@jbrowse/plugin-variants 1.6.8 → 1.7.1

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 (52) hide show
  1. package/dist/ChordVariantDisplay/index.d.ts +3 -3
  2. package/dist/ChordVariantDisplay/index.js +33 -0
  3. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.d.ts +5 -5
  4. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js +76 -0
  5. package/dist/LinearVariantDisplay/configSchema.d.ts +5 -5
  6. package/dist/LinearVariantDisplay/configSchema.js +18 -0
  7. package/dist/LinearVariantDisplay/configSchema.test.js +92 -0
  8. package/dist/LinearVariantDisplay/index.d.ts +2 -2
  9. package/dist/LinearVariantDisplay/index.js +23 -0
  10. package/dist/LinearVariantDisplay/model.d.ts +207 -207
  11. package/dist/LinearVariantDisplay/model.js +75 -0
  12. package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +24 -24
  13. package/dist/StructuralVariantChordRenderer/ReactComponent.js +228 -0
  14. package/dist/StructuralVariantChordRenderer/index.d.ts +3 -3
  15. package/dist/StructuralVariantChordRenderer/index.js +48 -0
  16. package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts +10 -10
  17. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +127 -0
  18. package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts +4 -4
  19. package/dist/VariantFeatureWidget/VariantFeatureWidget.js +251 -0
  20. package/dist/VariantFeatureWidget/VariantFeatureWidget.test.js +56 -0
  21. package/dist/VariantFeatureWidget/index.d.ts +11 -11
  22. package/dist/VariantFeatureWidget/index.js +35 -0
  23. package/dist/VcfAdapter/VcfAdapter.d.ts +24 -24
  24. package/dist/VcfAdapter/VcfAdapter.js +383 -0
  25. package/dist/VcfAdapter/VcfAdapter.test.js +55 -0
  26. package/dist/VcfAdapter/configSchema.d.ts +2 -2
  27. package/dist/VcfAdapter/configSchema.js +22 -0
  28. package/dist/VcfAdapter/index.d.ts +1 -1
  29. package/dist/VcfAdapter/index.js +15 -0
  30. package/dist/VcfTabixAdapter/VcfFeature.d.ts +59 -59
  31. package/dist/VcfTabixAdapter/VcfFeature.js +261 -0
  32. package/dist/VcfTabixAdapter/VcfFeature.test.js +106 -0
  33. package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts +35 -35
  34. package/dist/VcfTabixAdapter/VcfTabixAdapter.js +392 -0
  35. package/dist/VcfTabixAdapter/VcfTabixAdapter.test.js +99 -0
  36. package/dist/VcfTabixAdapter/configSchema.d.ts +2 -2
  37. package/dist/VcfTabixAdapter/configSchema.js +38 -0
  38. package/dist/VcfTabixAdapter/index.d.ts +1 -1
  39. package/dist/VcfTabixAdapter/index.js +15 -0
  40. package/dist/index.d.ts +7 -7
  41. package/dist/index.js +214 -6
  42. package/dist/index.test.js +37 -0
  43. package/package.json +5 -7
  44. package/dist/LinearVariantDisplay/configSchema.test.d.ts +0 -1
  45. package/dist/VariantFeatureWidget/VariantFeatureWidget.test.d.ts +0 -1
  46. package/dist/index.test.d.ts +0 -1
  47. package/dist/plugin-variants.cjs.development.js +0 -2897
  48. package/dist/plugin-variants.cjs.development.js.map +0 -1
  49. package/dist/plugin-variants.cjs.production.min.js +0 -2
  50. package/dist/plugin-variants.cjs.production.min.js.map +0 -1
  51. package/dist/plugin-variants.esm.js +0 -2889
  52. package/dist/plugin-variants.esm.js.map +0 -1
@@ -1,207 +1,207 @@
1
- /// <reference types="react" />
2
- import { Feature } from '@jbrowse/core/util/simpleFeature';
3
- import { LinearVariantDisplayConfigModel } from './configSchema';
4
- export default function (configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
5
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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- type: import("mobx-state-tree").ISimpleType<string>;
7
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
8
- } & {
9
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
10
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
11
- key: import("mobx-state-tree").ISimpleType<string>;
12
- region: import("mobx-state-tree").IModelType<{
13
- refName: import("mobx-state-tree").ISimpleType<string>;
14
- start: import("mobx-state-tree").ISimpleType<number>;
15
- end: import("mobx-state-tree").ISimpleType<number>;
16
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
17
- } & {
18
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
19
- }, {
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- setRefName(newRefName: string): void;
21
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
22
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
23
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
24
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
25
- }, {
26
- renderInProgress: AbortController | undefined;
27
- filled: boolean;
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- reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
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- features: Map<string, Feature> | undefined;
30
- layout: any;
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- status: string;
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- error: unknown;
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- message: string | undefined;
