@jbrowse/plugin-linear-genome-view 1.6.9 → 1.7.3

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 (111) hide show
  1. package/dist/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +13 -13
  2. package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js +232 -0
  3. package/dist/BaseLinearDisplay/components/Block.d.ts +15 -15
  4. package/dist/BaseLinearDisplay/components/Block.js +86 -0
  5. package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts +12 -12
  6. package/dist/BaseLinearDisplay/components/LinearBlocks.js +110 -0
  7. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.d.ts +4 -4
  8. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +192 -0
  9. package/dist/BaseLinearDisplay/index.d.ts +5 -5
  10. package/dist/BaseLinearDisplay/index.js +41 -0
  11. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +227 -230
  12. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +763 -0
  13. package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts +1 -1
  14. package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js +24 -0
  15. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +96 -96
  16. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +328 -0
  17. package/dist/LinearBareDisplay/configSchema.d.ts +2 -2
  18. package/dist/LinearBareDisplay/configSchema.js +19 -0
  19. package/dist/LinearBareDisplay/index.d.ts +2 -2
  20. package/dist/LinearBareDisplay/index.js +21 -0
  21. package/dist/LinearBareDisplay/index.test.js +33 -0
  22. package/dist/LinearBareDisplay/model.d.ts +192 -192
  23. package/dist/LinearBareDisplay/model.js +44 -0
  24. package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts +10 -10
  25. package/dist/LinearBasicDisplay/components/SetMaxHeight.js +94 -0
  26. package/dist/LinearBasicDisplay/configSchema.d.ts +2 -2
  27. package/dist/LinearBasicDisplay/configSchema.js +25 -0
  28. package/dist/LinearBasicDisplay/index.d.ts +2 -2
  29. package/dist/LinearBasicDisplay/index.js +23 -0
  30. package/dist/LinearBasicDisplay/model.d.ts +213 -213
  31. package/dist/LinearBasicDisplay/model.js +162 -0
  32. package/dist/LinearGenomeView/components/CenterLine.d.ts +14 -14
  33. package/dist/LinearGenomeView/components/CenterLine.js +80 -0
  34. package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts +6 -6
  35. package/dist/LinearGenomeView/components/ExportSvgDialog.js +137 -0
  36. package/dist/LinearGenomeView/components/Header.d.ts +7 -7
  37. package/dist/LinearGenomeView/components/Header.js +144 -0
  38. package/dist/LinearGenomeView/components/HelpDialog.d.ts +5 -5
  39. package/dist/LinearGenomeView/components/HelpDialog.js +48 -0
  40. package/dist/LinearGenomeView/components/ImportForm.d.ts +7 -7
  41. package/dist/LinearGenomeView/components/ImportForm.js +330 -0
  42. package/dist/LinearGenomeView/components/LinearGenomeView.d.ts +7 -7
  43. package/dist/LinearGenomeView/components/LinearGenomeView.js +129 -0
  44. package/dist/LinearGenomeView/components/LinearGenomeView.test.js +234 -0
  45. package/dist/LinearGenomeView/components/LinearGenomeViewSvg.d.ts +4 -4
  46. package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js +349 -0
  47. package/dist/LinearGenomeView/components/MiniControls.d.ts +6 -6
  48. package/dist/LinearGenomeView/components/MiniControls.js +83 -0
  49. package/dist/LinearGenomeView/components/OverviewRubberBand.d.ts +22 -22
  50. package/dist/LinearGenomeView/components/OverviewRubberBand.js +310 -0
  51. package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts +132 -124
  52. package/dist/LinearGenomeView/components/OverviewScaleBar.js +403 -0
  53. package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts +21 -21
  54. package/dist/LinearGenomeView/components/RefNameAutocomplete.js +331 -0
  55. package/dist/LinearGenomeView/components/RubberBand.d.ts +9 -20
  56. package/dist/LinearGenomeView/components/RubberBand.js +309 -0
  57. package/dist/LinearGenomeView/components/Ruler.d.ts +27 -27
  58. package/dist/LinearGenomeView/components/Ruler.js +101 -0
  59. package/dist/LinearGenomeView/components/ScaleBar.d.ts +401 -401
  60. package/dist/LinearGenomeView/components/ScaleBar.js +184 -0
  61. package/dist/LinearGenomeView/components/ScaleBar.test.js +180 -0
  62. package/dist/LinearGenomeView/components/SearchBox.d.ts +8 -8
  63. package/dist/LinearGenomeView/components/SearchBox.js +201 -0
  64. package/dist/LinearGenomeView/components/SearchResultsDialog.d.ts +8 -8
  65. package/dist/LinearGenomeView/components/SearchResultsDialog.js +159 -0
  66. package/dist/LinearGenomeView/components/SequenceDialog.d.ts +8 -8
  67. package/dist/LinearGenomeView/components/SequenceDialog.js +304 -0
  68. package/dist/LinearGenomeView/components/TrackContainer.d.ts +9 -9
  69. package/dist/LinearGenomeView/components/TrackContainer.js +179 -0
  70. package/dist/LinearGenomeView/components/TrackLabel.d.ts +44 -44
