@jbrowse/plugin-wiggle 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 (11) hide show
  1. package/esm/LinearWiggleDisplay/model.d.ts +25 -47
  2. package/esm/LinearWiggleDisplay/model.js +20 -25
  3. package/esm/MultiLinearWiggleDisplay/model.d.ts +71 -31
  4. package/esm/MultiLinearWiggleDisplay/model.js +22 -20
  5. package/esm/getMultiWiggleSourcesAutorun.d.ts +1 -0
  6. package/esm/getMultiWiggleSourcesAutorun.js +3 -0
  7. package/esm/getQuantitativeStatsAutorun.d.ts +1 -0
  8. package/esm/getQuantitativeStatsAutorun.js +3 -0
  9. package/esm/shared/SharedWiggleMixin.d.ts +22 -4
  10. package/esm/shared/SharedWiggleMixin.js +31 -20
  11. package/package.json +7 -7
package/esm/LinearWiggleDisplay/model.d.ts CHANGED
@@ -156,6 +156,7 @@ 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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  } & {
@@ -212,6 +213,7 @@ 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<{
@@ -265,6 +267,7 @@ 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>>;
@@ -546,6 +549,7 @@ 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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  } & {
@@ -602,6 +606,7 @@ 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<{
@@ -655,6 +660,7 @@ 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>>;
@@ -881,6 +887,7 @@ 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;
886
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  } & {
@@ -937,6 +944,7 @@ 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<{
@@ -990,6 +998,7 @@ 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>>;
@@ -1133,13 +1142,22 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  readonly minScore: number;
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  } & {
1135
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  readonly adapterCapabilities: string[];
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- readonly rendererConfig: any;
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+ readonly rendererConfig: {
1146
+ scaleType: string;
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+ filled: any;
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+ displayCrossHatches: any;
1149
+ summaryScoreMode: any;
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+ color: any;
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+ negColor: any;
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+ posColor: any;
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+ minSize: any;
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+ };
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  readonly autoscaleType: string;
1138
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  } & {
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  readonly domain: number[] | undefined;
1140
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  } & {
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- readonly filled: boolean;
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- readonly summaryScoreModeSetting: string;
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+ readonly filled: any;
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+ readonly summaryScoreModeSetting: any;
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  readonly scaleOpts: {
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  domain: number[] | undefined;
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  stats: {
@@ -1153,7 +1171,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  inverted: boolean;
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  };
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  readonly canHaveFill: boolean;
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- readonly displayCrossHatchesSetting: boolean;
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+ readonly displayCrossHatchesSetting: any;
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  readonly hasResolution: boolean;
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  readonly hasGlobalStats: boolean;
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  } & {
@@ -1229,13 +1247,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  })[];
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  })[];
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  wiggleOnlyTrackMenuItems(): ({
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- label: string;
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- type: string;
1234
- checked: boolean;
1235
- onClick: () => void;
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- subMenu?: undefined;
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- icon?: undefined;
1238
- } | {
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  label: string;
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  subMenu: {
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  label: string;
@@ -1243,27 +1254,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  checked: boolean;
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  onClick: () => void;
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  }[];
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- type?: undefined;
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- checked?: undefined;
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- onClick?: undefined;
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  icon?: undefined;
