@jbrowse/plugin-sv-inspector 2.13.1 → 2.14.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. package/dist/LaunchSvInspectorView/index.js +2 -6
  2. package/dist/SvInspectorView/components/CircularViewOptions.js +3 -1
  3. package/dist/SvInspectorView/models/SvInspectorView.d.ts +36 -9
  4. package/dist/SvInspectorView/models/SvInspectorView.js +12 -19
  5. package/dist/SvInspectorView/models/adhocFeatureUtils.d.ts +4 -4
  6. package/dist/SvInspectorView/models/adhocFeatureUtils.js +6 -5
  7. package/dist/SvInspectorView/models/breakpointSplitViewFromTableRow.d.ts +4 -4
  8. package/dist/SvInspectorView/models/breakpointSplitViewFromTableRow.js +1 -0
  9. package/esm/LaunchSvInspectorView/index.js +2 -6
  10. package/esm/SvInspectorView/components/CircularViewOptions.js +3 -1
  11. package/esm/SvInspectorView/models/SvInspectorView.d.ts +36 -9
  12. package/esm/SvInspectorView/models/SvInspectorView.js +13 -20
  13. package/esm/SvInspectorView/models/adhocFeatureUtils.d.ts +4 -4
  14. package/esm/SvInspectorView/models/adhocFeatureUtils.js +6 -5
  15. package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.d.ts +4 -4
  16. package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.js +1 -0
  17. package/package.json +3 -3
package/dist/LaunchSvInspectorView/index.js CHANGED
@@ -6,15 +6,11 @@ function LaunchSvInspectorViewF(pluginManager) {
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  // @ts-expect-error
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  async ({ session, assembly, uri, fileType, }) => {
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  var _a, _b;
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- // add view, make typescript happy with return type
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  const view = session.addView('SvInspectorView');
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- if (!view) {
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- throw new Error('Failed to initialize view');
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- }
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  const exts = uri.split('.');
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- let ext = (_a = exts === null || exts === void 0 ? void 0 : exts.pop()) === null || _a === void 0 ? void 0 : _a.toUpperCase();
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+ let ext = (_a = exts.pop()) === null || _a === void 0 ? void 0 : _a.toUpperCase();
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  if (ext === 'GZ') {
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- ext = (_b = exts === null || exts === void 0 ? void 0 : exts.pop()) === null || _b === void 0 ? void 0 : _b.toUpperCase();
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+ ext = (_b = exts.pop()) === null || _b === void 0 ? void 0 : _b.toUpperCase();
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  }
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  view.spreadsheetView.importWizard.setFileType(fileType || ext || '');
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  view.spreadsheetView.importWizard.setSelectedAssemblyName(assembly);
package/dist/SvInspectorView/components/CircularViewOptions.js CHANGED
@@ -16,6 +16,8 @@ const CircularViewOptions = (0, mobx_react_1.observer)(function ({ svInspector,
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  const { classes } = useStyles();
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  return (react_1.default.createElement(material_1.Grid, { container: true, className: classes.circularViewOptions, style: { height: svInspector.circularViewOptionsBarHeight } },
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  react_1.default.createElement(material_1.Grid, { item: true },
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- react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked) }), label: "show only regions with data" }))));
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+ react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => {
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+ svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked);
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+ } }), label: "show only regions with data" }))));
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  });
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  exports.default = CircularViewOptions;
package/dist/SvInspectorView/models/SvInspectorView.d.ts CHANGED
@@ -736,7 +736,6 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
736
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
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  setImportMode(): void;
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  setDisplayMode(): void;
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- closeView(): void;
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  } & {
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  menuItems(): {
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  label: string;
@@ -831,7 +830,6 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
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  zoomOutButton(): void;
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  setBpPerPx(newVal: number): void;
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  setModelViewWhenAdjust(secondCondition: boolean): void;
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- closeView(): void;
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  setDisplayedRegions(regions: import("mobx-state-tree").SnapshotOrInstance<typeof import("@jbrowse/core/util/types/mst").Region>[]): void;