  71. package/dist/LinearGenomeView/components/TrackLabel.js +165 -0
  72. package/dist/LinearGenomeView/components/TracksContainer.d.ts +10 -10
  73. package/dist/LinearGenomeView/components/TracksContainer.js +214 -0
  74. package/dist/LinearGenomeView/components/VerticalGuides.d.ts +9 -9
  75. package/dist/LinearGenomeView/components/VerticalGuides.js +116 -0
  76. package/dist/LinearGenomeView/components/ZoomControls.d.ts +7 -7
  77. package/dist/LinearGenomeView/components/ZoomControls.js +92 -0
  78. package/dist/LinearGenomeView/components/util.d.ts +2 -2
  79. package/dist/LinearGenomeView/components/util.js +16 -0
  80. package/dist/LinearGenomeView/index.d.ts +292 -292
  81. package/dist/LinearGenomeView/index.js +1418 -0
  82. package/dist/LinearGenomeView/index.test.js +1170 -0
  83. package/dist/LinearGenomeView/util.d.ts +14 -14
  84. package/dist/LinearGenomeView/util.js +93 -0
  85. package/dist/LinearGenomeView/util.test.js +78 -0
  86. package/dist/index.d.ts +565 -565
  87. package/dist/index.js +293 -6
  88. package/package.json +6 -9
  89. package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +2 -0
  90. package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +10 -8
  91. package/src/LinearBasicDisplay/components/SetMaxHeight.tsx +1 -1
  92. package/src/LinearBasicDisplay/model.ts +17 -18
  93. package/src/LinearGenomeView/components/Header.tsx +1 -1
  94. package/src/LinearGenomeView/components/ImportForm.tsx +10 -4
  95. package/src/LinearGenomeView/components/LinearGenomeView.test.js +1 -0
  96. package/src/LinearGenomeView/components/OverviewScaleBar.tsx +2 -2
  97. package/src/LinearGenomeView/components/RubberBand.tsx +14 -24
  98. package/src/LinearGenomeView/components/ScaleBar.test.tsx +1 -0
  99. package/src/LinearGenomeView/components/ScaleBar.tsx +3 -6
  100. package/src/LinearGenomeView/components/SequenceDialog.tsx +1 -1
  101. package/src/LinearGenomeView/components/TrackLabel.tsx +1 -1
  102. package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap +0 -4
  103. package/src/LinearGenomeView/index.tsx +2 -3
  104. package/dist/LinearBareDisplay/index.test.d.ts +0 -1
  105. package/dist/LinearGenomeView/components/LinearGenomeView.test.d.ts +0 -1
  106. package/dist/plugin-linear-genome-view.cjs.development.js +0 -8121
  107. package/dist/plugin-linear-genome-view.cjs.development.js.map +0 -1
  108. package/dist/plugin-linear-genome-view.cjs.production.min.js +0 -2
  109. package/dist/plugin-linear-genome-view.cjs.production.min.js.map +0 -1
  110. package/dist/plugin-linear-genome-view.esm.js +0 -8105
  111. package/dist/plugin-linear-genome-view.esm.js.map +0 -1
@@ -1,213 +1,213 @@
1
- /// <reference types="react" />
2
- import { MenuItem } from '@jbrowse/core/ui';
3
- import { Instance } from 'mobx-state-tree';
4
- import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema';
5
- declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
6
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
7
- type: import("mobx-state-tree").ISimpleType<string>;
8
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
9
- } & {
10
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
11
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
12
- key: import("mobx-state-tree").ISimpleType<string>;
13
- region: import("mobx-state-tree").IModelType<{
14
- refName: import("mobx-state-tree").ISimpleType<string>;
15
- start: import("mobx-state-tree").ISimpleType<number>;
16
- end: import("mobx-state-tree").ISimpleType<number>;
17
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
18
- } & {
19
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
20
- }, {
21
- setRefName(newRefName: string): void;
22
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
23
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
24
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
25
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
26
- }, {
27
- renderInProgress: AbortController | undefined;
28
- filled: boolean;
29
- reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
30
- features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
31
- layout: any;
32
- status: string;
33
- error: unknown;
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- message: string | undefined;
35
- maxHeightReached: boolean;
36
- ReactComponent: ({ model, }: {
37
- model: any;
38
- }) => any;
39
- renderProps: any;
40
- } & {
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- doReload(): void;
42
- afterAttach(): void;
43
- setStatus(message: string): void;
44
- setLoading(abortController: AbortController): void;
45
- setMessage(messageText: string): void;
46
- setRendered(props: {
47
- reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)>;
48
- features: Map<string, import("@jbrowse/core/util").Feature>;
49
- layout: any;
50
- maxHeightReached: boolean;
51
