@jbrowse/plugin-alignments 4.0.2 → 4.0.4

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 (15) hide show
  1. package/esm/LinearAlignmentsDisplay/model.d.ts +3 -0
  2. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +20 -1
  3. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +22 -14
  4. package/esm/LinearPileupDisplay/doAfterAttach.js +3 -3
  5. package/esm/LinearPileupDisplay/model.d.ts +29 -2
  6. package/esm/LinearPileupDisplay/model.js +11 -13
  7. package/esm/LinearPileupDisplay/sharedDoAfterAttach.js +1 -1
  8. package/esm/LinearReadArcsDisplay/model.d.ts +3 -0
  9. package/esm/LinearReadCloudDisplay/model.d.ts +3 -0
  10. package/esm/LinearSNPCoverageDisplay/model.js +9 -10
  11. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +6 -2
  12. package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.js +1 -1
  13. package/esm/shared/createRPCRenderingSetup.js +11 -6
  14. package/esm/shared/types.d.ts +0 -1
  15. package/package.json +6 -6
package/esm/LinearAlignmentsDisplay/model.d.ts CHANGED
@@ -64,6 +64,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
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  } & {
@@ -120,6 +121,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -173,6 +175,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts CHANGED
@@ -148,6 +148,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
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  } & {
@@ -204,6 +205,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
208
+ readonly isMinimized: boolean;
207
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  readonly parentDisplay: any;
208
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  readonly effectiveRpcDriverName: any;
209
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -257,6 +259,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  }> | null;
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  readonly adapterConfig: any;
259
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
262
+ readonly isMinimized: boolean;
260
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  readonly parentDisplay: any;
261
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  readonly effectiveRpcDriverName: any;
262
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -538,6 +541,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
538
541
  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
541
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
543
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  } & {
@@ -594,6 +598,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  }> | null;
595
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
601
+ readonly isMinimized: boolean;
597
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  readonly parentDisplay: any;
598
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  readonly effectiveRpcDriverName: any;
599
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -647,6 +652,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
652
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -873,6 +879,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
873
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
877
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  readonly effectiveRpcDriverName: any;
878
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  } & {
@@ -929,6 +936,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
934
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -982,6 +990,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
982
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
986
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  readonly effectiveRpcDriverName: any;
987
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1114,10 +1123,18 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  setHideLargeIndels(arg: boolean): void;
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  } & {
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  copyFeatureToClipboard(feature: Feature): Promise<void>;
1117
- readonly rendererConfig: any;
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+ readonly rendererConfig: {
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+ height: any;
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+ noSpacing: any;
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+ maxHeight: any;
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+ hideSmallIndels: any;
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+ hideMismatches: any;
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+ hideLargeIndels: any;
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+ };
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  } & {
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  readonly maxHeight: any;
1120
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  readonly featureHeightSetting: any;
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+ readonly noSpacingSetting: any;
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  readonly featureUnderMouse: Feature | undefined;