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  activateTrackSelector(): import("@jbrowse/core/util").Widget;
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  toggleTrack(trackId: string): boolean;
@@ -858,11 +856,44 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
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  /**
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  * #getter
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  */
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- readonly selectedRows: any;
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+ readonly selectedRows: ({
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+ id: string;
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+ cells: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
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+ text: import("mobx-state-tree").ISimpleType<string>;
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+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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+ text: import("mobx-state-tree").ISimpleType<string>;
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+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
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+ extendedData: any;
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+ isSelected: boolean;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ toggleSelect(): void;
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+ unSelect(): void;
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+ select(): void;
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+ setExtendedData(data: unknown): void;
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+ } & {
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+ readonly cellsWithDerived: any;
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+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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+ id: import("mobx-state-tree").ISimpleType<string>;
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+ cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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+ text: import("mobx-state-tree").ISimpleType<string>;
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+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
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+ isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ }, {
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+ toggleSelect(): void;
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+ unSelect(): void;
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+ select(): void;
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+ setExtendedData(data: unknown): void;
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+ } & {
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+ readonly cellsWithDerived: any;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[] | undefined;
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  /**
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  * #getter
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  */
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- readonly assemblyName: any;
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+ readonly assemblyName: string | undefined;
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  /**
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  * #getter
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  */
@@ -893,7 +924,7 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
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  type: string;
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  features: any[];
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  };
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- assemblyNames: any[];
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+ assemblyNames: (string | undefined)[];
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  displays: {
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  type: string;
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  displayId: string;
@@ -948,10 +979,6 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
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  * #action
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  */
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  setDisplayMode(): void;
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- /**
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- * #action
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- */
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- closeView(): void;
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  /**
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  * #action
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  */
package/dist/SvInspectorView/models/SvInspectorView.js CHANGED
@@ -83,15 +83,17 @@ function SvInspectorViewF(pluginManager) {
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  * #getter
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  */
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  get selectedRows() {
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- // @ts-expect-error
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- return self.spreadsheetView.rowSet.selectedRows;
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+ var _a;
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+ return (_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.rowSet.selectedRows;
