@jbrowse/plugin-linear-genome-view 3.4.0 → 3.5.0

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Files changed (23) hide show
  1. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +1 -1
  2. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +20 -18
  3. package/dist/LinearBareDisplay/model.d.ts +1 -1
  4. package/dist/LinearBasicDisplay/model.d.ts +1 -1
  5. package/dist/LinearGenomeView/components/HeaderPanControls.js +0 -3
  6. package/dist/LinearGenomeView/components/MiniControls.js +1 -0
  7. package/dist/LinearGenomeView/components/TrackLabel.js +1 -0
  8. package/dist/LinearGenomeView/components/TrackLabelMenu.js +2 -9
  9. package/dist/LinearGenomeView/model.d.ts +2 -1
  10. package/dist/LinearGenomeView/model.js +5 -1
  11. package/dist/index.d.ts +1 -1
  12. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +1 -1
  13. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js +20 -18
  14. package/esm/LinearBareDisplay/model.d.ts +1 -1
  15. package/esm/LinearBasicDisplay/model.d.ts +1 -1
  16. package/esm/LinearGenomeView/components/HeaderPanControls.js +0 -3
  17. package/esm/LinearGenomeView/components/MiniControls.js +1 -0
  18. package/esm/LinearGenomeView/components/TrackLabel.js +1 -0
  19. package/esm/LinearGenomeView/components/TrackLabelMenu.js +2 -9
  20. package/esm/LinearGenomeView/model.d.ts +2 -1
  21. package/esm/LinearGenomeView/model.js +5 -1
  22. package/esm/index.d.ts +1 -1
  23. package/package.json +3 -3
package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts CHANGED
@@ -206,7 +206,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
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206
  } & {
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  addBlock(key: string, block: BaseBlock): void;
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  deleteBlock(key: string): void;
209
- selectFeature(feature: Feature): Promise<void>;
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+ selectFeature(feature: Feature): void;
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  navToFeature(feature: Feature): void;
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  clearFeatureSelection(): void;
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  setFeatureIdUnderMouse(feature?: string): void;
package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js CHANGED
@@ -138,7 +138,7 @@ function stateModelFactory() {
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  deleteBlock(key) {
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  self.blockState.delete(key);
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  },
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- async selectFeature(feature) {
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+ selectFeature(feature) {
142
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  const session = (0, util_1.getSession)(self);
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  if ((0, util_1.isSessionModelWithWidgets)(session)) {
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  const { rpcManager } = session;
@@ -146,15 +146,23 @@ function stateModelFactory() {
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  const track = (0, util_1.getContainingTrack)(self);
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  const view = (0, util_1.getContainingView)(self);
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  const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
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- const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
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- adapterConfig,
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- });
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- session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
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- featureData: feature.toJSON(),
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- view,
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- track,
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- descriptions,
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- }));
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+ (async () => {
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+ try {
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+ const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
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+ adapterConfig,
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+ });
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+ session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
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+ featureData: feature.toJSON(),
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+ view,
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+ track,
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+ descriptions,
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+ }));
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+ }
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+ catch (e) {
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+ console.error(e);
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+ (0, util_1.getSession)(e).notifyError(`${e}`, e);
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+ }
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+ })();
