  handleClose: () => void;
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10
  }) => React.JSX.Element;
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
5
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  * #stateModel LinearPileupDisplay
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6
  * #category display
7
7
  * extends
8
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
8
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
9
9
  */
10
10
  declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
11
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -96,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
96
96
  } & {
97
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  configuration: AnyConfigurationSchemaType;
98
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  featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
99
- /**
100
- * #action
101
- */
102
99
  noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
103
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  fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
104
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
105
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  colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
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  type: import("mobx-state-tree").ISimpleType<string>;
107
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  tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
108
- extra: import("mobx-state-tree").IType<any, any, any>;
105
+ extra: import("mobx-state-tree").IType<any, any, any>; /**
106
+ * #action
107
+ */
109
108
  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
110
109
  filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
111
110
  flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -185,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
185
184
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
186
185
  regionCannotBeRendered(): null;
187
186
  } & {
188
- setMessage(arg?: string | undefined): void; /**
189
- * #getter
190
- */
187
+ setMessage(arg?: string | undefined): void;
191
188
  setError(error?: unknown): void;
192
189
  setRpcDriverName(rpcDriverName: string): void;
193
190
  reload(): void;
@@ -237,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
237
234
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
238
235
  } & {
239
236
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
240
- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
237
+ readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
238
+ * #getter
239
+ */
241
240
  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
242
241
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
243
242
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -246,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
246
245
  deleteBlock(key: string): void;
247
246
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
248
247
  clearFeatureSelection(): void;
249
- setFeatureIdUnderMouse(feature?: string | undefined): void;
248
+ setFeatureIdUnderMouse(feature?: string | undefined): void; /**
249
+ * #method
250
+ */
250
251
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
251
252
  } & {
252
253
  reload(): Promise<void>;
@@ -375,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
375
376
  * #action
376
377
  */
377
378
  setSortedBy(type: string, tag?: string): void;
379
+ /**
380
+ * #action
381
+ * overrides base from SharedLinearPileupDisplay to make sortReady false
382
+ * since changing feature height destroys the sort-induced layout
383
+ */
384
+ setFeatureHeight(n?: number): void;
378
385
  } & {
379
386
  /**
380
387
  * #action
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -11,14 +11,14 @@ import SortIcon from '@mui/icons-material/Sort';
11
11
  // locals
12
12
  import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
13
13
  import { observable } from 'mobx';
14
- // async
14
+ // lzies
15
15
  const SortByTagDialog = lazy(() => import('./components/SortByTag'));
16
16
  const ModificationsDialog = lazy(() => import('./components/ColorByModifications'));
17
17
  /**
18
18
  * #stateModel LinearPileupDisplay
19
19
  * #category display
20
20
  * extends
21
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
21
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
22
22
  */
23
23
  function stateModelFactory(configSchema) {
24
24
  return types
@@ -125,6 +125,15 @@ function stateModelFactory(configSchema) {
125
125
  tag,
126
126
  };
127
127
  },
128
+ /**
129
+ * #action
130
+ * overrides base from SharedLinearPileupDisplay to make sortReady false
131
+ * since changing feature height destroys the sort-induced layout
132
+ */
133
+ setFeatureHeight(n) {
134
+ self.sortReady = false;
135
+ self.featureHeight = n;
136
+ },
128
137
  }))
129
138
  .actions(self => {
130
139
  // resets the sort object and refresh whole display on reload
package/esm/PileupRenderer/components/PileupRendering.d.ts CHANGED
@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
12
12
  type: string;
13
13
  pos: number;
14
14
  refName: string;
15
- } | undefined;
15
+ };
16
16
  colorBy?: {
17
17
  type: string;
18
- tag?: string | undefined;
19
- } | undefined;
18
+ tag?: string;
19
+ };
20
20
  filterBy?: {
21
21
  tagFilter?: {
22
22
  tag: string;
23
- } | undefined;
24
- } | undefined;
25
- onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
23
+ };
24
+ };
25
+ onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
26
26
  }) => React.JSX.Element;
27
27
  export default PileupRendering;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "2.10.3",
3
+ "version": "2.11.0",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
66
+ "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
67
67
  }