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  },
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  /**
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  * #getter
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  */
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  get assemblyName() {
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  const { assembly } = self.spreadsheetView;
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- return assembly ? (0, configuration_1.readConfObject)(assembly, 'name') : undefined;
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+ return assembly
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+ ? (0, configuration_1.readConfObject)(assembly, 'name')
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+ : undefined;
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  },
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  /**
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  * #getter
@@ -141,7 +143,7 @@ function SvInspectorViewF(pluginManager) {
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  {
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  type: 'ChordVariantDisplay',
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  displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
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- onChordClick: `jexl:defaultOnChordClick(feature, track, pluginManager)`,
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+ onChordClick: 'jexl:defaultOnChordClick(feature, track, pluginManager)',
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  renderer: { type: 'StructuralVariantChordRenderer' },
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  },
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  ],
@@ -179,13 +181,6 @@ function SvInspectorViewF(pluginManager) {
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  setDisplayMode() {
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  self.spreadsheetView.setDisplayMode();
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  },
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- /**
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- * #action
184
- */
185
- closeView() {
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- // eslint-disable-next-line @typescript-eslint/no-explicit-any
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- (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
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- },
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  /**
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  * #action
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  */
@@ -207,7 +202,9 @@ function SvInspectorViewF(pluginManager) {
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  return [
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  {
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  label: 'Return to import form',
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- onClick: () => self.setImportMode(),
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+ onClick: () => {
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+ self.setImportMode();
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+ },
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  icon: FolderOpen_1.default,
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  },
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  ];
@@ -273,18 +270,15 @@ function SvInspectorViewF(pluginManager) {
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  }, { name: 'SvInspectorView displayed regions bind' }));
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  // bind circularview tracks to our track snapshot view
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  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => ({
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- generatedTrackConf: self === null || self === void 0 ? void 0 : self.featuresCircularTrackConfiguration,
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- assemblyName: self === null || self === void 0 ? void 0 : self.assemblyName,
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+ generatedTrackConf: self.featuresCircularTrackConfiguration,
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+ assemblyName: self.assemblyName,
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  }), data => {
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- if (!data) {
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- return;
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- }
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  const { assemblyName, generatedTrackConf } = data;
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  const { circularView } = self;
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  // hide any visible tracks
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  circularView.tracks.forEach(t => circularView.hideTrack(t.configuration.trackId));
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  // put our track in as the only track
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- if (assemblyName && generatedTrackConf) {
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+ if (assemblyName) {
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  // @ts-expect-error
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  circularView.addTrackConf(generatedTrackConf, {
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  assemblyName,
@@ -308,7 +302,6 @@ function SvInspectorViewF(pluginManager) {
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  disabled(spreadsheetView, spreadsheet, rowNumber, row) {