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  }
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  if ((0, util_1.isSelectionContainer)(session)) {
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  session.setSelection(feature);
@@ -205,11 +213,7 @@ function stateModelFactory() {
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  icon: MenuOpen_1.default,
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  onClick: () => {
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  if (self.contextMenuFeature) {
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- self
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- .selectFeature(self.contextMenuFeature)
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- .catch((e) => {
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- (0, util_1.getSession)(e).notifyError(`${e}`, e);
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- });
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+ self.selectFeature(self.contextMenuFeature);
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  }
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  },
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  },
@@ -240,9 +244,7 @@ function stateModelFactory() {
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  else {
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  const feature = self.features.get(f);
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  if (feature) {
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- self.selectFeature(feature).catch((e) => {
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- (0, util_1.getSession)(e).notifyError(`${e}`, e);
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- });
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+ self.selectFeature(feature);
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  }
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  }
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  },
package/dist/LinearBareDisplay/model.d.ts CHANGED
@@ -190,7 +190,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  } & {
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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  deleteBlock(key: string): void;
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- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
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+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
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  clearFeatureSelection(): void;
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  setFeatureIdUnderMouse(feature?: string): void;
package/dist/LinearBasicDisplay/model.d.ts CHANGED
@@ -198,7 +198,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  } & {
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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  deleteBlock(key: string): void;
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- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
201
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
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  clearFeatureSelection(): void;
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  setFeatureIdUnderMouse(feature?: string): void;
package/dist/LinearGenomeView/components/HeaderPanControls.js CHANGED
@@ -16,9 +16,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  color: theme.palette.text.primary,
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  margin: consts_1.SPACING,
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  },
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- buttonSpacer: {
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- marginRight: theme.spacing(2),
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- },
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19
  }));
23
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  function HeaderPanControls({ model }) {
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  const { classes } = useStyles();
package/dist/LinearGenomeView/components/MiniControls.js CHANGED
@@ -17,6 +17,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  position: 'absolute',
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  right: 0,
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  background: theme.palette.background.paper,
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+ zIndex: 2,
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  },
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  focusedBackground: {
22
23
  background: (0, material_1.alpha)(theme.palette.secondary.light, 0.2),
package/dist/LinearGenomeView/components/TrackLabel.js CHANGED
@@ -17,6 +17,7 @@ const TrackLabelDragHandle_1 = __importDefault(require("./TrackLabelDragHandle")
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  const TrackLabelMenu_1 = __importDefault(require("./TrackLabelMenu"));
18
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  root: {
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+ zIndex: 200,
20
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  background: (0, material_1.alpha)(theme.palette.background.paper, 0.8),
21
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  '&:hover': {
22
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  background: theme.palette.background.paper,
package/dist/LinearGenomeView/components/TrackLabelMenu.js CHANGED