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+ onClick?: undefined;
1250
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  } | {
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  label: string;
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  icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
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  muiName: string;
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  };
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  onClick: () => void;
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- type?: undefined;
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- checked?: undefined;
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- subMenu?: undefined;
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- } | {
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- type: string;
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- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
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- muiName: string;
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- };
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- label: string;
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- checked: boolean;
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- onClick: () => void;
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  subMenu?: undefined;
1268
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  })[];
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  } & {
@@ -1293,13 +1291,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  onClick: () => void;
1294
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  subMenu?: undefined;
1295
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  })[];
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- } | {
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- label: string;
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- type: string;
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- checked: boolean;
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- onClick: () => void;
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- subMenu?: undefined;
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- icon?: undefined;
1303
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  } | {
1304
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  label: string;
1305
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  subMenu: {
@@ -1308,27 +1299,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  checked: boolean;
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  onClick: () => void;
1310
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  }[];
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- type?: undefined;
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- checked?: undefined;
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- onClick?: undefined;
1314
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  icon?: undefined;
1303
+ onClick?: undefined;
1315
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  } | {
1316
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  label: string;
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  icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1318
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  muiName: string;
1319
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  };
1320
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  onClick: () => void;
1321
- type?: undefined;
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- checked?: undefined;
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- subMenu?: undefined;
1324
- } | {
1325
- type: string;
1326
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1327
- muiName: string;
1328
- };
1329
- label: string;
1330
- checked: boolean;
1331
- onClick: () => void;
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  subMenu?: undefined;
1333
1311
  } | {
1334
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  label: string;
@@ -1338,7 +1316,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
1338
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  subMenu: {
1339
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  label: string;
1340
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  type: string;
1341
- checked: boolean;
1319
+ checked: any;
1342
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  onClick: () => void;
1343
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  }[];
1344
1322
  })[];
package/esm/LinearWiggleDisplay/model.js CHANGED
@@ -140,18 +140,6 @@ function stateModelFactory(pluginManager, configSchema) {
140
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  },
141
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  wiggleOnlyTrackMenuItems() {
142
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  return [
143
- ...(self.graphType
144
- ? [
145
- {
146
- label: 'Inverted',
147
- type: 'checkbox',
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- checked: self.inverted,
149
- onClick: () => {
150
- self.setInverted(!self.inverted);
151
- },
152
- },
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- ]
154
- : []),
155
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  ...(self.canHaveFill
156
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  ? [
157