- renderProps: any;
52
- } | undefined): void;
53
- setError(error: unknown): void;
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- reload(): void;
55
- beforeDestroy(): void;
56
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
57
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
58
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
59
- } & {
60
- type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
61
- trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
62
- trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
63
- trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
64
- trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
65
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
66
- }, {
67
- rendererTypeName: string;
68
- error: unknown;
69
- } & {
70
- readonly RenderingComponent: import("react").FC<{
71
- model: import("mobx-state-tree").ModelInstanceTypeProps<{
72
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
73
- type: import("mobx-state-tree").ISimpleType<string>;
74
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
75
- }> & {
76
- rendererTypeName: string;
77
- error: unknown;
78
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
79
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
80
- type: import("mobx-state-tree").ISimpleType<string>;
81
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
82
- }, {
83
- rendererTypeName: string;
84
- error: unknown;
85
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
86
- onHorizontalScroll?: Function | undefined;
87
- blockState?: Record<string, any> | undefined;
88
- }>;
89
- readonly DisplayBlurb: import("react").FC<{
90
- model: import("mobx-state-tree").ModelInstanceTypeProps<{
91
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
92
- type: import("mobx-state-tree").ISimpleType<string>;
93
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
94
- }> & {
95
- rendererTypeName: string;
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- error: unknown;
97
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
98
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
99
- type: import("mobx-state-tree").ISimpleType<string>;
100
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
101
- }, {
102
- rendererTypeName: string;
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- error: unknown;
104
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
105
- }> | null;
106
- readonly adapterConfig: any;
107
- readonly parentTrack: any;
108
- renderProps(): any;
109
- readonly rendererType: any;
110
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
111
- trackMenuItems(): MenuItem[];
112
- readonly viewMenuActions: MenuItem[];
113
- regionCannotBeRendered(): undefined;
114
- } & {
115
- setError(error?: unknown): void;
116
- setRpcDriverName(rpcDriverName: string): void;
117
- reload(): void;
118
- } & {
119
- currBpPerPx: number;
120
- message: string;
121
- featureIdUnderMouse: string | undefined;
122
- contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
123
- scrollTop: number;
124
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
125
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
126
- } & {
127
- readonly blockType: "staticBlocks" | "dynamicBlocks";
128
- readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
129
- } & {
130
- readonly renderDelay: number;
131
- readonly TooltipComponent: import("react").FC<any>;
132
- readonly selectedFeatureId: string | undefined;
133
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
134
- } & {
135
- readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
136
- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
137
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
138
- getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
139
- searchFeatureByID(id: string): [number, number, number, number] | undefined;
140
- readonly currentBytesRequested: number;
141
- readonly currentFeatureScreenDensity: number;
142
- readonly maxFeatureScreenDensity: any;
143
- readonly estimatedStatsReady: boolean;
144
- readonly maxAllowableBytes: number;
145
- } & {
146
- setMessage(message: string): void;
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- afterAttach(): void;
148
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
149
- headers?: Record<string, string> | undefined;
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- signal?: AbortSignal | undefined;
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- filters?: string[] | undefined;
152
- }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
153
- 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;
156
- setHeight(displayHeight: number): number;
157
- resizeHeight(distance: number): number;
158
- setScrollTop(scrollTop: number): void;
159
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
160
- addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