@@ -22,16 +22,9 @@ const TrackLabelMenu = (0, mobx_react_1.observer)(function ({ track, }) {
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  const trackConf = track.configuration;
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  const minimized = track.minimized;
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  const pinned = track.pinned;
25
- let lgvHasParentView;
26
- try {
27
- (0, util_1.getContainingView)(view);
28
- lgvHasParentView = true;
29
- }
30
- catch (error) {
31
- lgvHasParentView = false;
32
- }
25
+ const { isTopLevelView } = view;
33
26
  const items = [
34
- ...(lgvHasParentView
27
+ ...(isTopLevelView
35
28
  ? []
36
29
  : [
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  {
package/dist/LinearGenomeView/model.d.ts CHANGED
@@ -58,7 +58,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  readonly width: number;
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  readonly interRegionPaddingWidth: number;
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  readonly assemblyNames: string[];
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- readonly stickyViewHeaders: boolean;
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+ readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
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+ readonly stickyViewHeaders: boolean | undefined;
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  readonly rubberbandTop: number;
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  readonly pinnedTracksTop: number;
64
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  } & {
package/dist/LinearGenomeView/model.js CHANGED
@@ -136,10 +136,14 @@ function stateModelFactory(pluginManager) {
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  ...new Set(self.displayedRegions.map(region => region.assemblyName)),
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  ];
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  },
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+ get isTopLevelView() {
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+ const session = (0, util_1.getSession)(self);
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+ return session.views.find(r => r.id === self.id);
142
+ },
139
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  get stickyViewHeaders() {
140
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  const session = (0, util_1.getSession)(self);
141
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  return (0, product_core_1.isSessionWithMultipleViews)(session)
142
- ? session.stickyViewHeaders
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+ ? this.isTopLevelView && session.stickyViewHeaders
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147
  : false;
144
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  },
145
149
  get rubberbandTop() {
package/dist/index.d.ts CHANGED
@@ -195,7 +195,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
195
195
  } & {
196
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
197
197
  deleteBlock(key: string): void;
198
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
198
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
199
199
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
200
200
  clearFeatureSelection(): void;
201
201
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts CHANGED
@@ -206,7 +206,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
206
206
  } & {
207
207
  addBlock(key: string, block: BaseBlock): void;
208
208
  deleteBlock(key: string): void;
209
- selectFeature(feature: Feature): Promise<void>;
209
+ selectFeature(feature: Feature): void;
210
210
  navToFeature(feature: Feature): void;
211
211
  clearFeatureSelection(): void;
212
212
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js CHANGED
@@ -99,7 +99,7 @@ function stateModelFactory() {
99
99
  deleteBlock(key) {
100
100
  self.blockState.delete(key);
101
101
  },
102
- async selectFeature(feature) {
102
+ selectFeature(feature) {
103
103
  const session = getSession(self);
104
104
  if (isSessionModelWithWidgets(session)) {
105
105
  const { rpcManager } = session;
@@ -107,15 +107,23 @@ function stateModelFactory() {
107
107
  const track = getContainingTrack(self);
108
108
  const view = getContainingView(self);
109
109
  const adapterConfig = getConf(track, 'adapter');
110
- const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
111
- adapterConfig,
112
- });
113
- session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
114
- featureData: feature.toJSON(),
115
- view,
116
- track,
117
- descriptions,
118
- }));
110
+ (async () => {
111
+ try {
112
+ const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
113
+ adapterConfig,
114
+ });
115
+ session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
116
+ featureData: feature.toJSON(),
117
+ view,
118
+ track,
119
+ descriptions,
120
+ }));
121
+ }
122
+ catch (e) {
123
+ console.error(e);
124
+ getSession(e).notifyError(`${e}`, e);
125
+ }
126
+ })();
119
127
  }
120
128
  if (isSelectionContainer(session)) {
121
129
  session.setSelection(feature);
@@ -166,11 +174,7 @@ function stateModelFactory() {
166
174
  icon: MenuOpenIcon,
167
175
  onClick: () => {
168
176
  if (self.contextMenuFeature) {
169
- self
170
- .selectFeature(self.contextMenuFeature)
171
- .catch((e) => {
172
- getSession(e).notifyError(`${e}`, e);
173
- });
177
+ self.selectFeature(self.contextMenuFeature);
174
178
  }
175