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  return !(0, breakpointSplitViewFromTableRow_1.canOpenBreakpointSplitViewFromTableRow)(self, spreadsheetView, spreadsheet, row, rowNumber);
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  },
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- // @ts-expect-error
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  onClick(spreadsheetView, spreadsheet, rowNumber, row) {
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  (0, breakpointSplitViewFromTableRow_1.openBreakpointSplitViewFromTableRow)(self, spreadsheetView, spreadsheet, row, rowNumber);
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  },
package/dist/SvInspectorView/models/adhocFeatureUtils.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: any, row: any, loc1: any, loc2: any, rowNumber: any): {
1
+ export declare function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: any, row: any, loc1: any, loc2: any, rowNumber: any): {
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  uniqueId: string;
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  refName: any;
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  start: any;
@@ -9,7 +9,7 @@ export function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: an
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  end: any;
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  };
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  };
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- export function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnNumbers: any, row: any, rowNumber: any, isValidRefName: any): {
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+ export declare function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnNumbers: any, row: any, rowNumber: any, isValidRefName: any): {
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  uniqueId: string;
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  refName: any;
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  start: any;
@@ -20,7 +20,7 @@ export function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnN
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  end: any;
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  };
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  };
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- export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefColumnNumbers: any, locStartColumnNumbers: any, locEndColumnNumbers: any, row: any, rowNumber: any): {
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+ export declare function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefColumnNumbers: any, locStartColumnNumbers: any, locEndColumnNumbers: any, row: any, rowNumber: any): {
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  uniqueId: string;
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  refName: any;
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  start: any;
@@ -31,7 +31,7 @@ export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefCol
31
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  end: any;
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  };
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  };
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- export function makeAdHocSvFeature(sheet: any, rowNumber: any, row: any, isValidRefName: any): {
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+ export declare function makeAdHocSvFeature(sheet: any, rowNumber: any, row: any, isValidRefName: any): {
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  uniqueId: string;
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  refName: any;
37
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  start: any;
package/dist/SvInspectorView/models/adhocFeatureUtils.js CHANGED
@@ -4,6 +4,7 @@ exports.makeAdHocFeature = makeAdHocFeature;
4
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  exports.makeAdHocSvFeatureFromTwoLocations = makeAdHocSvFeatureFromTwoLocations;
5
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  exports.makeAdHocSvFeatureFromTwoRefStartEndSets = makeAdHocSvFeatureFromTwoRefStartEndSets;
6
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  exports.makeAdHocSvFeature = makeAdHocSvFeature;
7
+ // @ts-nocheck
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  // this file contains the rather verbose functions for
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  // creating features from CSV/TSV lines
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  const util_1 = require("@jbrowse/core/util");
@@ -16,7 +17,7 @@ function makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc
16
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  }
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  let { text } = row.cells[columnNumber];
18
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  if (column.dataType.type === 'Number') {
19
- text = parseFloat(text);
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+ text = Number.parseFloat(text);
20
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  }
21
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  otherData[column.name] = text;
22
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  });
@@ -48,13 +49,13 @@ function makeAdHocSvFeatureFromTwoRefStartEndSets(columns, locRefColumnNumbers,
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  const textOf = colno => row.cells[colno].text;
49
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  const loc1 = {
50