161
- setCurrBpPerPx(n: number): void;
162
- deleteBlock(key: string): void;
163
- selectFeature(feature: import("@jbrowse/core/util").Feature): void;
164
- clearFeatureSelection(): void;
165
- setFeatureIdUnderMouse(feature: string | undefined): void;
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- reload(): void;
167
- setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
168
- } & {
169
- readonly regionTooLarge: boolean;
170
- readonly regionTooLargeReason: string;
171
- } & {
172
- reload(): Promise<void>;
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- afterAttach(): void;
174
- } & {
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- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
176
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
177
- trackMenuItems(): MenuItem[];
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- contextMenuItems(): {
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- label: string;
180
- icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
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- onClick: () => void;
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- }[];
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- renderProps(): any;
184
- } & {
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- renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
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- overrideHeight: number;
187
- }): Promise<JSX.Element>;
188
- } & {
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- readonly rendererTypeName: any;
190
- readonly showLabels: any;
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- readonly showDescriptions: any;
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- readonly maxHeight: any;
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- readonly displayMode: any;
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- readonly rendererConfig: any;
195
- } & {
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- toggleShowLabels(): void;
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- toggleShowDescriptions(): void;
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- setDisplayMode(val: string): void;
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- setMaxHeight(val: number): void;
200
- } & {
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- renderProps(): any;
202
- trackMenuItems(): MenuItem[];
203
- }, import("mobx-state-tree")._NotCustomized, {
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- id: string;
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- type: string;
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- rpcDriverName: string | undefined;
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- height: number;
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- userBpPerPxLimit: number | undefined;
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- userByteSizeLimit: number | undefined;
210
- } & import("mobx-state-tree")._NotCustomized>;
211
- export declare type FeatureTrackStateModel = ReturnType<typeof stateModelFactory>;
212
- export declare type FeatureTrackModel = Instance<FeatureTrackStateModel>;
213
- export default stateModelFactory;
1
+ /// <reference types="react" />
2
+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
3
+ import { MenuItem } from '@jbrowse/core/ui';
4
+ import { Instance } from 'mobx-state-tree';
5
+ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
6
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
7
+ type: import("mobx-state-tree").ISimpleType<string>;
8
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
9
+ } & {
10
+ height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
11
+ blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
12
+ key: import("mobx-state-tree").ISimpleType<string>;
13
+ region: import("mobx-state-tree").IModelType<{
14
+ refName: import("mobx-state-tree").ISimpleType<string>;
15
+ start: import("mobx-state-tree").ISimpleType<number>;
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+ end: import("mobx-state-tree").ISimpleType<number>;
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+ reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
18
+ } & {
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+ assemblyName: import("mobx-state-tree").ISimpleType<string>;
20
+ }, {
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+ setRefName(newRefName: string): void;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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+ reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
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+ isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
26
+ }, {
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+ renderInProgress: AbortController | undefined;
28
+ filled: boolean;
29
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