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  {
@@ -195,19 +183,6 @@ function stateModelFactory(pluginManager, configSchema) {
195
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  ]);
196
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  },
197
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  },
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- ...(self.graphType
199
- ? [
200
- {
201
- type: 'checkbox',
202
- icon: VisibilityIcon,
203
- label: 'Show cross hatches',
204
- checked: self.displayCrossHatchesSetting,
205
- onClick: () => {
206
- self.toggleCrossHatches();
207
- },
208
- },
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- ]
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- : []),
211
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  ];
212
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  },
213
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  };
@@ -228,6 +203,26 @@ function stateModelFactory(pluginManager, configSchema) {
228
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  self.setShowTooltips(!self.showTooltipsEnabled);
229
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  },
230
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  },
206
+ ...(self.graphType
207
+ ? [
208
+ {
209
+ label: 'Show inverted',
210
+ type: 'checkbox',
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+ checked: self.inverted,
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+ onClick: () => {
213
+ self.setInverted(!self.inverted);
214
+ },
215
+ },
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+ {
217
+ label: 'Show cross hatches',
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+ type: 'checkbox',
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+ checked: self.displayCrossHatchesSetting,
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+ onClick: () => {
221
+ self.toggleCrossHatches();
222
+ },
223
+ },
224
+ ]
225
+ : []),
231
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  ],
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  },
233
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  ...self.wiggleOnlyTrackMenuItems(),
package/esm/MultiLinearWiggleDisplay/model.d.ts CHANGED
@@ -159,6 +159,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
159
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  }> | null;
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  readonly adapterConfig: any;
161
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
162
+ readonly isMinimized: boolean;
162
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  readonly parentDisplay: any;
163
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  readonly effectiveRpcDriverName: any;
164
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  } & {
@@ -215,6 +216,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
215
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  }> | null;
216
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  readonly adapterConfig: any;
217
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
219
+ readonly isMinimized: boolean;
218
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  readonly parentDisplay: any;
219
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  readonly effectiveRpcDriverName: any;
220
222
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -268,6 +270,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
268
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  }> | null;
269
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  readonly adapterConfig: any;
270
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
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+ readonly isMinimized: boolean;
271
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  readonly parentDisplay: any;
272
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  readonly effectiveRpcDriverName: any;
273
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -549,6 +552,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
549
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  }> | null;
550
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  readonly adapterConfig: any;
551
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
555
+ readonly isMinimized: boolean;
552
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  readonly parentDisplay: any;
553
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  readonly effectiveRpcDriverName: any;
554
558
  } & {
@@ -605,6 +609,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
605
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  }> | null;
606
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  readonly adapterConfig: any;
607
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
612
+ readonly isMinimized: boolean;
608
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  readonly parentDisplay: any;
609
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  readonly effectiveRpcDriverName: any;
610
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -658,6 +663,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
658
663
  }> | null;
659
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  readonly adapterConfig: any;
660
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
666
+ readonly isMinimized: boolean;
661
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  readonly parentDisplay: any;
662