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  refName: textOf(locRefColumnNumbers[0]),
51
- start: parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
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- end: parseInt(textOf(locEndColumnNumbers[0]), 10),
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+ start: Number.parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
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+ end: Number.parseInt(textOf(locEndColumnNumbers[0]), 10),
53
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  };
54
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  const loc2 = {
55
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  refName: textOf(locRefColumnNumbers[1]),
56
- start: parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
57
- end: parseInt(textOf(locEndColumnNumbers[1]), 10),
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+ start: Number.parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
58
+ end: Number.parseInt(textOf(locEndColumnNumbers[1]), 10),
58
59
  };
59
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  const columnsAlreadyUsedInLocations = [
60
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  locRefColumnNumbers[0],
package/dist/SvInspectorView/models/breakpointSplitViewFromTableRow.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export function getFeatureForRow(session: any, spreadsheetView: any, row: any, rowNumber: any): any;
2
- export function breakpointSplitViewSnapshotFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): any;
3
- export function openBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): void;
4
- export function canOpenBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): boolean;
1
+ export declare function getFeatureForRow(session: any, spreadsheetView: any, row: any, rowNumber: any): any;
2
+ export declare function breakpointSplitViewSnapshotFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): any;
3
+ export declare function openBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): void;
4
+ export declare function canOpenBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): boolean;
package/dist/SvInspectorView/models/breakpointSplitViewFromTableRow.js CHANGED
@@ -4,6 +4,7 @@ exports.getFeatureForRow = getFeatureForRow;
4
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  exports.breakpointSplitViewSnapshotFromTableRow = breakpointSplitViewSnapshotFromTableRow;
5
5
  exports.openBreakpointSplitViewFromTableRow = openBreakpointSplitViewFromTableRow;
6
6
  exports.canOpenBreakpointSplitViewFromTableRow = canOpenBreakpointSplitViewFromTableRow;
7
+ // @ts-nocheck
7
8
  const util_1 = require("@jbrowse/core/util");
8
9
  const adhocFeatureUtils_1 = require("./adhocFeatureUtils");
9
10
  function getFeatureForRow(session, spreadsheetView, row, rowNumber) {
package/esm/LaunchSvInspectorView/index.js CHANGED
@@ -3,15 +3,11 @@ export default function LaunchSvInspectorViewF(pluginManager) {
3
3
  // @ts-expect-error
4
4
  async ({ session, assembly, uri, fileType, }) => {
5
5
  var _a, _b;
6
- // add view, make typescript happy with return type
7
6
  const view = session.addView('SvInspectorView');
8
- if (!view) {
9
- throw new Error('Failed to initialize view');
10
- }
11
7
  const exts = uri.split('.');
12
- let ext = (_a = exts === null || exts === void 0 ? void 0 : exts.pop()) === null || _a === void 0 ? void 0 : _a.toUpperCase();
8
+ let ext = (_a = exts.pop()) === null || _a === void 0 ? void 0 : _a.toUpperCase();
13
9
  if (ext === 'GZ') {
14
- ext = (_b = exts === null || exts === void 0 ? void 0 : exts.pop()) === null || _b === void 0 ? void 0 : _b.toUpperCase();
10
+ ext = (_b = exts.pop()) === null || _b === void 0 ? void 0 : _b.toUpperCase();
15
11
  }
16
12
  view.spreadsheetView.importWizard.setFileType(fileType || ext || '');
17
13
  view.spreadsheetView.importWizard.setSelectedAssemblyName(assembly);
package/esm/SvInspectorView/components/CircularViewOptions.js CHANGED
@@ -11,6 +11,8 @@ const CircularViewOptions = observer(function ({ svInspector, }) {
11
11
  const { classes } = useStyles();
12
12
  return (React.createElement(Grid, { container: true, className: classes.circularViewOptions, style: { height: svInspector.circularViewOptionsBarHeight } },
13
13
  React.createElement(Grid, { item: true },
14
- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked) }), label: "show only regions with data" }))));
14
+ React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => {
15
+ svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked);
16
+ } }), label: "show only regions with data" }))));
15
17
  });
16
18
  export default CircularViewOptions;
package/esm/SvInspectorView/models/SvInspectorView.d.ts CHANGED
@@ -736,7 +736,6 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
736
736
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
737
737
  setImportMode(): void;
738
738
  setDisplayMode(): void;
739
- closeView(): void;
740
739
  } & {
741
740
  menuItems(): {
742
741
  label: string;
@@ -831,7 +830,6 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
831
830
  zoomOutButton(): void;
832
831
  setBpPerPx(newVal: number): void;
833
832
  setModelViewWhenAdjust(secondCondition: boolean): void;
834
- closeView(): void;
835
833
  setDisplayedRegions(regions: import("mobx-state-tree").SnapshotOrInstance<typeof import("@jbrowse/core/util/types/mst").Region>[]): void;
836
834
  activateTrackSelector(): import("@jbrowse/core/util").Widget;
837
835
  toggleTrack(trackId: string): boolean;
@@ -858,11 +856,44 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
858
856
  /**
859
857
  * #getter
860
858
  */
861
