react-msaview 5.0.16 → 5.1.0

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Files changed (85) hide show
  1. package/bundle/index.js +23 -23
  2. package/bundle/index.js.LICENSE.txt +1 -1
  3. package/bundle/index.js.map +1 -1
  4. package/dist/clustalX.d.ts +5 -0
  5. package/dist/clustalX.js +88 -0
  6. package/dist/clustalX.js.map +1 -0
  7. package/dist/components/SequenceTextArea.js +2 -2
  8. package/dist/components/SequenceTextArea.js.map +1 -1
  9. package/dist/components/TextTrack.js +3 -5
  10. package/dist/components/TextTrack.js.map +1 -1
  11. package/dist/components/Track.d.ts +2 -1
  12. package/dist/components/Track.js +4 -3
  13. package/dist/components/Track.js.map +1 -1
  14. package/dist/components/VerticalScrollbar.js +6 -31
  15. package/dist/components/VerticalScrollbar.js.map +1 -1
  16. package/dist/components/dialogs/InterProScanDialog.js +5 -3
  17. package/dist/components/dialogs/InterProScanDialog.js.map +1 -1
  18. package/dist/components/header/HeaderStatusArea.js +4 -2
  19. package/dist/components/header/HeaderStatusArea.js.map +1 -1
  20. package/dist/components/header/MSASettingsMenu.js +2 -27
  21. package/dist/components/header/MSASettingsMenu.js.map +1 -1
  22. package/dist/components/header/SettingsMenu.js +4 -69
  23. package/dist/components/header/SettingsMenu.js.map +1 -1
  24. package/dist/components/header/TreeSettingsMenu.js +3 -41
  25. package/dist/components/header/TreeSettingsMenu.js.map +1 -1
  26. package/dist/components/header/settingsMenuItems.d.ts +4 -0
  27. package/dist/components/header/settingsMenuItems.js +59 -0
  28. package/dist/components/header/settingsMenuItems.js.map +1 -0
  29. package/dist/components/minimap/Minimap.js +6 -31
  30. package/dist/components/minimap/Minimap.js.map +1 -1
  31. package/dist/components/msa/MSACanvasBlock.js +31 -33
  32. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  33. package/dist/components/msa/renderMSABlock.js +15 -9
  34. package/dist/components/msa/renderMSABlock.js.map +1 -1
  35. package/dist/components/tree/TreeCanvas.js +12 -14
  36. package/dist/components/tree/TreeCanvas.js.map +1 -1
  37. package/dist/components/tree/renderTreeCanvas.d.ts +9 -3
  38. package/dist/components/tree/renderTreeCanvas.js +14 -40
  39. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  40. package/dist/fetchUtils.d.ts +2 -1
  41. package/dist/fetchUtils.js +16 -2
  42. package/dist/fetchUtils.js.map +1 -1
  43. package/dist/hierarchy.d.ts +2 -0
  44. package/dist/hierarchy.js +25 -0
  45. package/dist/hierarchy.js.map +1 -1
  46. package/dist/launchInterProScan.d.ts +2 -1
  47. package/dist/launchInterProScan.js +31 -15
  48. package/dist/launchInterProScan.js.map +1 -1
  49. package/dist/model.d.ts +150 -494
  50. package/dist/model.js +23 -116
  51. package/dist/model.js.map +1 -1
  52. package/dist/useColorContrast.d.ts +10 -0
  53. package/dist/useColorContrast.js +13 -0
  54. package/dist/useColorContrast.js.map +1 -0
  55. package/dist/useDragScroll.d.ts +12 -0
  56. package/dist/useDragScroll.js +47 -0
  57. package/dist/useDragScroll.js.map +1 -0
  58. package/dist/version.d.ts +1 -1
  59. package/dist/version.js +1 -1
  60. package/dist/version.js.map +1 -1
  61. package/package.json +6 -6
  62. package/src/clustalX.test.ts +76 -0
  63. package/src/clustalX.ts +131 -0
  64. package/src/components/SequenceTextArea.tsx +2 -2
  65. package/src/components/TextTrack.tsx +3 -8
  66. package/src/components/Track.tsx +6 -9
  67. package/src/components/VerticalScrollbar.tsx +13 -40
  68. package/src/components/dialogs/InterProScanDialog.tsx +7 -1
  69. package/src/components/header/HeaderStatusArea.tsx +6 -1
  70. package/src/components/header/MSASettingsMenu.tsx +3 -27
  71. package/src/components/header/SettingsMenu.tsx +7 -79
  72. package/src/components/header/TreeSettingsMenu.tsx +4 -48
  73. package/src/components/header/settingsMenuItems.ts +68 -0
  74. package/src/components/minimap/Minimap.tsx +13 -38
  75. package/src/components/msa/MSACanvasBlock.tsx +53 -36
  76. package/src/components/msa/renderMSABlock.ts +16 -9
  77. package/src/components/tree/TreeCanvas.tsx +13 -35
  78. package/src/components/tree/renderTreeCanvas.ts +23 -38
  79. package/src/fetchUtils.ts +16 -2
  80. package/src/hierarchy.ts +27 -0
  81. package/src/launchInterProScan.ts +34 -10
  82. package/src/model.ts +32 -143
  83. package/src/useColorContrast.ts +18 -0
  84. package/src/useDragScroll.ts +55 -0
  85. package/src/version.ts +1 -1
package/dist/model.d.ts CHANGED
@@ -7,9 +7,9 @@ import type { Theme } from '@mui/material';
7
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  /**
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  * #stateModel MsaView
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  * extends
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- * - DialogQueueSessionMixin
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- * - MSAModel
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- * - Tree
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+ * - [DialogQueueSessionMixin](../dialogqueuesessionmixin)
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+ * - [MSAModel](../msamodel)
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+ * - [Tree](../tree)
13
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  */
14
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  declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
15
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  drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -35,27 +35,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
35
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  scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
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  scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
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  colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
38
- treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
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- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
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- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
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- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
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- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
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- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
52
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
53
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
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- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
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- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- }>>, {
38
+ treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
59
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  locationType: "UriLocation";
60
40
  uri: string;
61
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  internetAccountId: string | undefined;
@@ -63,62 +43,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
63
43
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
64
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  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
65
45
  }> | undefined;
66
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
67
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
68
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
69
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
70
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
71
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
72
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
73
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
74
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
75
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
76
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
77
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
78
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
79
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