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  renderReady(): boolean;
1123
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  readonly filters: SerializableFilterChain;
@@ -1207,6 +1224,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
1207
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
1211
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  readonly effectiveRpcDriverName: any;
1212
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1260,6 +1278,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
1260
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  }> | null;
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  readonly adapterConfig: any;
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
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  readonly parentDisplay: any;
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  readonly effectiveRpcDriverName: any;
1265
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -52,6 +52,9 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  }))
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  .views(self => ({
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  get autorunReady() {
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+ if (self.isMinimized) {
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+ return false;
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+ }
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  const view = getContainingView(self);
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  return (view.initialized && self.featureDensityStatsReadyAndRegionNotTooLarge);
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  },
@@ -152,25 +155,27 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  session.notify('Copied to clipboard', 'success');
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  },
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  get rendererConfig() {
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- const { featureHeight: height, noSpacing, hideSmallIndels, hideMismatches, hideLargeIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
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- const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
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+ const { featureHeight, noSpacing, hideSmallIndels, hideMismatches, hideLargeIndels, trackMaxHeight, rendererTypeName, } = self;
159
+ const conf = self.configuration.renderers?.[rendererTypeName];
157
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  return {
158
- ...configBlob,
159
- ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
160
- ...(hideMismatches !== undefined ? { hideMismatches } : {}),
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- ...(hideLargeIndels !== undefined ? { hideLargeIndels } : {}),
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- ...(height !== undefined ? { height } : {}),
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- ...(noSpacing !== undefined ? { noSpacing } : {}),
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- ...(maxHeight !== undefined ? { maxHeight } : {}),
161
+ height: featureHeight ?? readConfObject(conf, 'height'),
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+ noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
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+ maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
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+ hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
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+ hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
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+ hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
165
167
  };
166
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  },
167
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  }))
168
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  .views(self => ({
169
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  get maxHeight() {
170
- return readConfObject(self.rendererConfig, 'maxHeight');
172
+ return self.rendererConfig.maxHeight;
171
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  },
172
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  get featureHeightSetting() {
173
- return readConfObject(self.rendererConfig, 'height');
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+ return self.rendererConfig.height;
176
+ },
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+ get noSpacingSetting() {
178
+ return self.rendererConfig.noSpacing;
174
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  },
175
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  get featureUnderMouse() {
176
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  return self.featureUnderMouseVolatile;
@@ -391,7 +396,8 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
391
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  {
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  label: 'Normal',
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  type: 'radio',