- readonly selectedRows: any;
859
+ readonly selectedRows: ({
860
+ id: string;
861
+ cells: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
862
+ text: import("mobx-state-tree").ISimpleType<string>;
863
+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
864
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
865
+ text: import("mobx-state-tree").ISimpleType<string>;
866
+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
867
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
868
+ extendedData: any;
869
+ isSelected: boolean;
870
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
871
+ toggleSelect(): void;
872
+ unSelect(): void;
873
+ select(): void;
874
+ setExtendedData(data: unknown): void;
875
+ } & {
876
+ readonly cellsWithDerived: any;
877
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
878
+ id: import("mobx-state-tree").ISimpleType<string>;
879
+ cells: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
880
+ text: import("mobx-state-tree").ISimpleType<string>;
881
+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
882
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
883
+ extendedData: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<any, any, any>>;
884
+ isSelected: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
885
+ }, {
886
+ toggleSelect(): void;
887
+ unSelect(): void;
888
+ select(): void;
889
+ setExtendedData(data: unknown): void;
890
+ } & {
891
+ readonly cellsWithDerived: any;
892
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[] | undefined;
862
893
  /**
863
894
  * #getter
864
895
  */
865
- readonly assemblyName: any;
896
+ readonly assemblyName: string | undefined;
866
897
  /**
867
898
  * #getter
868
899
  */
@@ -893,7 +924,7 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
893
924
  type: string;
894
925
  features: any[];
895
926
  };
896
- assemblyNames: any[];
927
+ assemblyNames: (string | undefined)[];
897
928
  displays: {
898
929
  type: string;
899
930
  displayId: string;
@@ -948,10 +979,6 @@ declare function SvInspectorViewF(pluginManager: PluginManager): import("mobx-st
948
979
  * #action
949
980
  */
950
981
  setDisplayMode(): void;
951
- /**
952
- * #action
953
- */
954
- closeView(): void;
955
982
  /**
956
983
  * #action
957
984
  */
package/esm/SvInspectorView/models/SvInspectorView.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import clone from 'clone';
2
2
  import { autorun, reaction } from 'mobx';
3
- import { types, getParent, addDisposer } from 'mobx-state-tree';
3
+ import { types, addDisposer } from 'mobx-state-tree';
4
4
  import { getSession } from '@jbrowse/core/util';
5
5
  import { readConfObject } from '@jbrowse/core/configuration';
6
6
  import { ElementId } from '@jbrowse/core/util/types/mst';
@@ -78,15 +78,17 @@ function SvInspectorViewF(pluginManager) {
78
78
  * #getter
79
79
  */
80
80
  get selectedRows() {
81
- // @ts-expect-error
82
- return self.spreadsheetView.rowSet.selectedRows;
81
+ var _a;
82
+ return (_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.rowSet.selectedRows;
83
83
  },
84
84
  /**
85
85
  * #getter
86
86
  */
87
87
  get assemblyName() {
88
88
  const { assembly } = self.spreadsheetView;
89
- return assembly ? readConfObject(assembly, 'name') : undefined;
89
+ return assembly
90
+ ? readConfObject(assembly, 'name')
91
+ : undefined;
90
92
  },
91
93
  /**
92
94
  * #getter
@@ -136,7 +138,7 @@ function SvInspectorViewF(pluginManager) {
136
138
  {
137
139
  type: 'ChordVariantDisplay',
138
140
  displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
139
- onChordClick: `jexl:defaultOnChordClick(feature, track, pluginManager)`,
141
+ onChordClick: 'jexl:defaultOnChordClick(feature, track, pluginManager)',
140
142
  renderer: { type: 'StructuralVariantChordRenderer' },
141
143
  },
142
144
  ],
@@ -174,13 +176,6 @@ function SvInspectorViewF(pluginManager) {
174
176
  setDisplayMode() {
175
177
  self.spreadsheetView.setDisplayMode();
176
178
  },
177
- /**
178
- * #action
179
- */
180
- closeView() {
181
- // eslint-disable-next-line @typescript-eslint/no-explicit-any
182
- getParent(self, 2).removeView(self);
183
- },
184
179
  /**
185
180
  * #action
186
181
  */
@@ -202,7 +197,9 @@ function SvInspectorViewF(pluginManager) {
202
197
  return [
203
198
  {
204
199
  label: 'Return to import form',
205
- onClick: () => self.setImportMode(),
200
+ onClick: () => {
201
+ self.setImportMode();
202
+ },
206
203
  icon: FolderOpenIcon,
207
204
  },
208
205
  ];
@@ -268,18 +265,15 @@ function SvInspectorViewF(pluginManager) {
268
265
  }, { name: 'SvInspectorView displayed regions bind' }));
269
266
  // bind circularview tracks to our track snapshot view
270
267
  addDisposer(self, reaction(() => ({
271
- generatedTrackConf: self === null || self === void 0 ? void 0 : self.featuresCircularTrackConfiguration,
272
- assemblyName: self === null || self === void 0 ? void 0 : self.assemblyName,
268
+ generatedTrackConf: self.featuresCircularTrackConfiguration,
269
+ assemblyName: self.assemblyName,
273
270
  }), data => {
274
- if (!data) {
275
- return;
276
- }
277
271
  const { assemblyName, generatedTrackConf } = data;
278
272
  const { circularView } = self;
279
273
  // hide any visible tracks
280
274
  circularView.tracks.forEach(t => circularView.hideTrack(t.configuration.trackId));
281
275
  // put our track in as the only track
282
- if (assemblyName && generatedTrackConf) {
276
+ if (assemblyName) {
283
277
  // @ts-expect-error
284
278
  circularView.addTrackConf(generatedTrackConf, {
285
279
  assemblyName,
@@ -303,7 +297,6 @@ function SvInspectorViewF(pluginManager) {
303
297