80
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
81
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
82
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
83
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
84
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
85
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
86
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
87
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
88
- }, {}> | ({
89
- locationType: "UriLocation";
90
- uri: string;
91
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
92
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
93
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
94
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
95
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
96
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
97
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
98
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
99
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
100
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
101
- msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
102
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
103
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
104
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
105
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
106
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
107
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
108
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
109
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
110
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
111
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
112
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
113
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
114
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
115
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
116
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
117
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
118
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
119
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
120
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
121
- }>>, {
46
+ } | {
47
+ locationType: "BlobLocation";
48
+ name: string;
49
+ blobId: string;
50
+ } | {
51
+ locationType: "FileHandleLocation";
52
+ name: string;
53
+ handleId: string;
54
+ } | {
55
+ locationType: "LocalPathLocation";
56
+ localPath: string;
57
+ }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
58
+ msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
122
59
  locationType: "UriLocation";
123
60
  uri: string;
124
61
  internetAccountId: string | undefined;
@@ -126,62 +63,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
126
63
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
127
64
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
128
65
  }> | undefined;
129
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
130
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
131
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
132
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
133
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
134
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
135
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
136
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
137
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
138
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
139
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
140
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
141
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
142
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
143
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
144
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
145
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
146
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
147
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
148
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
149
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
150
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
151
- }, {}> | ({
152
- locationType: "UriLocation";
153
- uri: string;
154
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
155
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
156
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
157
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
158
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
159
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
160
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
161
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
162
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
163
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
164
- treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
165
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
166
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
167
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
168
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
169
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
170
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
171
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
172
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
173
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
174
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
175
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
176
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
177
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
178
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
179
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
180
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
181
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
182
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
183
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
184
- }>>, {
66
+ } | {
67
+ locationType: "BlobLocation";
68
+ name: string;
69
+ blobId: string;
70
+ } | {
71
+ locationType: "FileHandleLocation";
72
+ name: string;
73
+ handleId: string;
74
+ } | {
75
+ locationType: "LocalPathLocation";
76
+ localPath: string;
77
+ }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
78
+ treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
185
79
  locationType: "UriLocation";
186
80
  uri: string;
187
81
  internetAccountId: string | undefined;
@@ -189,62 +83,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
189
83
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
190
84
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
191
85
  }> | undefined;
192
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
193
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
194
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
195
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
196
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
197
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
198
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
199
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
200
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
201
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
202
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
203
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
204
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
205
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
206
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
207
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
208
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
209
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
210
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
211
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
212
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
213
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
214
- }, {}> | ({
215
- locationType: "UriLocation";
216
- uri: string;
217
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
218