179
  },
176
180
  },
@@ -201,9 +205,7 @@ function stateModelFactory() {
201
205
  else {
202
206
  const feature = self.features.get(f);
203
207
  if (feature) {
204
- self.selectFeature(feature).catch((e) => {
205
- getSession(e).notifyError(`${e}`, e);
206
- });
208
+ self.selectFeature(feature);
207
209
  }
208
210
  }
209
211
  },
package/esm/LinearBareDisplay/model.d.ts CHANGED
@@ -190,7 +190,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
190
190
  } & {
191
191
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
192
192
  deleteBlock(key: string): void;
193
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
193
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
194
194
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
195
195
  clearFeatureSelection(): void;
196
196
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/LinearBasicDisplay/model.d.ts CHANGED
@@ -198,7 +198,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
198
198
  } & {
199
199
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
200
200
  deleteBlock(key: string): void;
201
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
201
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
202
202
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
203
203
  clearFeatureSelection(): void;
204
204
  setFeatureIdUnderMouse(feature?: string): void;
package/esm/LinearGenomeView/components/HeaderPanControls.js CHANGED
@@ -10,9 +10,6 @@ const useStyles = makeStyles()(theme => ({
10
10
  color: theme.palette.text.primary,
11
11
  margin: SPACING,
12
12
  },
13
- buttonSpacer: {
14
- marginRight: theme.spacing(2),
15
- },
16
13
  }));
17
14
  export default function HeaderPanControls({ model }) {
18
15
  const { classes } = useStyles();
package/esm/LinearGenomeView/components/MiniControls.js CHANGED
@@ -12,6 +12,7 @@ const useStyles = makeStyles()(theme => ({
12
12
  position: 'absolute',
13
13
  right: 0,
14
14
  background: theme.palette.background.paper,
15
+ zIndex: 2,
15
16
  },
16
17
  focusedBackground: {
17
18
  background: alpha(theme.palette.secondary.light, 0.2),
package/esm/LinearGenomeView/components/TrackLabel.js CHANGED
@@ -12,6 +12,7 @@ import TrackLabelDragHandle from './TrackLabelDragHandle';
12
12
  import TrackLabelMenu from './TrackLabelMenu';
13
13
  const useStyles = makeStyles()(theme => ({
14
14
  root: {
15
+ zIndex: 200,
15
16
  background: alpha(theme.palette.background.paper, 0.8),
16
17
  '&:hover': {
17
18
  background: theme.palette.background.paper,
package/esm/LinearGenomeView/components/TrackLabelMenu.js CHANGED
@@ -17,16 +17,9 @@ const TrackLabelMenu = observer(function ({ track, }) {
17
17
  const trackConf = track.configuration;
18
18
  const minimized = track.minimized;
19
19
  const pinned = track.pinned;
20
- let lgvHasParentView;
21
- try {
22
- getContainingView(view);
23
- lgvHasParentView = true;
24
- }
25
- catch (error) {
26
- lgvHasParentView = false;
27
- }
20
+ const { isTopLevelView } = view;
28
21
  const items = [
29
- ...(lgvHasParentView
22
+ ...(isTopLevelView
30
23
  ? []
31
24
  : [
32
25
  {
package/esm/LinearGenomeView/model.d.ts CHANGED
@@ -58,7 +58,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
58
58
  readonly width: number;
59
59
  readonly interRegionPaddingWidth: number;
60
60
  readonly assemblyNames: string[];
61
- readonly stickyViewHeaders: boolean;
61
+ readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
62
+ readonly stickyViewHeaders: boolean | undefined;
62
63
  readonly rubberbandTop: number;
63
64
  readonly pinnedTracksTop: number;
64
65
  } & {
package/esm/LinearGenomeView/model.js CHANGED
@@ -96,10 +96,14 @@ export function stateModelFactory(pluginManager) {
96
96
  ...new Set(self.displayedRegions.map(region => region.assemblyName)),
97
97
  ];
98
98
  },
99
+ get isTopLevelView() {
100
+ const session = getSession(self);
101
+ return session.views.find(r => r.id === self.id);
102
+ },
99
103
  get stickyViewHeaders() {
100
104
  const session = getSession(self);
101
105
  return isSessionWithMultipleViews(session)
102
- ? session.stickyViewHeaders
106
+ ? this.isTopLevelView && session.stickyViewHeaders
103
107
  : false;
104
108
  },
105
109
  get rubberbandTop() {
package/esm/index.d.ts CHANGED
@@ -195,7 +195,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
195
195
  } & {
196
196
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
197
197
  deleteBlock(key: string): void;
198
- selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
198
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
199
199
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
200
200
  clearFeatureSelection(): void;
201
201
  setFeatureIdUnderMouse(feature?: string): void;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-linear-genome-view",
3
- "version": "3.4.0",
3
+ "version": "3.5.0",
4
4
  "description": "JBrowse 2 linear genome view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -38,7 +38,7 @@
38
38
  "useSrc": "node ../../scripts/useSrc.js"
39
39
  },
40
40
  "dependencies": {
41
- "@jbrowse/core": "^3.4.0",
41
+ "@jbrowse/core": "^3.5.0",
42
42
  "@mui/icons-material": "^7.0.0",
43
43
  "@mui/material": "^7.0.0",
44
44
  "@types/file-saver": "^2.0.1",
@@ -58,5 +58,5 @@
58
58
  "access": "public"
59
59
  },
60
60
  "module": "esm/index.js",
61
- "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
61
+ "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
62
62
  }