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  readonly effectiveRpcDriverName: any;
663
669
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -884,6 +890,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
884
890
  }> | null;
885
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  readonly adapterConfig: any;
886
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  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
893
+ readonly isMinimized: boolean;
887
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  readonly parentDisplay: any;
888
895
  readonly effectiveRpcDriverName: any;
889
896
  } & {
@@ -940,6 +947,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
940
947
  }> | null;
941
948
  readonly adapterConfig: any;
942
949
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
950
+ readonly isMinimized: boolean;
943
951
  readonly parentDisplay: any;
944
952
  readonly effectiveRpcDriverName: any;
945
953
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -993,6 +1001,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
993
1001
  }> | null;
994
1002
  readonly adapterConfig: any;
995
1003
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1004
+ readonly isMinimized: boolean;
996
1005
  readonly parentDisplay: any;
997
1006
  readonly effectiveRpcDriverName: any;
998
1007
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1136,13 +1145,22 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1136
1145
  readonly minScore: number;
1137
1146
  } & {
1138
1147
  readonly adapterCapabilities: string[];
1139
- readonly rendererConfig: any;
1148
+ readonly rendererConfig: {
1149
+ scaleType: string;
1150
+ filled: any;
1151
+ displayCrossHatches: any;
1152
+ summaryScoreMode: any;
1153
+ color: any;
1154
+ negColor: any;
1155
+ posColor: any;
1156
+ minSize: any;
1157
+ };
1140
1158
  readonly autoscaleType: string;
1141
1159
  } & {
1142
1160
  readonly domain: number[] | undefined;
1143
1161
  } & {
1144
- readonly filled: boolean;
1145
- readonly summaryScoreModeSetting: string;
1162
+ readonly filled: any;
1163
+ readonly summaryScoreModeSetting: any;
1146
1164
  readonly scaleOpts: {
1147
1165
  domain: number[] | undefined;
1148
1166
  stats: {
@@ -1156,7 +1174,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1156
1174
  inverted: boolean;
1157
1175
  };
1158
1176
  readonly canHaveFill: boolean;
1159
- readonly displayCrossHatchesSetting: boolean;
1177
+ readonly displayCrossHatchesSetting: any;
1160
1178
  readonly hasResolution: boolean;
1161
1179
  readonly hasGlobalStats: boolean;
1162
1180
  } & {
@@ -1449,6 +1467,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1449
1467
  }> | null;
1450
1468
  readonly adapterConfig: any;
1451
1469
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1470
+ readonly isMinimized: boolean;
1452
1471
  readonly parentDisplay: any;
1453
1472
  readonly effectiveRpcDriverName: any;
1454
1473
  } & {
@@ -1505,6 +1524,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1505
1524
  }> | null;
1506
1525
  readonly adapterConfig: any;
1507
1526
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1527
+ readonly isMinimized: boolean;
1508
1528
  readonly parentDisplay: any;
1509
1529
  readonly effectiveRpcDriverName: any;
1510
1530
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1558,6 +1578,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1558
1578
  }> | null;
1559
1579
  readonly adapterConfig: any;
1560
1580
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1581
+ readonly isMinimized: boolean;
1561
1582
  readonly parentDisplay: any;
1562
1583
  readonly effectiveRpcDriverName: any;
1563
1584
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1839,6 +1860,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1839
1860
  }> | null;
1840
1861
  readonly adapterConfig: any;
1841
1862
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1863
+ readonly isMinimized: boolean;
1842
1864
  readonly parentDisplay: any;
1843
1865
  readonly effectiveRpcDriverName: any;
1844
1866
  } & {
@@ -1895,6 +1917,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1895
1917
  }> | null;
1896
1918
  readonly adapterConfig: any;
1897
1919
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1920
+ readonly isMinimized: boolean;
1898
1921
  readonly parentDisplay: any;
1899
1922
  readonly effectiveRpcDriverName: any;
1900
1923
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1948,6 +1971,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
1948
1971
  }> | null;
1949
1972
  readonly adapterConfig: any;
1950
1973
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
1974
+ readonly isMinimized: boolean;
1951
1975
  readonly parentDisplay: any;
1952
1976
  readonly effectiveRpcDriverName: any;
1953
1977
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -2174,6 +2198,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2174
2198
  }> | null;
2175
2199
  readonly adapterConfig: any;
2176
2200
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
2201
+ readonly isMinimized: boolean;
2177
2202
  readonly parentDisplay: any;
2178
2203
  readonly effectiveRpcDriverName: any;
2179
2204
  } & {
@@ -2230,6 +2255,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2230
2255
  }> | null;
2231
2256
  readonly adapterConfig: any;
2232
2257
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
2258
+ readonly isMinimized: boolean;
2233
2259
  readonly parentDisplay: any;