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- maxHeightReached: boolean;
35
- ReactComponent: ({ model, }: {
36
- model: any;
37
- }) => any;
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- renderProps: any;
39
- } & {
40
- doReload(): void;
41
- afterAttach(): void;
42
- setStatus(message: string): void;
43
- setLoading(abortController: AbortController): void;
44
- setMessage(messageText: string): void;
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- setRendered(props: {
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- reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)>;
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- features: Map<string, Feature>;
48
- layout: any;
49
- maxHeightReached: boolean;
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- renderProps: any;
51
- } | undefined): void;
52
- setError(error: unknown): void;
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- reload(): void;
54
- beforeDestroy(): void;
55
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
56
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
57
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
58
- } & {
59
- type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
60
- trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
61
- trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
62
- trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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- trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
65
- } & {
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- type: import("mobx-state-tree").ISimpleType<"LinearVariantDisplay">;
67
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
68
- }, {
69
- rendererTypeName: string;
70
- error: unknown;
71
- } & {
72
- readonly RenderingComponent: import("react").FC<{
73
- model: import("mobx-state-tree").ModelInstanceTypeProps<{
74
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
75
- type: import("mobx-state-tree").ISimpleType<string>;
76
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
77
- }> & {
78
- rendererTypeName: string;
79
- error: unknown;
80
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
81
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
82
- type: import("mobx-state-tree").ISimpleType<string>;
83
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
84
- }, {
85
- rendererTypeName: string;
86
- error: unknown;
87
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
88
- onHorizontalScroll?: Function | undefined;
89
- blockState?: Record<string, any> | undefined;
90
- }>;
91
- readonly DisplayBlurb: import("react").FC<{
92
- model: import("mobx-state-tree").ModelInstanceTypeProps<{
93
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
94
- type: import("mobx-state-tree").ISimpleType<string>;
95
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
96
- }> & {
97
- rendererTypeName: string;
98
- error: unknown;
99
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
100
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
101
- type: import("mobx-state-tree").ISimpleType<string>;
102
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
103
- }, {
104
- rendererTypeName: string;
105
- error: unknown;
106
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
107
- }> | null;
108
- readonly adapterConfig: any;
109
- readonly parentTrack: any;
110
- renderProps(): any;
111
- readonly rendererType: any;
112
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
113
- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
114
- readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
115
- regionCannotBeRendered(): undefined;
116
- } & {
117
- setError(error?: unknown): void;
118
- setRpcDriverName(rpcDriverName: string): void;
119
- reload(): void;
120
- } & {
121
- currBpPerPx: number;
122
- message: string;
123
- featureIdUnderMouse: string | undefined;
124
- contextMenuFeature: Feature | undefined;
125
- scrollTop: number;
126
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
127
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
128
- } & {
129
- readonly blockType: "staticBlocks" | "dynamicBlocks";
130
- readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
131
- } & {
132
- readonly renderDelay: number;
133
- readonly TooltipComponent: import("react").FC<any>;
134
- readonly selectedFeatureId: string | undefined;
135
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
136
- } & {
137
- readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
138
- readonly featureUnderMouse: Feature | undefined;
139
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
140
- getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
141
- searchFeatureByID(id: string): [number, number, number, number] | undefined;
142
- readonly currentBytesRequested: number;
143
- readonly currentFeatureScreenDensity: number;
144
- readonly maxFeatureScreenDensity: any;
145
- readonly estimatedStatsReady: boolean;
146
- readonly maxAllowableBytes: number;
147
- } & {
148
- setMessage(message: string): void;
149
- afterAttach(): void;
150
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