30
+ features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
31
+ layout: any;
32
+ status: string;
33
+ error: unknown;
34
+ message: string | undefined;
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+ maxHeightReached: boolean;
36
+ ReactComponent: ({ model, }: {
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+ model: any;
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+ }) => any;
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+ renderProps: any;
40
+ } & {
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+ doReload(): void;
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+ afterAttach(): void;
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+ setStatus(message: string): void;
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+ setLoading(abortController: AbortController): void;
45
+ setMessage(messageText: string): void;
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+ setRendered(props: {
47
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
48
+ features: Map<string, import("@jbrowse/core/util").Feature>;
49
+ layout: any;
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+ maxHeightReached: boolean;
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+ renderProps: any;
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+ } | undefined): void;
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+ setError(error: unknown): void;
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+ reload(): void;
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+ beforeDestroy(): void;
56
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
57
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
58
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
59
+ } & {
60
+ type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
61
+ trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
62
+ trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
63
+ trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
64
+ trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
65
+ configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
66
+ }, {
67
+ rendererTypeName: string;
68
+ error: unknown;
69
+ } & {
70
+ readonly RenderingComponent: import("react").FC<{
71
+ model: import("mobx-state-tree").ModelInstanceTypeProps<{
72
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
73
+ type: import("mobx-state-tree").ISimpleType<string>;
74
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
75
+ }> & {
76
+ rendererTypeName: string;
77
+ error: unknown;
78
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
79
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
80
+ type: import("mobx-state-tree").ISimpleType<string>;
81
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
82
+ }, {
83
+ rendererTypeName: string;
84
+ error: unknown;
85
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
86
+ onHorizontalScroll?: Function | undefined;
87
+ blockState?: Record<string, any> | undefined;
88
+ }>;
89
+ readonly DisplayBlurb: import("react").FC<{
90
+ model: import("mobx-state-tree").ModelInstanceTypeProps<{
91
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
92
+ type: import("mobx-state-tree").ISimpleType<string>;
93
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
94
+ }> & {
95
+ rendererTypeName: string;
96
+ error: unknown;
97
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
98
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
99
+ type: import("mobx-state-tree").ISimpleType<string>;
100
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
101
+ }, {
102
+ rendererTypeName: string;
103
+ error: unknown;
104
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
105
+ }> | null;
106
+ readonly adapterConfig: any;
107
+ readonly parentTrack: any;
108
+ renderProps(): any;
109
+ readonly rendererType: any;
110
+ readonly DisplayMessageComponent: import("react").FC<any> | undefined;
111
+ trackMenuItems(): MenuItem[];
112
+ readonly viewMenuActions: MenuItem[];
113
+ regionCannotBeRendered(): undefined;
114
+ } & {
115
+ setError(error?: unknown): void;
116
+ setRpcDriverName(rpcDriverName: string): void;
117
+ reload(): void;
118
+ } & {
119
+ currBpPerPx: number;
120
+ message: string;
121
+ featureIdUnderMouse: string | undefined;
122
+ contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
123
+ scrollTop: number;
124
+ estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
125
+ estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
126
+ } & {
127
+ readonly blockType: "staticBlocks" | "dynamicBlocks";
128
+ readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
129
+ } & {
130
+ readonly renderDelay: number;
131
+ readonly TooltipComponent: import("react").FC<any>;
132
+ readonly selectedFeatureId: string | undefined;
133
+ readonly DisplayMessageComponent: import("react").FC<any> | undefined;