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
219
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
220
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
221
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
222
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
223
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
224
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
225
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
226
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
227
- gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
228
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
229
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
230
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
231
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
232
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
233
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
234
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
235
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
236
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
237
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
238
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
239
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
240
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
241
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
242
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
243
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
244
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
245
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
246
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
247
- }>>, {
86
+ } | {
87
+ locationType: "BlobLocation";
88
+ name: string;
89
+ blobId: string;
90
+ } | {
91
+ locationType: "FileHandleLocation";
92
+ name: string;
93
+ handleId: string;
94
+ } | {
95
+ locationType: "LocalPathLocation";
96
+ localPath: string;
97
+ }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
98
+ gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
248
99
  locationType: "UriLocation";
249
100
  uri: string;
250
101
  internetAccountId: string | undefined;
@@ -252,41 +103,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
252
103
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
253
104
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
254
105
  }> | undefined;
255
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
256
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
257
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
258
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
259
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
260
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
261
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
262
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
263
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
264
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
265
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
266
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
267
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
268
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
269
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
270
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
271
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
272
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
273
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
274
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
275
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
276
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
277
- }, {}> | ({
278
- locationType: "UriLocation";
279
- uri: string;
280
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
281
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
282
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
283
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
284
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
285
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
286
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
287
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
288
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
289
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
106
+ } | {
107
+ locationType: "BlobLocation";
108
+ name: string;
109
+ blobId: string;
110
+ } | {
111
+ locationType: "FileHandleLocation";
112
+ name: string;
113
+ handleId: string;
114
+ } | {
115
+ locationType: "LocalPathLocation";
116
+ localPath: string;
117
+ }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
290
118
  currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
291
119
  collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
292
120
  showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -339,6 +167,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
339
167
  status: {
340
168
  msg: string;
341
169
  url?: string;
170
+ onCancel?: () => void;
342
171
  } | undefined;
343
172
  /**
344
173
  * #volatile
@@ -732,6 +561,16 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
732
561
  * #getter
733
562
  */
734
563
  readonly leaves: HierarchyNode<NodeWithIdsAndLength>[];
564
+ /**
565
+ * #getter
566
+ * max branch length across the tree, used to scale phylogram x-positions
567
+ */
568
+ readonly maxBranchLength: number;
569
+ /**
570
+ * #getter
571
+ * max topological depth to a tip, used to scale cladogram x-positions
572
+ */
573
+ readonly maxDepthToLeaf: number;
735
574
  /**
736
575
  * #getter
737
576
  */
@@ -842,6 +681,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
842
681
  setStatus(status?: {
843
682
  msg: string;
844
683
  url?: string;
684
+ onCancel?: () => void;
845
685
  }): void;
846
686
  } & {
847
687
  /**
@@ -1056,51 +896,29 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
1056
896
  */
1057
897
  fitHorizontally(): void;
1058
898
  afterCreate(): void;
1059
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1060
- drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1061
- labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1062
- treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
1063
- treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
1064
- showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1065
- drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1066
- drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1067
- } & {
1068
- bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1069
- colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
1070
- } & {
1071
- id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
1072
- showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1073
- hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1074
- allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1075
- subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1076
- type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
1077
- drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1078
- height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
1079
- rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1080
- scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1081
- scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1082
- colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1083
- treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1084
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1085
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1086
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1087
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1088
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1089
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1090
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1091
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1092
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1093
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1094
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1095
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1096
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1097