151
- headers?: Record<string, string> | undefined;
152
- signal?: AbortSignal | undefined;
153
- filters?: string[] | undefined;
154
- }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
155
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
156
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
157
- clearRegionStats(): void;
158
- setHeight(displayHeight: number): number;
159
- resizeHeight(distance: number): number;
160
- setScrollTop(scrollTop: number): void;
161
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
162
- addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
163
- setCurrBpPerPx(n: number): void;
164
- deleteBlock(key: string): void;
165
- selectFeature(feature: Feature): void;
166
- clearFeatureSelection(): void;
167
- setFeatureIdUnderMouse(feature: string | undefined): void;
168
- reload(): void;
169
- setContextMenuFeature(feature?: Feature | undefined): void;
170
- } & {
171
- readonly regionTooLarge: boolean;
172
- readonly regionTooLargeReason: string;
173
- } & {
174
- reload(): Promise<void>;
175
- afterAttach(): void;
176
- } & {
177
- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
178
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
179
- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
180
- contextMenuItems(): {
181
- label: string;
182
- icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
183
- onClick: () => void;
184
- }[];
185
- renderProps(): any;
186
- } & {
187
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
188
- overrideHeight: number;
189
- }): Promise<JSX.Element>;
190
- } & {
191
- readonly rendererTypeName: any;
192
- readonly showLabels: any;
193
- readonly showDescriptions: any;
194
- readonly maxHeight: any;
195
- readonly displayMode: any;
196
- readonly rendererConfig: any;
197
- } & {
198
- toggleShowLabels(): void;
199
- toggleShowDescriptions(): void;
200
- setDisplayMode(val: string): void;
201
- setMaxHeight(val: number): void;
202
- } & {
203
- renderProps(): any;
204
- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
205
- } & {
206
- selectFeature(feature: Feature): Promise<void>;
207
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1
+ /// <reference types="react" />
2
+ import { Feature } from '@jbrowse/core/util/simpleFeature';
3
+ import { LinearVariantDisplayConfigModel } from './configSchema';
4
+ export default function (configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
5
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
6
+ type: import("mobx-state-tree").ISimpleType<string>;
7
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
8
+ } & {
9
+ height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
10
+ blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
11
+ key: import("mobx-state-tree").ISimpleType<string>;
12
+ region: import("mobx-state-tree").IModelType<{
13
+ refName: import("mobx-state-tree").ISimpleType<string>;
14
+ start: import("mobx-state-tree").ISimpleType<number>;
15
+ end: import("mobx-state-tree").ISimpleType<number>;
16
+ reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
17
+ } & {
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+ assemblyName: import("mobx-state-tree").ISimpleType<string>;
19
+ }, {
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+ setRefName(newRefName: string): void;
21
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
22
+ reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
23
+ isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
24
+ isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
25
+ }, {
26
+ renderInProgress: AbortController | undefined;
27
+ filled: boolean;
28
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
29
+ features: Map<string, Feature> | undefined;
30
+ layout: any;
31
+ status: string;
32
+ error: unknown;
33
+ message: string | undefined;
34
+ maxHeightReached: boolean;
35
+ ReactComponent: ({ model, }: {
36
+ model: any;
37
+ }) => any;
38
+ renderProps: any;
39
+ } & {
40
+ doReload(): void;
41
+ afterAttach(): void;
42
+ setStatus(message: string): void;
43
+ setLoading(abortController: AbortController): void;
44
+ setMessage(messageText: string): void;
45
+ setRendered(props: {
46
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
47
+ features: Map<string, Feature>;
48
+ layout: any;
49
+ maxHeightReached: boolean;
50
+ renderProps: any;
51
+ } | undefined): void;
52
+ setError(error: unknown): void;
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+ reload(): void;
54
+ beforeDestroy(): void;
55
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
56
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
57
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
58
+ } & {
59
+ type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
60
+ trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
61
+ trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
62
+ trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
63
+ trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
64
+ configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
65
+ } & {
66