134
+ } & {
135
+ readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
136
+ readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
137
+ getFeatureOverlapping(blockKey: string, x: number, y: number): any;
138
+ getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
139
+ searchFeatureByID(id: string): [number, number, number, number] | undefined;
140
+ readonly currentBytesRequested: number;
141
+ readonly currentFeatureScreenDensity: number;
142
+ readonly maxFeatureScreenDensity: any;
143
+ readonly estimatedStatsReady: boolean;
144
+ readonly maxAllowableBytes: number;
145
+ } & {
146
+ setMessage(message: string): void;
147
+ afterAttach(): void;
148
+ estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
149
+ headers?: Record<string, string> | undefined;
150
+ signal?: AbortSignal | undefined;
151
+ filters?: string[] | undefined;
152
+ }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
153
+ setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
154
+ setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
155
+ clearRegionStats(): void;
156
+ setHeight(displayHeight: number): number;
157
+ resizeHeight(distance: number): number;
158
+ setScrollTop(scrollTop: number): void;
159
+ updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
160
+ addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
161
+ setCurrBpPerPx(n: number): void;
162
+ deleteBlock(key: string): void;
163
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
164
+ clearFeatureSelection(): void;
165
+ setFeatureIdUnderMouse(feature: string | undefined): void;
166
+ reload(): void;
167
+ setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
168
+ } & {
169
+ readonly regionTooLarge: boolean;
170
+ readonly regionTooLargeReason: string;
171
+ } & {
172
+ reload(): Promise<void>;
173
+ afterAttach(): void;
174
+ } & {
175
+ regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
176
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
177
+ trackMenuItems(): MenuItem[];
178
+ contextMenuItems(): {
179
+ label: string;
180
+ icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
181
+ onClick: () => void;
182
+ }[];
183
+ renderProps(): any;
184
+ } & {
185
+ renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
186
+ overrideHeight: number;
187
+ }): Promise<JSX.Element>;
188
+ } & {
189
+ readonly rendererTypeName: any;
190
+ readonly showLabels: any;
191
+ readonly showDescriptions: any;
192
+ readonly maxHeight: any;
193
+ readonly displayMode: any;
194
+ readonly rendererConfig: any;
195
+ } & {
196
+ toggleShowLabels(): void;
197
+ toggleShowDescriptions(): void;
198
+ setDisplayMode(val: string): void;
199
+ setMaxHeight(val: number): void;
200
+ } & {
201
+ renderProps(): any;
202
+ trackMenuItems(): MenuItem[];
203
+ }, import("mobx-state-tree")._NotCustomized, {
204
+ id: string;
205
+ type: string;
206
+ rpcDriverName: string | undefined;
207
+ height: number;
208
+ userBpPerPxLimit: number | undefined;
209
+ userByteSizeLimit: number | undefined;
210
+ } & import("mobx-state-tree")._NotCustomized>;
211
+ export declare type FeatureTrackStateModel = ReturnType<typeof stateModelFactory>;
212
+ export declare type FeatureTrackModel = Instance<FeatureTrackStateModel>;
213
+ export default stateModelFactory;
@@ -0,0 +1,162 @@
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"] = void 0;
9
+
10
+ var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
11
+
12
+ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
13
+
14
+ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
15
+
16
+ var _react = require("react");
17
+
18
+ var _configuration = require("@jbrowse/core/configuration");
19
+
20
+ var _util = require("@jbrowse/core/util");
21
+
22
+ var _mobxStateTree = require("mobx-state-tree");
23
+
24
+ var _Visibility = _interopRequireDefault(require("@material-ui/icons/Visibility"));
25
+
26
+ var _BaseLinearDisplay = require("../BaseLinearDisplay");
27
+
28
+ function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
29
+
30
+ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
31
+
32
+ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
33
+
34
+ function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
35
+
36
+ var SetMaxHeightDlg = /*#__PURE__*/(0, _react.lazy)(function () {
37
+ return Promise.resolve().then(function () {
38
+ return _interopRequireWildcard(require('./components/SetMaxHeight'));
39
+ });
40
+ });
41
+
42
+ var stateModelFactory = function stateModelFactory(configSchema) {
43
+ return _mobxStateTree.types.compose('LinearBasicDisplay', _BaseLinearDisplay.BaseLinearDisplay, _mobxStateTree.types.model({
44
+ type: _mobxStateTree.types.literal('LinearBasicDisplay'),
45
+ trackShowLabels: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
46
+ trackShowDescriptions: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
47