394
- checked: self.featureHeight === 7 && self.noSpacing === false,
399
+ checked: self.featureHeightSetting === 7 &&
400
+ self.noSpacingSetting === false,
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  onClick: () => {
396
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  self.setFeatureHeight(7);
397
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  self.setNoSpacing(false);
@@ -400,7 +406,8 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
400
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  {
401
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  label: 'Compact',
402
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  type: 'radio',
403
- checked: self.featureHeight === 2 && self.noSpacing === true,
409
+ checked: self.featureHeightSetting === 2 &&
410
+ self.noSpacingSetting === true,
404
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  onClick: () => {
405
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  self.setFeatureHeight(2);
406
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  self.setNoSpacing(true);
@@ -409,7 +416,8 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  {
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  label: 'Super-compact',
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  type: 'radio',
412
- checked: self.featureHeight === 1 && self.noSpacing === true,
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+ checked: self.featureHeightSetting === 1 &&
420
+ self.noSpacingSetting === true,
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  onClick: () => {
414
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  self.setFeatureHeight(1);
415
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  self.setNoSpacing(true);
package/esm/LinearPileupDisplay/doAfterAttach.js CHANGED
@@ -5,21 +5,21 @@ import { setupModificationsAutorun } from "../shared/setupModificationsAutorun.j
5
5
  import { createAutorun } from "../util.js";
6
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  export function doAfterAttach(model) {
7
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  createAutorun(model, async () => {
8
- const view = getContainingView(model);
9
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  if (!model.autorunReady) {
10
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  return;
11
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  }
11
+ const view = getContainingView(model);
12
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  model.setCurrSortBpPerPx(view.bpPerPx);
13
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  }, {
14
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  delay: 1000,
15
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  name: 'CurrBpPerPx',
16
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  });
17
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  createAutorun(model, async () => {
18
- const { rpcManager } = getSession(model);
19
- const view = getContainingView(model);
20
18
  if (!model.autorunReady) {
21
19
  return;
22
20
  }
21
+ const { rpcManager } = getSession(model);
22
+ const view = getContainingView(model);
23
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  const { sortedBy, adapterConfig, rendererType, sortReady } = model;
24
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  const { bpPerPx } = view;
25
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  if (sortedBy && (!sortReady || model.currSortBpPerPx === view.bpPerPx)) {
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -151,6 +151,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
151
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  }> | null;
152
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  readonly adapterConfig: any;
153
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
154
+ readonly isMinimized: boolean;
154
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  readonly parentDisplay: any;
155
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  readonly effectiveRpcDriverName: any;
156
157
  } & {
@@ -207,6 +208,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
207
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  }> | null;
208
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  readonly adapterConfig: any;
209
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
211
+ readonly isMinimized: boolean;
210
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  readonly parentDisplay: any;
211
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  readonly effectiveRpcDriverName: any;
212
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -260,6 +262,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
260
262
  }> | null;
261
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  readonly adapterConfig: any;
262
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
265
+ readonly isMinimized: boolean;
263
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  readonly parentDisplay: any;
264
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  readonly effectiveRpcDriverName: any;
265