+ type: import("mobx-state-tree").ISimpleType<"LinearVariantDisplay">;
67
+ configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
68
+ }, {
69
+ rendererTypeName: string;
70
+ error: unknown;
71
+ } & {
72
+ readonly RenderingComponent: import("react").FC<{
73
+ model: import("mobx-state-tree").ModelInstanceTypeProps<{
74
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
75
+ type: import("mobx-state-tree").ISimpleType<string>;
76
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
77
+ }> & {
78
+ rendererTypeName: string;
79
+ error: unknown;
80
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
81
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
82
+ type: import("mobx-state-tree").ISimpleType<string>;
83
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
84
+ }, {
85
+ rendererTypeName: string;
86
+ error: unknown;
87
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
88
+ onHorizontalScroll?: Function | undefined;
89
+ blockState?: Record<string, any> | undefined;
90
+ }>;
91
+ readonly DisplayBlurb: import("react").FC<{
92
+ model: import("mobx-state-tree").ModelInstanceTypeProps<{
93
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
94
+ type: import("mobx-state-tree").ISimpleType<string>;
95
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
96
+ }> & {
97
+ rendererTypeName: string;
98
+ error: unknown;
99
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
100
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
101
+ type: import("mobx-state-tree").ISimpleType<string>;
102
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
103
+ }, {
104
+ rendererTypeName: string;
105
+ error: unknown;
106
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
107
+ }> | null;
108
+ readonly adapterConfig: any;
109
+ readonly parentTrack: any;
110
+ renderProps(): any;
111
+ readonly rendererType: any;
112
+ readonly DisplayMessageComponent: import("react").FC<any> | undefined;
113
+ trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
114
+ readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
115
+ regionCannotBeRendered(): undefined;
116
+ } & {
117
+ setError(error?: unknown): void;
118
+ setRpcDriverName(rpcDriverName: string): void;
119
+ reload(): void;
120
+ } & {
121
+ currBpPerPx: number;
122
+ message: string;
123
+ featureIdUnderMouse: string | undefined;
124
+ contextMenuFeature: Feature | undefined;
125
+ scrollTop: number;
126
+ estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
127
+ estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
128
+ } & {
129
+ readonly blockType: "staticBlocks" | "dynamicBlocks";
130
+ readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
131
+ } & {
132
+ readonly renderDelay: number;
133
+ readonly TooltipComponent: import("react").FC<any>;
134
+ readonly selectedFeatureId: string | undefined;
135
+ readonly DisplayMessageComponent: import("react").FC<any> | undefined;
136
+ } & {
137
+ readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
138
+ readonly featureUnderMouse: Feature | undefined;
139
+ getFeatureOverlapping(blockKey: string, x: number, y: number): any;
140
+ getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
141
+ searchFeatureByID(id: string): [number, number, number, number] | undefined;
142
+ readonly currentBytesRequested: number;
143
+ readonly currentFeatureScreenDensity: number;
144
+ readonly maxFeatureScreenDensity: any;
145
+ readonly estimatedStatsReady: boolean;
146
+ readonly maxAllowableBytes: number;
147
+ } & {
148
+ setMessage(message: string): void;
149
+ afterAttach(): void;
150
+ estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
151
+ headers?: Record<string, string> | undefined;
152
+ signal?: AbortSignal | undefined;
153
+ filters?: string[] | undefined;
154
+ }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
155
+ setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
156
+ setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
157
+ clearRegionStats(): void;
158
+ setHeight(displayHeight: number): number;
159
+ resizeHeight(distance: number): number;
160
+ setScrollTop(scrollTop: number): void;
161
+ updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
162
+ addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
163
+ setCurrBpPerPx(n: number): void;
164
+ deleteBlock(key: string): void;
165
+ selectFeature(feature: Feature): void;
166
+ clearFeatureSelection(): void;
167
+ setFeatureIdUnderMouse(feature: string | undefined): void;
168
+ reload(): void;
169
+ setContextMenuFeature(feature?: Feature | undefined): void;
170
+ } & {
171
+ readonly regionTooLarge: boolean;
172
+ readonly regionTooLargeReason: string;
173
+ } & {
174
+ reload(): Promise<void>;
175
+ afterAttach(): void;
176
+ } & {
177
+ regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
178
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
179
+ trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
180
+ contextMenuItems(): {
181
+ label: string;
182
+ icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
183
+ onClick: () => void;
184
+ }[];
185
+ renderProps(): any;
186
+ } & {
187
+ renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
188
+ overrideHeight: number;
189
+ }): Promise<JSX.Element>;
190
+ } & {
191
+ readonly rendererTypeName: any;
192
+ readonly showLabels: any;
193
+ readonly showDescriptions: any;
194
+ readonly maxHeight: any;
195
+ readonly displayMode: any;
196
+ readonly rendererConfig: any;
197
+ } & {
198
+ toggleShowLabels(): void;
199
+ toggleShowDescriptions(): void;
200
+ setDisplayMode(val: string): void;
201
+ setMaxHeight(val: number): void;
202
+ } & {
203
+ renderProps(): any;
204
+ trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
205
+ } & {
206
+ selectFeature(feature: Feature): Promise<void>;
207
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -0,0 +1,75 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+
5
+ Object.defineProperty(exports, "__esModule", {
6
+ value: true
7
+ });
8
+ exports["default"] = _default;
9
+
10
+ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
+
12
+ var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
13
+
14
+ var _configuration = require("@jbrowse/core/configuration");
15
+
16
+ var _tracks = require("@jbrowse/core/util/tracks");
17
+
18
+ var _util = require("@jbrowse/core/util");
19
+
20
+ var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
21
+
22
+ var _mobxStateTree = require("mobx-state-tree");
23
+
24
+ function _default(configSchema) {
25
+ return _mobxStateTree.types.compose('LinearVariantDisplay', (0, _pluginLinearGenomeView.linearBasicDisplayModelFactory)(configSchema), _mobxStateTree.types.model({
26
+ type: _mobxStateTree.types.literal('LinearVariantDisplay'),
27
+ configuration: (0, _configuration.ConfigurationReference)(configSchema)
28
+ })).actions(function (self) {
29
+ return {
30
+ selectFeature: function selectFeature(feature) {
31
+ return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
32
+ var session, rpcManager, sessionId, track, adapterConfig, header, featureWidget;
33
+ return _regenerator["default"].wrap(function _callee$(_context) {
34
+ while (1) {
35
+ switch (_context.prev = _context.next) {
36
+ case 0:
37
+ session = (0, _util.getSession)(self);
38
+
39
+ if (!(0, _util.isSessionModelWithWidgets)(session)) {
40
+ _context.next = 11;
41
+ break;
42
+ }
43
+
44
+ rpcManager = session.rpcManager;
45
+ sessionId = (0, _tracks.getRpcSessionId)(self);
46
+ track = (0, _util.getContainingTrack)(self);
47
+ adapterConfig = (0, _configuration.getConf)(track, 'adapter');
48
+ _context.next = 8;
49
+ return rpcManager.call(sessionId, 'CoreGetMetadata', {
50
+ adapterConfig: adapterConfig
51
+ });
52
+
53
+ case 8:
54
+ header = _context.sent;
55
+ featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
56
+ featureData: feature.toJSON(),
57
+ view: (0, _util.getContainingView)(self),
58
+ descriptions: header
59
+ });
60
+ session.showWidget(featureWidget);
61
+
62
+ case 11:
63
+ session.setSelection(feature);
64
+
65
+ case 12:
66
+ case "end":
67
+ return _context.stop();
68
+ }
69
+ }
70
+ }, _callee);
71
+ }))();
72
+ }
73
+ };
74
+ });
75
+ }
@@ -1,24 +1,24 @@
1
- declare function _default(props: any): JSX.Element;
2
- declare namespace _default {
3
- export namespace propTypes {
4
- export const features: PropTypes.Validator<Map<unknown, unknown>>;
5
- export const config: PropTypes.Validator<any>;
6
- export const displayModel: React.Requireable<any>;
7
- export const blockDefinitions: PropTypes.Validator<any[]>;
8
- export const radius: PropTypes.Validator<number>;
9
- export const bezierRadius: PropTypes.Validator<number>;
10
- export const selectedFeatureId: PropTypes.Requireable<string>;
11
- export const onChordClick: PropTypes.Requireable<string | ((...args: any[]) => any)>;
12
- }
13
- export namespace defaultProps {
14
- const displayModel_1: undefined;
15
- export { displayModel_1 as displayModel };
16
- const selectedFeatureId_1: string;
17
- export { selectedFeatureId_1 as selectedFeatureId };
18
- const onChordClick_1: undefined;
19
- export { onChordClick_1 as onChordClick };
20
- }
21
- }
22
- export default _default;
23
- import PropTypes from "prop-types";
24
- import React from "react";
1
+ declare function _default(props: any): JSX.Element;
2
+ declare namespace _default {
3
+ namespace propTypes {
4
+ const features: PropTypes.Validator<Map<unknown, unknown>>;
5
+ const config: PropTypes.Validator<any>;
6
+ const displayModel: React.Requireable<any>;
7
+ const blockDefinitions: PropTypes.Validator<any[]>;
8
+ const radius: PropTypes.Validator<number>;
9
+ const bezierRadius: PropTypes.Validator<number>;
10
+ const selectedFeatureId: PropTypes.Requireable<string>;
11
+ const onChordClick: PropTypes.Requireable<string | ((...args: any[]) => any)>;
12
+ }
13
+ namespace defaultProps {
14
+ const displayModel_1: undefined;
15
+ export { displayModel_1 as displayModel };
16
+ const selectedFeatureId_1: string;
17
+ export { selectedFeatureId_1 as selectedFeatureId };
18
+ const onChordClick_1: undefined;
19
+ export { onChordClick_1 as onChordClick };
20
+ }
21
+ }
22
+ export default _default;
23
+ import PropTypes from "prop-types";
24
+ import React from "react";