2234
2260
  readonly effectiveRpcDriverName: any;
2235
2261
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -2283,6 +2309,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2283
2309
  }> | null;
2284
2310
  readonly adapterConfig: any;
2285
2311
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
2312
+ readonly isMinimized: boolean;
2286
2313
  readonly parentDisplay: any;
2287
2314
  readonly effectiveRpcDriverName: any;
2288
2315
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -2426,13 +2453,22 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2426
2453
  readonly minScore: number;
2427
2454
  } & {
2428
2455
  readonly adapterCapabilities: string[];
2429
- readonly rendererConfig: any;
2456
+ readonly rendererConfig: {
2457
+ scaleType: string;
2458
+ filled: any;
2459
+ displayCrossHatches: any;
2460
+ summaryScoreMode: any;
2461
+ color: any;
2462
+ negColor: any;
2463
+ posColor: any;
2464
+ minSize: any;
2465
+ };
2430
2466
  readonly autoscaleType: string;
2431
2467
  } & {
2432
2468
  readonly domain: number[] | undefined;
2433
2469
  } & {
2434
- readonly filled: boolean;
2435
- readonly summaryScoreModeSetting: string;
2470
+ readonly filled: any;
2471
+ readonly summaryScoreModeSetting: any;
2436
2472
  readonly scaleOpts: {
2437
2473
  domain: number[] | undefined;
2438
2474
  stats: {
@@ -2446,7 +2482,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2446
2482
  inverted: boolean;
2447
2483
  };
2448
2484
  readonly canHaveFill: boolean;
2449
- readonly displayCrossHatchesSetting: boolean;
2485
+ readonly displayCrossHatchesSetting: any;
2450
2486
  readonly hasResolution: boolean;
2451
2487
  readonly hasGlobalStats: boolean;
2452
2488
  } & {
@@ -2679,6 +2715,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2679
2715
  }> | null;
2680
2716
  readonly adapterConfig: any;
2681
2717
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
2718
+ readonly isMinimized: boolean;
2682
2719
  readonly parentDisplay: any;
2683
2720
  readonly effectiveRpcDriverName: any;
2684
2721
  } & {
@@ -2735,6 +2772,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2735
2772
  }> | null;
2736
2773
  readonly adapterConfig: any;
2737
2774
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
2775
+ readonly isMinimized: boolean;
2738
2776
  readonly parentDisplay: any;
2739
2777
  readonly effectiveRpcDriverName: any;
2740
2778
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -2788,6 +2826,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
2788
2826
  }> | null;
2789
2827
  readonly adapterConfig: any;
2790
2828
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
2829
+ readonly isMinimized: boolean;
2791
2830
  readonly parentDisplay: any;
2792
2831
  readonly effectiveRpcDriverName: any;
2793
2832
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -3069,6 +3108,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3069
3108
  }> | null;
3070
3109
  readonly adapterConfig: any;
3071
3110
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
3111
+ readonly isMinimized: boolean;
3072
3112
  readonly parentDisplay: any;
3073
3113
  readonly effectiveRpcDriverName: any;
3074
3114
  } & {
@@ -3125,6 +3165,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3125
3165
  }> | null;
3126
3166
  readonly adapterConfig: any;
3127
3167
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
3168
+ readonly isMinimized: boolean;
3128
3169
  readonly parentDisplay: any;
3129
3170
  readonly effectiveRpcDriverName: any;
3130
3171
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -3178,6 +3219,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3178
3219
  }> | null;
3179
3220
  readonly adapterConfig: any;
3180
3221
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
3222
+ readonly isMinimized: boolean;
3181
3223
  readonly parentDisplay: any;
3182
3224
  readonly effectiveRpcDriverName: any;
3183
3225
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -3404,6 +3446,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3404
3446
  }> | null;
3405
3447
  readonly adapterConfig: any;
3406
3448
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
3449
+ readonly isMinimized: boolean;
3407
3450
  readonly parentDisplay: any;
3408
3451
  readonly effectiveRpcDriverName: any;
3409
3452
  } & {
@@ -3460,6 +3503,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3460
3503
  }> | null;
3461
3504
  readonly adapterConfig: any;
3462
3505
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
3506
+ readonly isMinimized: boolean;
3463
3507
  readonly parentDisplay: any;
3464
3508
  readonly effectiveRpcDriverName: any;
3465
3509
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -3513,6 +3557,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3513
3557
  }> | null;
3514
3558
  readonly adapterConfig: any;
3515
3559
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
3560
+ readonly isMinimized: boolean;
3516
3561
  readonly parentDisplay: any;
3517
3562
  readonly effectiveRpcDriverName: any;
3518
3563
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -3656,13 +3701,22 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3656
3701
  readonly minScore: number;
3657
3702
  } & {
3658
3703
  readonly adapterCapabilities: string[];
3659
- readonly rendererConfig: any;
3704
+ readonly rendererConfig: {
3705
+ scaleType: string;
3706
+ filled: any;
3707
+ displayCrossHatches: any;
3708