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -541,6 +544,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
541
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  }> | null;
542
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  readonly adapterConfig: any;
543
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
547
+ readonly isMinimized: boolean;
544
548
  readonly parentDisplay: any;
545
549
  readonly effectiveRpcDriverName: any;
546
550
  } & {
@@ -597,6 +601,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
597
601
  }> | null;
598
602
  readonly adapterConfig: any;
599
603
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
604
+ readonly isMinimized: boolean;
600
605
  readonly parentDisplay: any;
601
606
  readonly effectiveRpcDriverName: any;
602
607
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -650,6 +655,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
650
655
  }> | null;
651
656
  readonly adapterConfig: any;
652
657
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
658
+ readonly isMinimized: boolean;
653
659
  readonly parentDisplay: any;
654
660
  readonly effectiveRpcDriverName: any;
655
661
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -876,6 +882,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
876
882
  }> | null;
877
883
  readonly adapterConfig: any;
878
884
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
885
+ readonly isMinimized: boolean;
879
886
  readonly parentDisplay: any;
880
887
  readonly effectiveRpcDriverName: any;
881
888
  } & {
@@ -932,6 +939,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
932
939
  }> | null;
933
940
  readonly adapterConfig: any;
934
941
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
942
+ readonly isMinimized: boolean;
935
943
  readonly parentDisplay: any;
936
944
  readonly effectiveRpcDriverName: any;
937
945
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -985,6 +993,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
985
993
  }> | null;
986
994
  readonly adapterConfig: any;
987
995
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
996
+ readonly isMinimized: boolean;
988
997
  readonly parentDisplay: any;
989
998
  readonly effectiveRpcDriverName: any;
990
999
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1117,10 +1126,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
1117
1126
  setHideLargeIndels(arg: boolean): void;
1118
1127
  } & {
1119
1128
  copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): Promise<void>;
1120
- readonly rendererConfig: any;
1129
+ readonly rendererConfig: {
1130
+ height: any;
1131
+ noSpacing: any;
1132
+ maxHeight: any;
1133
+ hideSmallIndels: any;
1134
+ hideMismatches: any;
1135
+ hideLargeIndels: any;
1136
+ };
1121
1137
  } & {
1122
1138
  readonly maxHeight: any;
1123
1139
  readonly featureHeightSetting: any;
1140
+ readonly noSpacingSetting: any;
1124
1141
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
1125
1142
  renderReady(): boolean;
1126
1143
  readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
@@ -1210,6 +1227,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
1210
1227
  }> | null;
1211
1228
  readonly adapterConfig: any;
1212
1229
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1230
+ readonly isMinimized: boolean;
1213
1231
  readonly parentDisplay: any;
1214
1232
  readonly effectiveRpcDriverName: any;
1215
1233
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1263,6 +1281,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
1263
1281
  }> | null;
1264
1282
  readonly adapterConfig: any;
1265
1283
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1284
+ readonly isMinimized: boolean;
1266
1285
  readonly parentDisplay: any;
1267
1286
  readonly effectiveRpcDriverName: any;
1268
1287
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1351,7 +1370,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
1351
1370
  reload(): void;
1352
1371
  } & {
1353
1372
  readonly modificationThreshold: any;
1354
- readonly rendererConfig: any;
1373
+ readonly rendererConfig: {
1374
+ height: any;
1375
+ noSpacing: any;
1376
+ maxHeight: any;
1377
+ mismatchAlpha: any;
1378
+ hideSmallIndels: any;
1379
+ hideMismatches: any;
1380
+ hideLargeIndels: any;
1381
+ };
1355
1382
  } & {
1356
1383
  readonly mismatchAlphaSetting: any;
1357
1384
  renderReady(): boolean;
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -1,5 +1,5 @@
1
1
  import { lazy } from 'react';
2
- import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
2
+ import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
3
3
  import { getContainingView, getSession } from '@jbrowse/core/util';
4
4
  import { types } from '@jbrowse/mobx-state-tree';
5
5
  import ColorLensIcon from '@mui/icons-material/ColorLens';
@@ -91,18 +91,16 @@ function stateModelFactory(configSchema) {
91
91
  return self.colorBy?.modifications?.threshold ?? 10;
92
92
  },
93
93
  get rendererConfig() {
94
- const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, hideSmallIndels, hideMismatches, } = self;
95
- const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