  disabled(spreadsheetView, spreadsheet, rowNumber, row) {
304
298
  return !canOpenBreakpointSplitViewFromTableRow(self, spreadsheetView, spreadsheet, row, rowNumber);
305
299
  },
306
- // @ts-expect-error
307
300
  onClick(spreadsheetView, spreadsheet, rowNumber, row) {
308
301
  openBreakpointSplitViewFromTableRow(self, spreadsheetView, spreadsheet, row, rowNumber);
309
302
  },
package/esm/SvInspectorView/models/adhocFeatureUtils.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: any, row: any, loc1: any, loc2: any, rowNumber: any): {
1
+ export declare function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: any, row: any, loc1: any, loc2: any, rowNumber: any): {
2
2
  uniqueId: string;
3
3
  refName: any;
4
4
  start: any;
@@ -9,7 +9,7 @@ export function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: an
9
9
  end: any;
10
10
  };
11
11
  };
12
- export function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnNumbers: any, row: any, rowNumber: any, isValidRefName: any): {
12
+ export declare function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnNumbers: any, row: any, rowNumber: any, isValidRefName: any): {
13
13
  uniqueId: string;
14
14
  refName: any;
15
15
  start: any;
@@ -20,7 +20,7 @@ export function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnN
20
20
  end: any;
21
21
  };
22
22
  };
23
- export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefColumnNumbers: any, locStartColumnNumbers: any, locEndColumnNumbers: any, row: any, rowNumber: any): {
23
+ export declare function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefColumnNumbers: any, locStartColumnNumbers: any, locEndColumnNumbers: any, row: any, rowNumber: any): {
24
24
  uniqueId: string;
25
25
  refName: any;
26
26
  start: any;
@@ -31,7 +31,7 @@ export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefCol
31
31
  end: any;
32
32
  };
33
33
  };
34
- export function makeAdHocSvFeature(sheet: any, rowNumber: any, row: any, isValidRefName: any): {
34
+ export declare function makeAdHocSvFeature(sheet: any, rowNumber: any, row: any, isValidRefName: any): {
35
35
  uniqueId: string;
36
36
  refName: any;
37
37
  start: any;
package/esm/SvInspectorView/models/adhocFeatureUtils.js CHANGED
@@ -1,3 +1,4 @@
1
+ // @ts-nocheck
1
2
  // this file contains the rather verbose functions for
2
3
  // creating features from CSV/TSV lines
3
4
  import { parseLocString } from '@jbrowse/core/util';
@@ -10,7 +11,7 @@ export function makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, lo
10
11
  }
11
12
  let { text } = row.cells[columnNumber];
12
13
  if (column.dataType.type === 'Number') {
13
- text = parseFloat(text);
14
+ text = Number.parseFloat(text);
14
15
  }
15
16
  otherData[column.name] = text;
16
17
  });
@@ -42,13 +43,13 @@ export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns, locRefColumnNu
42
43
  const textOf = colno => row.cells[colno].text;
43
44
  const loc1 = {
44
45
  refName: textOf(locRefColumnNumbers[0]),
45
- start: parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
46
- end: parseInt(textOf(locEndColumnNumbers[0]), 10),
46
+ start: Number.parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
47
+ end: Number.parseInt(textOf(locEndColumnNumbers[0]), 10),
47
48
  };
48
49
  const loc2 = {
49
50
  refName: textOf(locRefColumnNumbers[1]),
50
- start: parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
51
- end: parseInt(textOf(locEndColumnNumbers[1]), 10),
51
+ start: Number.parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
52
+ end: Number.parseInt(textOf(locEndColumnNumbers[1]), 10),
52
53
  };
53
54
  const columnsAlreadyUsedInLocations = [
54
55
  locRefColumnNumbers[0],
package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export function getFeatureForRow(session: any, spreadsheetView: any, row: any, rowNumber: any): any;
2
- export function breakpointSplitViewSnapshotFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): any;
3
- export function openBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): void;
4
- export function canOpenBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): boolean;
1
+ export declare function getFeatureForRow(session: any, spreadsheetView: any, row: any, rowNumber: any): any;
2
+ export declare function breakpointSplitViewSnapshotFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): any;
3
+ export declare function openBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): void;
4
+ export declare function canOpenBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): boolean;
package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.js CHANGED
@@ -1,3 +1,4 @@
1
+ // @ts-nocheck
1
2
  import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util';
2
3
  import { makeAdHocSvFeature } from './adhocFeatureUtils';
3
4
  export function getFeatureForRow(session, spreadsheetView, row, rowNumber) {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sv-inspector",
3
- "version": "2.13.1",
3
+ "version": "2.14.0",
4
4
  "description": "JBrowse 2 SV inspector view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -24,7 +24,7 @@
24
24
  ],
25
25
  "scripts": {
26
26
  "build": "npm-run-all build:*",
27
- "test": "cd ../..; jest plugins/sv-inspector",
27
+ "test": "cd ../..; jest --passWithNoTests plugins/sv-inspector",
28
28
  "prepublishOnly": "yarn test",
29
29
  "prepack": "yarn build && yarn useDist",
30
30
  "postpack": "yarn useSrc",
@@ -57,5 +57,5 @@
57
57
  "publishConfig": {
58
58
  "access": "public"
59
59
  },
60
- "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
60
+ "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
61
61
  }