+ trackDisplayMode: _mobxStateTree.types.maybe(_mobxStateTree.types.string),
48
+ trackMaxHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
49
+ configuration: (0, _configuration.ConfigurationReference)(configSchema)
50
+ })).views(function (self) {
51
+ return {
52
+ get rendererTypeName() {
53
+ return (0, _configuration.getConf)(self, ['renderer', 'type']);
54
+ },
55
+
56
+ get showLabels() {
57
+ var _self$trackShowLabels;
58
+
59
+ return (_self$trackShowLabels = self.trackShowLabels) !== null && _self$trackShowLabels !== void 0 ? _self$trackShowLabels : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
60
+ },
61
+
62
+ get showDescriptions() {
63
+ var _self$trackShowDescri;
64
+
65
+ return (_self$trackShowDescri = self.trackShowDescriptions) !== null && _self$trackShowDescri !== void 0 ? _self$trackShowDescri : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
66
+ },
67
+
68
+ get maxHeight() {
69
+ var _self$trackMaxHeight;
70
+
71
+ return (_self$trackMaxHeight = self.trackMaxHeight) !== null && _self$trackMaxHeight !== void 0 ? _self$trackMaxHeight : (0, _configuration.getConf)(self, ['renderer', 'maxHeight']);
72
+ },
73
+
74
+ get displayMode() {
75
+ var _self$trackDisplayMod;
76
+
77
+ var displayMode = (0, _configuration.getConf)(self, ['renderer', 'displayMode']);
78
+ return (_self$trackDisplayMod = self.trackDisplayMode) !== null && _self$trackDisplayMod !== void 0 ? _self$trackDisplayMod : displayMode;
79
+ },
80
+
81
+ get rendererConfig() {
82
+ var configBlob = (0, _configuration.getConf)(self, ['renderer']) || {};
83
+ return self.rendererType.configSchema.create(_objectSpread(_objectSpread({}, configBlob), {}, {
84
+ showLabels: this.showLabels,
85
+ showDescriptions: this.showDescriptions,
86
+ displayMode: this.displayMode,
87
+ maxHeight: this.maxHeight
88
+ }), (0, _mobxStateTree.getEnv)(self));
89
+ }
90
+
91
+ };
92
+ }).actions(function (self) {
93
+ return {
94
+ toggleShowLabels: function toggleShowLabels() {
95
+ self.trackShowLabels = !self.showLabels;
96
+ },
97
+ toggleShowDescriptions: function toggleShowDescriptions() {
98
+ self.trackShowDescriptions = !self.showDescriptions;
99
+ },
100
+ setDisplayMode: function setDisplayMode(val) {
101
+ self.trackDisplayMode = val;
102
+ },
103
+ setMaxHeight: function setMaxHeight(val) {
104
+ self.trackMaxHeight = val;
105
+ }
106
+ };
107
+ }).views(function (self) {
108
+ var superTrackMenuItems = self.trackMenuItems,
109
+ superRenderProps = self.renderProps;
110
+ return {
111
+ renderProps: function renderProps() {
112
+ var config = self.rendererConfig;
113
+ return _objectSpread(_objectSpread({}, superRenderProps()), {}, {
114
+ config: config
115
+ });
116
+ },
117
+ trackMenuItems: function trackMenuItems() {
118
+ return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
119
+ label: 'Show labels',
120
+ icon: _Visibility["default"],
121
+ type: 'checkbox',
122
+ checked: self.showLabels,
123
+ onClick: function onClick() {
124
+ self.toggleShowLabels();
125
+ }
126
+ }, {
127
+ label: 'Show descriptions',
128
+ icon: _Visibility["default"],
129
+ type: 'checkbox',
130
+ checked: self.showDescriptions,
131
+ onClick: function onClick() {
132
+ self.toggleShowDescriptions();
133
+ }
134
+ }, {
135
+ label: 'Display mode',
136
+ icon: _Visibility["default"],
137
+ subMenu: ['compact', 'reducedRepresentation', 'normal', 'collapse'].map(function (val) {
138
+ return {
139
+ label: val,
140
+ onClick: function onClick() {
141
+ self.setDisplayMode(val);
142
+ }
143
+ };
144
+ })
145
+ }, {
146
+ label: 'Set max height',
147
+ onClick: function onClick() {
148
+ (0, _util.getSession)(self).queueDialog(function (doneCallback) {
149
+ return [SetMaxHeightDlg, {
150
+ model: self,
151
+ handleClose: doneCallback
152
+ }];
153
+ });
154
+ }
155
+ }]);
156
+ }
157
+ };
158
+ });
159
+ };
160
+
161
+ var _default = stateModelFactory;
162
+ exports["default"] = _default;
@@ -1,14 +1,14 @@
1
- /// <reference types="react" />
2
- import { Instance } from 'mobx-state-tree';
3
- import { LinearGenomeViewStateModel } from '..';
4
- declare type LGV = Instance<LinearGenomeViewStateModel>;
5
- declare function CenterLine({ model }: {
6
- model: LGV;
7
- }): JSX.Element | null;
8
- declare namespace CenterLine {
9
- var propTypes: {
10
- model: import("prop-types").Validator<any>;
11
- };
12
- }
13
- declare const _default: typeof CenterLine;
14
- export default _default;
1
+ /// <reference types="react" />
2
+ import { Instance } from 'mobx-state-tree';
3
+ import { LinearGenomeViewStateModel } from '..';
4
+ declare type LGV = Instance<LinearGenomeViewStateModel>;
5
+ declare function CenterLine({ model }: {
6
+ model: LGV;
7
+ }): JSX.Element | null;
8
+ declare namespace CenterLine {
9
+ var propTypes: {
10
+ model: import("prop-types").Validator<any>;
11
+ };
12
+ }
13
+ declare const _default: typeof CenterLine;
14
+ export default _default;