94
+ const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, hideSmallIndels, hideMismatches, hideLargeIndels, } = self;
95
+ const conf = self.configuration.renderers?.PileupRenderer;
96
96
  return {
97
- ...configBlob,
98
- ...(featureHeight !== undefined ? { height: featureHeight } : {}),
99
- ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
100
- ...(hideMismatches !== undefined ? { hideMismatches } : {}),
101
- ...(noSpacing !== undefined ? { noSpacing } : {}),
102
- ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
103
- ...(trackMaxHeight !== undefined
104
- ? { maxHeight: trackMaxHeight }
105
- : {}),
97
+ height: featureHeight ?? readConfObject(conf, 'height'),
98
+ noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
99
+ maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
100
+ mismatchAlpha: mismatchAlpha ?? readConfObject(conf, 'mismatchAlpha'),
101
+ hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
102
+ hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
103
+ hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
106
104
  };
107
105
  },
108
106
  }))
@@ -110,7 +108,7 @@ function stateModelFactory(configSchema) {
110
108
  const { renderReady: superRenderReady } = self;
111
109
  return {
112
110
  get mismatchAlphaSetting() {
113
- return readConfObject(self.rendererConfig, 'mismatchAlpha');
111
+ return self.rendererConfig.mismatchAlpha;
114
112
  },
115
113
  renderReady() {
116
114
  const view = getContainingView(self);
package/esm/LinearPileupDisplay/sharedDoAfterAttach.js CHANGED
@@ -4,10 +4,10 @@ import { getUniqueTags } from "../shared/getUniqueTags.js";
4
4
  import { createAutorun } from "../util.js";
5
5
  export function sharedDoAfterAttach(self) {
6
6
  createAutorun(self, async () => {
7
- const view = getContainingView(self);
8
7
  if (!self.autorunReady) {
9
8
  return;
10
9
  }
10
+ const view = getContainingView(self);
11
11
  const { colorBy, tagsReady } = self;
12
12
  const { staticBlocks } = view;
13
13
  if (colorBy?.tag && !tagsReady) {
package/esm/LinearReadArcsDisplay/model.d.ts CHANGED
@@ -70,6 +70,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
70
70
  }> | null;
71
71
  readonly adapterConfig: any;
72
72
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
73
+ readonly isMinimized: boolean;
73
74
  readonly parentDisplay: any;
74
75
  readonly effectiveRpcDriverName: any;
75
76
  } & {
@@ -126,6 +127,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
126
127
  }> | null;
127
128
  readonly adapterConfig: any;
128
129
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
130
+ readonly isMinimized: boolean;
129
131
  readonly parentDisplay: any;
130
132
  readonly effectiveRpcDriverName: any;
131
133
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -179,6 +181,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
179
181
  }> | null;
180
182
  readonly adapterConfig: any;
181
183
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
184
+ readonly isMinimized: boolean;
182
185
  readonly parentDisplay: any;
183
186
  readonly effectiveRpcDriverName: any;
184
187
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
package/esm/LinearReadCloudDisplay/model.d.ts CHANGED
@@ -79,6 +79,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
79
79
  }> | null;
80
80
  readonly adapterConfig: any;
81
81
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
82
+ readonly isMinimized: boolean;
82
83
  readonly parentDisplay: any;
83
84
  readonly effectiveRpcDriverName: any;
84
85
  } & {
@@ -135,6 +136,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
135
136
  }> | null;
136
137
  readonly adapterConfig: any;
137
138
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
139
+ readonly isMinimized: boolean;
138
140
  readonly parentDisplay: any;
139
141
  readonly effectiveRpcDriverName: any;
140
142
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -188,6 +190,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
188
190
  }> | null;
189
191
  readonly adapterConfig: any;
190
192
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
193
+ readonly isMinimized: boolean;
191
194
  readonly parentDisplay: any;
192
195
  readonly effectiveRpcDriverName: any;
193
196
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
package/esm/LinearSNPCoverageDisplay/model.js CHANGED
@@ -61,17 +61,18 @@ function stateModelFactory(pluginManager, configSchema) {
61
61
  return self.colorBy?.modifications?.threshold ?? 10;
62
62
  },
63
63
  get rendererConfig() {
64
- const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
65
64
  const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
65
+ const conf = self.configuration.renderers?.[self.rendererTypeName];
66
66
  return {
67
- ...configBlob,
68
- showInterbaseCounts: showInterbaseCounts ?? configBlob.showInterbaseCounts,
69
- showInterbaseIndicators: showInterbaseIndicators ?? configBlob.showInterbaseIndicators,
70
- showArcs: showArcs ?? configBlob.showArcs,
67
+ showInterbaseCounts: showInterbaseCounts ??
68
+ readConfObject(conf, 'showInterbaseCounts'),
69