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1098
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1099
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1100
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1101
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1102
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1103
- }>>, {
899
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<{
900
+ drawLabels: boolean;
901
+ labelsAlignRight: boolean;
902
+ treeAreaWidth: number;
903
+ treeWidth: number;
904
+ showBranchLen: boolean;
905
+ drawTree: boolean;
906
+ drawNodeBubbles: boolean;
907
+ bgColor: boolean;
908
+ colorSchemeName: string;
909
+ id: string;
910
+ showDomains: boolean;
911
+ hideGaps: boolean;
912
+ allowedGappyness: number;
913
+ subFeatureRows: boolean;
914
+ type: "MsaView";
915
+ drawMsaLetters: boolean;
916
+ height: number;
917
+ rowHeight: number;
918
+ scrollY: number;
919
+ scrollX: number;
920
+ colWidth: number;
921
+ treeFilehandle: {
1104
922
  locationType: "UriLocation";
1105
923
  uri: string;
1106
924
  internetAccountId: string | undefined;
@@ -1108,62 +926,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
1108
926
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1109
927
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1110
928
  }> | undefined;
1111
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1112
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1113
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1114
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1115
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1116
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1117
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1118
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1119
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1120
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1121
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1122
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1123
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1124
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1125
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1126
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1127
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1128
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1129
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1130
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1131
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1132
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1133
- }, {}> | ({
1134
- locationType: "UriLocation";
1135
- uri: string;
1136
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1137
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1138
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1139
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1140
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1141
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1142
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1143
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1144
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1145
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1146
- msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1147
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1148
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1149
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1150
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1151
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1152
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1153
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1154
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1155
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1156
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1157
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1158
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1159
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1160
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1161
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1162
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1163
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1164
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1165
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1166
- }>>, {
929
+ } | {
930
+ locationType: "BlobLocation";
931
+ name: string;
932
+ blobId: string;
933
+ } | {
934
+ locationType: "FileHandleLocation";
935
+ name: string;
936
+ handleId: string;
937
+ } | {
938
+ locationType: "LocalPathLocation";
939
+ localPath: string;
940
+ } | undefined;
941
+ msaFilehandle: {
1167
942
  locationType: "UriLocation";
1168
943
  uri: string;
1169
944
  internetAccountId: string | undefined;
@@ -1171,62 +946,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
1171
946
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1172
947
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1173
948
  }> | undefined;
1174
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1175
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1176
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1177
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1178
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1179
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1180
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1181
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1182
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1183
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1184
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1185
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1186
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1187
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1188
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1189
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1190
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1191
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1192
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1193
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1194
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1195
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1196
- }, {}> | ({
1197
- locationType: "UriLocation";
1198
- uri: string;
1199
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1200
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1201
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1202
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1203
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1204
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1205
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1206
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1207
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1208
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1209
- treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1210
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1211
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1212
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1213
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1214
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1215
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1216
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1217
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1218
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1219
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1220
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1221
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1222
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1223
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1224
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1225
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1226
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1227
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1228
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1229
- }>>, {
949
+ } | {
950
+ locationType: "BlobLocation";