+ summaryScoreMode: any;
3709
+ color: any;
3710
+ negColor: any;
3711
+ posColor: any;
3712
+ minSize: any;
3713
+ };
3660
3714
  readonly autoscaleType: string;
3661
3715
  } & {
3662
3716
  readonly domain: number[] | undefined;
3663
3717
  } & {
3664
- readonly filled: boolean;
3665
- readonly summaryScoreModeSetting: string;
3718
+ readonly filled: any;
3719
+ readonly summaryScoreModeSetting: any;
3666
3720
  readonly scaleOpts: {
3667
3721
  domain: number[] | undefined;
3668
3722
  stats: {
@@ -3676,7 +3730,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3676
3730
  inverted: boolean;
3677
3731
  };
3678
3732
  readonly canHaveFill: boolean;
3679
- readonly displayCrossHatchesSetting: boolean;
3733
+ readonly displayCrossHatchesSetting: any;
3680
3734
  readonly hasResolution: boolean;
3681
3735
  readonly hasGlobalStats: boolean;
3682
3736
  } & {
@@ -3800,16 +3854,16 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3800
3854
  muiName: string;
3801
3855
  };
3802
3856
  subMenu: {
3803
- label: string;
3804
3857
  type: string;
3805
- checked: boolean;
3858
+ label: string;
3859
+ checked: any;
3806
3860
  onClick: () => void;
3807
3861
  }[];
3808
- type?: undefined;
3809
- checked?: undefined;
3810
- onClick?: undefined;
3811
3862
  } | {
3812
3863
  label: string;
3864
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
3865
+ muiName: string;
3866
+ };
3813
3867
  subMenu: ({
3814
3868
  label: string;
3815
3869
  subMenu: {
@@ -3831,10 +3885,6 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3831
3885
  onClick: () => void;
3832
3886
  subMenu?: undefined;
3833
3887
  })[];
3834
- icon?: undefined;
3835
- type?: undefined;
3836
- checked?: undefined;
3837
- onClick?: undefined;
3838
3888
  } | {
3839
3889
  label: string;
3840
3890
  subMenu: {
@@ -3844,16 +3894,6 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
3844
3894
  onClick: () => void;
3845
3895
  }[];
3846
3896
  icon?: undefined;
3847
- type?: undefined;
3848
- checked?: undefined;
3849
- onClick?: undefined;
3850
- } | {
3851
- type: string;
3852
- label: string;
3853
- checked: boolean;
3854
- onClick: () => void;
3855
- icon?: undefined;
3856
- subMenu?: undefined;
3857
3897
  })[];
3858
3898
  } & {
3859
3899
  afterAttach(): void;
package/esm/MultiLinearWiggleDisplay/model.js CHANGED
@@ -4,6 +4,7 @@ import { set1 as colors } from '@jbrowse/core/ui/colors';
4
4
  import { getContainingView, getSession, max, measureText, } from '@jbrowse/core/util';
5
5
  import { stopStopToken } from '@jbrowse/core/util/stopToken';
6
6
  import { isAlive, types } from '@jbrowse/mobx-state-tree';
7
+ import EqualizerIcon from '@mui/icons-material/Equalizer';
7
8
  import VisibilityIcon from '@mui/icons-material/Visibility';
8
9
  import deepEqual from 'fast-deep-equal';
9
10
  import SharedWiggleMixin from "../shared/SharedWiggleMixin.js";
@@ -267,10 +268,31 @@ export function stateModelFactory(_pluginManager, configSchema) {
267
268
  self.setShowTooltips(!self.showTooltipsEnabled);
268
269
  },
269
270
  },
271
+ {
272
+ label: 'Show sidebar',
273
+ type: 'checkbox',
274
+ checked: self.showSidebar,
275
+ onClick: () => {
276
+ self.setShowSidebar(!self.showSidebar);
277
+ },
278
+ },
279
+ ...(self.graphType
280
+ ? [
281
+ {
282
+ type: 'checkbox',
283
+ label: 'Show cross hatches',
284
+ checked: self.displayCrossHatchesSetting,
285
+ onClick: () => {
286
+ self.toggleCrossHatches();
287
+ },
288
+ },
289
+ ]
290
+ : []),
270
291
  ],
271
292
  },
272
293
  {
273
294
  label: 'Score',
295
+ icon: EqualizerIcon,
274
296
  subMenu: self.scoreTrackMenuItems(),
275
297
  },
276
298
  ...(self.canHaveFill
@@ -309,18 +331,6 @@ export function stateModelFactory(_pluginManager, configSchema) {
309
331
  },
310
332
  ]
311
333
  : []),
312
- ...(self.graphType
313
- ? [
314
- {
315
- type: 'checkbox',
316
- label: 'Draw cross hatches',
317
- checked: self.displayCrossHatchesSetting,
318
- onClick: () => {
319
- self.toggleCrossHatches();
320
- },
321
- },
322
- ]
323
- : []),
324
334
  ...(self.isMultiRow
325
335
  ? [
326
336
  {
@@ -337,14 +347,6 @@ export function stateModelFactory(_pluginManager, configSchema) {
337
347
  },
338
348
  ]
339
349
  : []),
340
- {
341
- label: 'Show sidebar',
342
- type: 'checkbox',
343
- checked: self.showSidebar,
344
- onClick: () => {
345
- self.setShowSidebar(!self.showSidebar);
346
- },
347
- },
348
350
  {
349
351
  label: 'Edit colors/arrangement...',
350
352
  onClick: () => {
package/esm/getMultiWiggleSourcesAutorun.d.ts CHANGED
@@ -11,6 +11,7 @@ export declare function getMultiWiggleSourcesAutorun(self: {
11
11
  configuration: AnyConfigurationModel;
12
12
  adapterConfig: AnyConfigurationModel;
13
13
  autoscaleType: string;
14
+ isMinimized: boolean;
14
15
  adapterProps: () => Record<string, unknown>;
15
16
  setSourcesLoading: (aborter: StopToken) => void;
16
17
  setError: (error: unknown) => void;
package/esm/getMultiWiggleSourcesAutorun.js CHANGED
@@ -7,6 +7,9 @@ import { autorun } from 'mobx';
7
7
  export function getMultiWiggleSourcesAutorun(self) {
8
8
  addDisposer(self, autorun(async () => {
9
9
  try {
10
+ if (self.isMinimized) {
11
+ return;
12
+ }
10
13
  const view = getContainingView(self);
11
14
  if (!view.initialized) {
12
15
  return;
package/esm/getQuantitativeStatsAutorun.d.ts CHANGED
@@ -6,6 +6,7 @@ export declare function getQuantitativeStatsAutorun(self: {
6
6