+ showInterbaseIndicators: showInterbaseIndicators ??
70
+ readConfObject(conf, 'showInterbaseIndicators'),
71
+ showArcs: showArcs ?? readConfObject(conf, 'showArcs'),
71
72
  };
72
73
  },
73
74
  get showArcsSetting() {
74
- return (self.showArcs ?? readConfObject(this.rendererConfig, 'showArcs'));
75
+ return this.rendererConfig.showArcs;
75
76
  },
76
77
  get skipFeatures() {
77
78
  if (!this.showArcsSetting) {
@@ -92,12 +93,10 @@ function stateModelFactory(pluginManager, configSchema) {
92
93
  return [...skipFeaturesMap.values()];
93
94
  },
94
95
  get showInterbaseCountsSetting() {
95
- return (self.showInterbaseCounts ??
96
- readConfObject(this.rendererConfig, 'showInterbaseCounts'));
96
+ return this.rendererConfig.showInterbaseCounts;
97
97
  },
98
98
  get showInterbaseIndicatorsSetting() {
99
- return (self.showInterbaseIndicators ??
100
- readConfObject(this.rendererConfig, 'showInterbaseIndicators'));
99
+ return this.rendererConfig.showInterbaseIndicators;
101
100
  },
102
101
  get autorunReady() {
103
102
  const view = getContainingView(self);
package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js CHANGED
@@ -156,10 +156,14 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
156
156
  }
157
157
  async getCoverageBins(region, opts = {}) {
158
158
  const { bpPerPx, statsEstimationMode } = opts;
159
- if (this.lastBpPerPx !== undefined && this.lastBpPerPx !== bpPerPx) {
159
+ if (bpPerPx !== undefined &&
160
+ this.lastBpPerPx !== undefined &&
161
+ this.lastBpPerPx !== bpPerPx) {
160
162
  this.cache.clear();
161
163
  }
162
- this.lastBpPerPx = bpPerPx;
164
+ if (bpPerPx !== undefined) {
165
+ this.lastBpPerPx = bpPerPx;
166
+ }
163
167
  if (statsEstimationMode) {
164
168
  const regionFilterKey = makeRegionFilterKey(region, opts);
165
169
  for (const key of this.cache.keys()) {
package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.js CHANGED
@@ -79,6 +79,7 @@ export async function generateCoverageBinsPrefixSum({ fetchSequence, features, r
79
79
  for (let i = 0, l = features.length; i < l; i++) {
80
80
  processFeature(region, features[i], skipmap, noncovEvents, snpEvents);
81
81
  }
82
+ featureCtx.feature = undefined;
82
83
  const deletionDepth = new Int32Array(regionSize);
83
84
  let dd = 0;
84
85
  for (let i = 0; i < regionSize; i++) {
@@ -346,7 +347,6 @@ function mismatchHandler(type, start, refLen, base, _qual, altbase, interbaseLen
346
347
  const hash = `${mstart}_${mend}_${effectiveStrand}`;
347
348
  if (skipmap[hash] === undefined) {
348
349
  skipmap[hash] = {
349
- feature: feature,
350
350
  start: mstart,
351
351
  end: mend,
352
352
  strand: fstrand,
package/esm/shared/createRPCRenderingSetup.js CHANGED
@@ -33,18 +33,23 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
33
33
  const stopToken = createStopToken();
34
34
  self.setRenderingStopToken(stopToken);
35
35
  self.setLoading(true);
36
- const viewSnapshot = structuredClone({
37
- ...getSnapshot(view),
38
- staticBlocks: view.staticBlocks,
36
+ const viewSnapshot = {
37
+ displayedRegions: structuredClone(view.displayedRegions),
38
+ bpPerPx: view.bpPerPx,
39
+ offsetPx: view.offsetPx,
40
+ interRegionPaddingWidth: view.interRegionPaddingWidth,
41
+ minimumBlockWidth: view.minimumBlockWidth,
39
42
  width: view.width,
40
- });
43
+ };
41
44
  const sessionId = getRpcSessionId(self);
45
+ const adapterConfig = self.adapterConfig;
46
+ const config = getSnapshot(self.configuration);
42
47
  const result = (await rpcManager.call(sessionId, rpcMethodName, {
43
48
  sessionId,
44
49
  view: viewSnapshot,
45
- adapterConfig: self.adapterConfig,
50
+ adapterConfig,
46
51
  sequenceAdapter,
47
- config: getSnapshot(self.configuration),
52
+ config,
48
53
  statusCallback: (msg) => {
49
54
  if (isAlive(self)) {
50
55
  self.setStatusMessage?.(msg);
package/esm/shared/types.d.ts CHANGED
@@ -2,7 +2,6 @@ import type { MismatchCallback } from './forEachMismatchTypes.ts';
2
2
  import type { Feature } from '@jbrowse/core/util';
3
3
  export type SkipMap = Record<string, {
4
4
  score: number;
5
- feature: unknown;
6
5
  start: number;
7
6
  end: number;
8
7
  strand: number;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "4.0.2",
3
+ "version": "4.0.4",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -25,7 +25,7 @@
25
25
  "@jbrowse/mobx-state-tree": "^5.5.0",
26
26
  "@mui/icons-material": "^7.3.6",
27
27
  "@mui/material": "^7.3.6",
28
- "@mui/x-charts-vendor": "^8.23.0",
28
+ "@mui/x-charts-vendor": "^8.25.0",
29
29
  "canvas2svg": "^1.0.16",
30
30
  "copy-to-clipboard": "^3.3.3",
31
31
  "fast-deep-equal": "^3.1.3",
@@ -33,10 +33,10 @@
33
33
  "mobx": "^6.15.0",
34
34
  "mobx-react": "^9.2.1",
35
35
  "rxjs": "^7.8.2",
36
- "@jbrowse/core": "^4.0.2",
37
- "@jbrowse/plugin-wiggle": "^4.0.2",
38
- "@jbrowse/sv-core": "^4.0.2",
39
- "@jbrowse/plugin-linear-genome-view": "^4.0.2"
36
+ "@jbrowse/core": "^4.0.4",
37
+ "@jbrowse/plugin-linear-genome-view": "^4.0.4",
38
+ "@jbrowse/plugin-wiggle": "^4.0.4",
39
+ "@jbrowse/sv-core": "^4.0.4"
40
40
  },
41
41
  "peerDependencies": {
42
42
  "react": ">=18.0.0"