@jbrowse/plugin-sequence 2.4.1 → 2.4.2

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Files changed (8) hide show
  1. package/dist/LinearReferenceSequenceDisplay/model.d.ts +25 -30
  2. package/dist/LinearReferenceSequenceDisplay/model.js +2 -2
  3. package/dist/LinearReferenceSequenceDisplay/model.js.map +1 -1
  4. package/esm/LinearReferenceSequenceDisplay/model.d.ts +25 -30
  5. package/esm/LinearReferenceSequenceDisplay/model.js +2 -2
  6. package/esm/LinearReferenceSequenceDisplay/model.js.map +1 -1
  7. package/package.json +2 -2
  8. package/src/LinearReferenceSequenceDisplay/model.ts +7 -4
package/dist/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -27,6 +27,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  }, {
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  renderInProgress: AbortController | undefined;
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+ /**
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+ * #method
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+ */
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  filled: boolean;
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -41,7 +44,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  renderProps: any;
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  } & {
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  doReload(): void;
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- afterAttach(): void;
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+ afterAttach(): void; /**
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+ * #action
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+ */
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  setStatus(message: string): void;
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  setLoading(abortController: AbortController): void;
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  setMessage(messageText: string): void;
@@ -71,15 +76,10 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly RenderingComponent: import("react").FC<{
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  model: {
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  id: string;
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- /**
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- * #property
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- */
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  type: string;
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  rpcDriverName: string | undefined;
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- rendererTypeName: string; /**
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- * #property
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- */
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+ rendererTypeName: string;
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  error: unknown;
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  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -99,9 +99,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  rpcDriverName: string | undefined;
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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  rendererTypeName: string;
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- error: unknown; /**
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- * #action
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- */
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+ error: unknown;
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  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
@@ -129,8 +127,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  message: string;
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  featureIdUnderMouse: string | undefined;
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  contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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  } & {
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  readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -143,7 +141,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  } & {
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
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- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
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+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
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  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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  searchFeatureByID(id: string): [number, number, number, number] | undefined;
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  readonly currentBytesRequested: number;
@@ -153,19 +151,16 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly maxAllowableBytes: number;
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  } & {
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  setMessage(message: string): void;
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+ } & {
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  afterAttach(): void;
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- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
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- headers?: Record<string, string> | undefined;
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- signal?: AbortSignal | undefined;
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- filters?: string[] | undefined;
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- }): Promise<{}>;
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- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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- clearRegionStats(): void;
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+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
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+ setRegionsStatsP(arg: any): void;
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+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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+ clearRegionsStats(): void;
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  setHeight(displayHeight: number): number;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
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+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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  setCurrBpPerPx(n: number): void;
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  deleteBlock(key: string): void;
@@ -179,18 +174,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly regionTooLargeReason: string;
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  } & {
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  reload(): Promise<void>;
177
+ } & {
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  afterAttach(): void;
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  } & {
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  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
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  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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- contextMenuItems(): {
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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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- }[];
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+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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  renderProps(): any;
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  } & {
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  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -260,6 +250,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
261
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  }, {
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  renderInProgress: AbortController | undefined;
253
+ /**
254
+ * #method
255
+ */
263
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  filled: boolean;
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
265
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -274,7 +267,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  renderProps: any;
275
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  } & {
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  doReload(): void;
277
- afterAttach(): void;
270
+ afterAttach(): void; /**
271
+ * #action
272
+ */
278
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  setStatus(message: string): void;
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  setLoading(abortController: AbortController): void;
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  setMessage(messageText: string): void;
package/dist/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -41,11 +41,11 @@ function modelFactory(configSchema) {
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  * #method
42
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  */