  configuration: AnyConfigurationModel;
7
7
  adapterConfig: AnyConfigurationModel;
8
8
  autoscaleType: string;
9
+ isMinimized: boolean;
9
10
  adapterProps: () => Record<string, unknown>;
10
11
  setStatsLoading: (token: StopToken) => void;
11
12
  setError: (error: unknown) => void;
package/esm/getQuantitativeStatsAutorun.js CHANGED
@@ -6,6 +6,9 @@ import { getQuantitativeStats } from "./getQuantitativeStats.js";
6
6
  export function getQuantitativeStatsAutorun(self) {
7
7
  addDisposer(self, autorun(async () => {
8
8
  try {
9
+ if (self.isMinimized) {
10
+ return;
11
+ }
9
12
  if (self.quantitativeStatsReady) {
10
13
  const view = getContainingView(self);
11
14
  const stopToken = createStopToken();
package/esm/shared/SharedWiggleMixin.d.ts CHANGED
@@ -151,6 +151,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
151
151
  }> | null;
152
152
  readonly adapterConfig: any;
153
153
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
154
+ readonly isMinimized: boolean;
154
155
  readonly parentDisplay: any;
155
156
  readonly effectiveRpcDriverName: any;
156
157
  } & {
@@ -207,6 +208,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
207
208
  }> | null;
208
209
  readonly adapterConfig: any;
209
210
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
211
+ readonly isMinimized: boolean;
210
212
  readonly parentDisplay: any;
211
213
  readonly effectiveRpcDriverName: any;
212
214
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -260,6 +262,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
260
262
  }> | null;
261
263
  readonly adapterConfig: any;
262
264
  readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
265
+ readonly isMinimized: boolean;
263
266
  readonly parentDisplay: any;
264
267
  readonly effectiveRpcDriverName: any;
265
268
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -541,6 +544,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
541
544
  }> | null;
542
545
  readonly adapterConfig: any;
543
546
  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 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
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 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
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 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
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 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
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 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
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>>;
@@ -1128,13 +1137,22 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
1128
1137
  readonly minScore: number;
1129
1138
  } & {
1130
1139
  readonly adapterCapabilities: string[];
1131
- readonly rendererConfig: any;
1140
+ readonly rendererConfig: {
1141
+ scaleType: string;
1142
+ filled: any;
1143
+ displayCrossHatches: any;
1144
+ summaryScoreMode: any;
1145
+ color: any;
1146
+ negColor: any;
1147
+ posColor: any;
1148
+ minSize: any;
1149
+ };
1132
1150
  readonly autoscaleType: string;
1133
1151
  } & {
1134
1152
  readonly domain: number[] | undefined;
1135
1153
  } & {
1136
- readonly filled: boolean;
1137
- readonly summaryScoreModeSetting: string;
1154
+ readonly filled: any;
1155
+ readonly summaryScoreModeSetting: any;
1138
1156
  readonly scaleOpts: {
1139
1157
  domain: number[] | undefined;
1140
1158
  stats: {
@@ -1148,7 +1166,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
1148
1166
  inverted: boolean;
1149
1167
  };
1150
1168
  readonly canHaveFill: boolean;
1151
- readonly displayCrossHatchesSetting: boolean;
1169
+ readonly displayCrossHatchesSetting: any;
1152
1170
  readonly hasResolution: boolean;
1153
1171
  readonly hasGlobalStats: boolean;
1154
1172
  } & {
package/esm/shared/SharedWiggleMixin.js CHANGED
@@ -143,17 +143,16 @@ export default function SharedWiggleMixin(configSchema) {
143
143
  },
144
144
  get rendererConfig() {
145
145
  const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
146
- const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
146
+ const conf = self.configuration.renderers?.[rendererTypeName];
147
147
  return {
148
- ...configBlob,
149
- ...(scaleType ? { scaleType } : {}),
150
- ...(fill !== undefined ? { filled: fill } : {}),
151
- ...(displayCrossHatches !== undefined ? { displayCrossHatches } : {}),
152
- ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
153
- ...(color !== undefined ? { color } : {}),
154
- ...(negColor !== undefined ? { negColor } : {}),
155
- ...(posColor !== undefined ? { posColor } : {}),
156
- ...(minSize !== undefined ? { minSize } : {}),
148
+ scaleType: scaleType ?? readConfObject(conf, 'scaleType'),
149
+ filled: fill ?? readConfObject(conf, 'filled'),
150
+ displayCrossHatches: displayCrossHatches ?? readConfObject(conf, 'displayCrossHatches'),
151
+ summaryScoreMode: summaryScoreMode ?? readConfObject(conf, 'summaryScoreMode'),
152
+ color: color ?? readConfObject(conf, 'color'),
153
+ negColor: negColor ?? readConfObject(conf, 'negColor'),
154
+ posColor: posColor ?? readConfObject(conf, 'posColor'),
155
+ minSize: minSize ?? readConfObject(conf, 'minSize'),
157
156
  };
158
157
  },
159
158
  get autoscaleType() {
@@ -185,12 +184,10 @@ export default function SharedWiggleMixin(configSchema) {
185
184
  })
186
185
  .views(self => ({
187
186
  get filled() {
188
- return (self.fill ??