951
+ name: string;
952
+ blobId: string;
953
+ } | {
954
+ locationType: "FileHandleLocation";
955
+ name: string;
956
+ handleId: string;
957
+ } | {
958
+ locationType: "LocalPathLocation";
959
+ localPath: string;
960
+ } | undefined;
961
+ treeMetadataFilehandle: {
1230
962
  locationType: "UriLocation";
1231
963
  uri: string;
1232
964
  internetAccountId: string | undefined;
@@ -1234,62 +966,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
1234
966
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1235
967
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1236
968
  }> | undefined;
1237
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1238
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1239
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1240
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1241
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1242
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1243
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1244
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1245
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1246
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1247
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1248
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1249
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1250
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1251
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1252
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1253
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1254
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1255
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1256
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1257
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1258
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1259
- }, {}> | ({
1260
- locationType: "UriLocation";
1261
- uri: string;
1262
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1263
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1264
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1265
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1266
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1267
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1268
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1269
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1270
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1271
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1272
- gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1273
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1274
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1275
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1276
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1277
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1278
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1279
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1280
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1281
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1282
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1283
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1284
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1285
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1286
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1287
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1288
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1289
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1290
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1291
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1292
- }>>, {
969
+ } | {
970
+ locationType: "BlobLocation";
971
+ name: string;
972
+ blobId: string;
973
+ } | {
974
+ locationType: "FileHandleLocation";
975
+ name: string;
976
+ handleId: string;
977
+ } | {
978
+ locationType: "LocalPathLocation";
979
+ localPath: string;
980
+ } | undefined;
981
+ gffFilehandle: {
1293
982
  locationType: "UriLocation";
1294
983
  uri: string;
1295
984
  internetAccountId: string | undefined;
@@ -1297,64 +986,31 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
1297
986
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1298
987
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1299
988
  }> | undefined;
1300
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1301
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1302
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1303
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1304
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1305
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1306
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1307
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1308
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1309
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1310
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1311
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1312
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1313
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1314
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1315
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1316
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1317
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1318
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1319
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1320
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1321
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1322
- }, {}> | ({
1323
- locationType: "UriLocation";
1324
- uri: string;
1325
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1326
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1327
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1328
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1329
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1330
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1331
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1332
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1333
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1334
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1335
- currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1336
- collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1337
- showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1338
- turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
1339
- data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
1340
- tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1341
- msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1342
- treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1343
- gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1344
- }, {
1345
- setTree(tree?: string): void;
1346
- setMSA(msa?: string): void;
1347
- setTreeMetadata(treeMetadata?: string): void;
1348
- setGFF(gff?: string): void;
1349
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
989
+ } | {
990
+ locationType: "BlobLocation";
991
+ name: string;
992
+ blobId: string;
993
+ } | {
994
+ locationType: "FileHandleLocation";
995
+ name: string;
996
+ handleId: string;
997
+ } | {
998
+ locationType: "LocalPathLocation";
999
+ localPath: string;
1000
+ } | undefined;
1001
+ currentAlignment: number;
1002
+ collapsed: string[];
1003
+ showOnly: string | undefined;
1004
+ turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
1005
+ data: {
1350
1006
  tree: string | undefined;
1351
1007
  msa: string | undefined;
1352
1008
  treeMetadata: string | undefined;
1353
1009
  gff: string | undefined;
1354
- }>, [undefined]>;
1355
- featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
1356
- relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1357
- }>, symbol>>;
1010
+ };
1011
+ featureFilters: import("mobx").IKeyValueMap<boolean>;
1012
+ relativeTo: string | undefined;
1013
+ }, symbol>>;
1358
1014
  export default stateModelFactory;
1359
1015
  export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;
1360
1016
  export type MsaViewModel = Instance<MsaViewStateModel>;