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  renderProps() {
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- const { showForward, showReverse, showTranslation } = self;
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+ const { showForward, rpcDriverName, showReverse, showTranslation } = self;
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  return {
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  ...superRenderProps(),
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- rpcDriverName: self.rpcDriverName,
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  config: self.configuration.renderer,
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+ rpcDriverName,
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  showForward,
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  showReverse,
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  showTranslation,
package/dist/LinearReferenceSequenceDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -27,6 +27,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
27
27
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
28
28
  }, {
29
29
  renderInProgress: AbortController | undefined;
30
+ /**
31
+ * #method
32
+ */
30
33
  filled: boolean;
31
34
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
32
35
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -41,7 +44,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
41
44
  renderProps: any;
42
45
  } & {
43
46
  doReload(): void;
44
- afterAttach(): void;
47
+ afterAttach(): void; /**
48
+ * #action
49
+ */
45
50
  setStatus(message: string): void;
46
51
  setLoading(abortController: AbortController): void;
47
52
  setMessage(messageText: string): void;
@@ -71,15 +76,10 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
71
76
  readonly RenderingComponent: import("react").FC<{
72
77
  model: {
73
78
  id: string;
74
- /**
75
- * #property
76
- */
77
79
  type: string;
78
80
  rpcDriverName: string | undefined;
79
81
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
80
- rendererTypeName: string; /**
81
- * #property
82
- */
82
+ rendererTypeName: string;
83
83
  error: unknown;
84
84
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
85
85
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -99,9 +99,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
99
99
  rpcDriverName: string | undefined;
100
100
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
101
101
  rendererTypeName: string;
102
- error: unknown; /**
103
- * #action
104
- */
102
+ error: unknown;
105
103
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
106
104
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
107
105
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -129,8 +127,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
129
127
  message: string;
130
128
  featureIdUnderMouse: string | undefined;
131
129
  contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
132
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
133
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
130
+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
131
+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
134
132
  } & {
135
133
  readonly height: number;
136
134
  readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -143,7 +141,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
143
141
  } & {
144
142
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
145
143
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
146
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
144
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
147
145
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
148
146
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
149
147
  readonly currentBytesRequested: number;
@@ -153,19 +151,16 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
153
151
  readonly maxAllowableBytes: number;
154
152
  } & {
155
153
  setMessage(message: string): void;
154
+ } & {
156
155
  afterAttach(): void;
157
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
158
- headers?: Record<string, string> | undefined;
159
- signal?: AbortSignal | undefined;
160
- filters?: string[] | undefined;
161
- }): Promise<{}>;
162
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
163
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
164
- clearRegionStats(): void;
156
+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
157
+ setRegionsStatsP(arg: any): void;
158
+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
159
+ clearRegionsStats(): void;
165
160
  setHeight(displayHeight: number): number;
166
161
  resizeHeight(distance: number): number;
167
162
  setScrollTop(scrollTop: number): void;
168
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
163
+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
164
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
170
165
  setCurrBpPerPx(n: number): void;
171
166
  deleteBlock(key: string): void;
@@ -179,18 +174,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
179
174
  readonly regionTooLargeReason: string;
180
175
  } & {
181
176
  reload(): Promise<void>;
177
+ } & {
182
178
  afterAttach(): void;
183
179
  } & {
184
180
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
185
181
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
186
182
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
187
- contextMenuItems(): {
188
- label: string;
189
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
190
- muiName: string;
191
- };
192
- onClick: () => void;
193
- }[];
183
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
194
184
  renderProps(): any;
195
185
  } & {
196
186
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -260,6 +250,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
260
250
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
261
251
  }, {
262
252
  renderInProgress: AbortController | undefined;
253
+ /**
254
+ * #method
255
+ */
263
256
  filled: boolean;
264
257
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
265
258
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -274,7 +267,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
274
267
  renderProps: any;
275
268
  } & {
276
269
  doReload(): void;
277
- afterAttach(): void;
270
+ afterAttach(): void; /**
271
+ * #action
272
+ */
278
273
  setStatus(message: string): void;
279
274
  setLoading(abortController: AbortController): void;
280
275
  setMessage(messageText: string): void;
package/esm/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -38,11 +38,11 @@ export function modelFactory(configSchema) {
38
38
  * #method
39
39
  */
40
40
  renderProps() {
41
- const { showForward, showReverse, showTranslation } = self;
41
+ const { showForward, rpcDriverName, showReverse, showTranslation } = self;
42
42
  return {
43
43
  ...superRenderProps(),
44
- rpcDriverName: self.rpcDriverName,
45
44
  config: self.configuration.renderer,
45
+ rpcDriverName,
46
46
  showForward,
47
47
  showReverse,
48
48
  showTranslation,
package/esm/LinearReferenceSequenceDisplay/model.js.map CHANGED
@@ -1 +1 @@
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1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.4.1",
3
+ "version": "2.4.2",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
58
  "distModule": "esm/index.js",
59
59
  "srcModule": "src/index.ts",
60
60
  "module": "esm/index.js",
61
- "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
61
+ "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
62
62
  }
package/src/LinearReferenceSequenceDisplay/model.ts CHANGED
@@ -10,6 +10,8 @@ import {
10
10
  import { getContainingView } from '@jbrowse/core/util'
11
11
  import { autorun } from 'mobx'
12
12
 
13
+ type LGV = LinearGenomeViewModel
14
+
13
15
  /**
14
16
  * #stateModel LinearReferenceSequenceDisplay
15
17
  * base model `BaseLinearDisplay`
@@ -49,11 +51,12 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
49
51
  * #method
50
52
  */
51
53
  renderProps() {
52
- const { showForward, showReverse, showTranslation } = self
54
+ const { showForward, rpcDriverName, showReverse, showTranslation } =
55
+ self
53
56
  return {
54
57
  ...superRenderProps(),
55
- rpcDriverName: self.rpcDriverName,
56
58
  config: self.configuration.renderer,
59
+ rpcDriverName,
57
60
  showForward,
58
61
  showReverse,
59
62
  showTranslation,
@@ -66,7 +69,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
66
69
  * #method
67
70
  */
68
71
  regionCannotBeRendered(/* region */) {
69
- const view = getContainingView(self) as LinearGenomeViewModel
72
+ const view = getContainingView(self) as LGV
70
73
  return view?.bpPerPx >= 1 ? 'Zoom in to see sequence' : undefined
71
74
  },
72
75
  /**
@@ -99,7 +102,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
99
102
  addDisposer(
100
103
  self,
101
104
  autorun(() => {
102
- const view = getContainingView(self) as LinearGenomeViewModel
105
+ const view = getContainingView(self) as LGV
103
106
  if (view?.bpPerPx >= 1) {
104
107
  self.setHeight(50)
105
108
  } else {