189
- readConfObject(self.rendererConfig, 'filled'));
187
+ return self.rendererConfig.filled;
190
188
  },
191
189
  get summaryScoreModeSetting() {
192
- return (self.summaryScoreMode ??
193
- readConfObject(self.rendererConfig, 'summaryScoreMode'));
190
+ return self.rendererConfig.summaryScoreMode;
194
191
  },
195
192
  get scaleOpts() {
196
193
  return {
@@ -205,8 +202,7 @@ export default function SharedWiggleMixin(configSchema) {
205
202
  return self.rendererTypeName === 'XYPlotRenderer';
206
203
  },
207
204
  get displayCrossHatchesSetting() {
208
- return (self.displayCrossHatches ??
209
- readConfObject(self.rendererConfig, 'displayCrossHatches'));
205
+ return self.rendererConfig.displayCrossHatches;
210
206
  },
211
207
  get hasResolution() {
212
208
  return self.adapterCapabilities.includes('hasResolution');
@@ -251,10 +247,25 @@ export default function SharedWiggleMixin(configSchema) {
251
247
  ]
252
248
  : []),
253
249
  {
254
- label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
255
- onClick: () => {
256
- self.toggleLogScale();
257
- },
250
+ label: 'Scale type',
251
+ subMenu: [
252
+ {
253
+ label: 'Linear scale',
254
+ type: 'radio',
255
+ checked: self.scaleType === 'linear',
256
+ onClick: () => {
257
+ self.setScaleType('linear');
258
+ },
259
+ },
260
+ {
261
+ label: 'Log scale',
262
+ type: 'radio',
263
+ checked: self.scaleType === 'log',
264
+ onClick: () => {
265
+ self.setScaleType('log');
266
+ },
267
+ },
268
+ ],
258
269
  },
259
270
  {
260
271
  label: 'Autoscale type',
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-wiggle",
3
- "version": "4.0.2",
3
+ "version": "4.0.4",
4
4
  "description": "JBrowse 2 wiggle adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -25,19 +25,19 @@
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",
29
- "@mui/x-data-grid": "^8.23.0",
28
+ "@mui/x-charts-vendor": "^8.25.0",
29
+ "@mui/x-data-grid": "^8.25.0",
30
+ "@types/file-saver-es": "^2.0.3",
30
31
  "colord": "^2.9.3",
31
32
  "copy-to-clipboard": "^3.3.3",
32
33
  "fast-deep-equal": "^3.1.3",
33
- "@types/file-saver-es": "^2.0.3",
34
34
  "file-saver-es": "^2.0.5",
35
35
  "mobx": "^6.15.0",
36
36
  "mobx-react": "^9.2.1",
37
37
  "rxjs": "^7.8.2",
38
- "@jbrowse/plugin-linear-genome-view": "^4.0.2",
39
- "@jbrowse/plugin-data-management": "^4.0.2",
40
- "@jbrowse/core": "^4.0.2"
38
+ "@jbrowse/core": "^4.0.4",
39
+ "@jbrowse/plugin-data-management": "^4.0.4",
40
+ "@jbrowse/plugin-linear-genome-view": "^4.0.4"
41
41
  },
42
42
  "peerDependencies": {
43
43
  "react": ">=18.0.0"