jbrowse-plugin-msaview 2.4.5 → 2.5.1

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Files changed (47) hide show
  1. package/dist/LaunchMsaView/util.js +1 -1
  2. package/dist/LaunchMsaViewExtensionPoint/index.js +2 -1
  3. package/dist/MsaViewPanel/afterCreateAutoruns.d.ts +15 -0
  4. package/dist/MsaViewPanel/afterCreateAutoruns.js +53 -0
  5. package/dist/MsaViewPanel/loadProteinDomains.d.ts +16 -0
  6. package/dist/MsaViewPanel/loadProteinDomains.js +33 -0
  7. package/dist/MsaViewPanel/model.d.ts +69 -399
  8. package/dist/MsaViewPanel/model.js +17 -39
  9. package/dist/MsaViewPanel/pairwiseAlignment.js +2 -9
  10. package/dist/MsaViewPanel/structureConnection.d.ts +0 -6
  11. package/dist/MsaViewPanel/structureConnection.js +0 -16
  12. package/dist/MsaViewPanel/structureConnection.test.js +1 -51
  13. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.d.ts +1 -0
  14. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js +92 -0
  15. package/dist/jbrowse-plugin-msaview.umd.production.min.js +30 -30
  16. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  17. package/dist/utils/domainCache.d.ts +8 -0
  18. package/dist/utils/domainCache.js +28 -0
  19. package/dist/utils/eutils.d.ts +3 -0
  20. package/dist/utils/eutils.js +14 -0
  21. package/dist/utils/msa.js +23 -19
  22. package/dist/utils/ncbiBlast.js +23 -25
  23. package/dist/utils/ncbiDomains.d.ts +39 -0
  24. package/dist/utils/ncbiDomains.js +154 -0
  25. package/dist/utils/poll.d.ts +11 -0
  26. package/dist/utils/poll.js +19 -0
  27. package/dist/utils/taxonomyNames.js +2 -1
  28. package/dist/version.d.ts +1 -1
  29. package/dist/version.js +1 -1
  30. package/package.json +17 -14
  31. package/src/LaunchMsaView/util.ts +1 -3
  32. package/src/LaunchMsaViewExtensionPoint/index.ts +3 -0
  33. package/src/MsaViewPanel/afterCreateAutoruns.ts +54 -0
  34. package/src/MsaViewPanel/loadProteinDomains.ts +57 -0
  35. package/src/MsaViewPanel/model.ts +23 -45
  36. package/src/MsaViewPanel/pairwiseAlignment.ts +2 -7
  37. package/src/MsaViewPanel/structureConnection.test.ts +1 -61
  38. package/src/MsaViewPanel/structureConnection.ts +0 -22
  39. package/src/MsaViewPanel/syncGenomeHoverToMsaColumn.test.ts +112 -0
  40. package/src/utils/domainCache.ts +44 -0
  41. package/src/utils/eutils.ts +16 -0
  42. package/src/utils/msa.ts +23 -19
  43. package/src/utils/ncbiBlast.ts +28 -33
  44. package/src/utils/ncbiDomains.ts +171 -0
  45. package/src/utils/poll.ts +28 -0
  46. package/src/utils/taxonomyNames.ts +3 -1
  47. package/src/version.ts +1 -1
package/dist/MsaViewPanel/model.d.ts CHANGED
@@ -1,3 +1,4 @@
1
+ export type { MSAFormat } from 'msa-parsers';
1
2
  import type { ProteinView, StructureConnection } from './structureConnection';
2
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  import type { MafRegion, MsaViewInitState } from './types';
3
4
  import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
@@ -25,11 +26,11 @@ export interface BlastParams {
25
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  * extends
26
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  * - MSAModel from https://github.com/GMOD/react-msaview
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  */
28
- export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
29
+ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
30
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  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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  minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- } & {
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+ }, "height" | "id" | "type" | "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "bgColor" | "colorSchemeName" | "msaFormat" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
33
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  drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
35
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  treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -37,10 +38,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
37
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  showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
39
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  drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
40
- } & {
41
+ }, "bgColor" | "colorSchemeName" | "msaFormat"> & {
41
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  bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
43
- } & {
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+ msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
45
+ }, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
44
46
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
45
47
  showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
46
48
  hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -48,32 +50,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
48
50
  subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
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  drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
51
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  height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
52
55
  rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
53
56
  scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
54
57
  scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
55
58
  colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
56
- 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<{
57
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
58
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
59
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
60
- 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>>;
65
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
66
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
67
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
69
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
70
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
71
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
72
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
73
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
74
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
75
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
76
- }>>, {
59
+ treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
77
60
  locationType: "UriLocation";
78
61
  uri: string;
79
62
  internetAccountId: string | undefined;
@@ -92,51 +75,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
92
75
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
93
76
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
94
77
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
95
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
96
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
97
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
98
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
99
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
100
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
101
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
102
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
103
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
104
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
105
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
106
- }, {}> | ({
107
- locationType: "UriLocation";
108
- uri: string;
109
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
110
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
111
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
112
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
113
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
114
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
115
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
116
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
117
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
118
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
119
- 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<{
120
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
121
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
122
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
123
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
124
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
125
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
126
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
127
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
128
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
129
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
130
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
131
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
132
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
133
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
134
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
135
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
136
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
137
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
138
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
139
- }>>, {
78
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
79
+ msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
140
80
  locationType: "UriLocation";
141
81
  uri: string;
142
82
  internetAccountId: string | undefined;
@@ -155,51 +95,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
155
95
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
156
96
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
157
97
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
158
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
159
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
160
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
161
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
162
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
163
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
164
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
165
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
166
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
167
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
168
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
169
- }, {}> | ({
170
- locationType: "UriLocation";
171
- uri: string;
172
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
173
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
174
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
175
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
176
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
177
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
178
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
179
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
180
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
181
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
182
- 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<{
183
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
184
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
185
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
186
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
187
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
188
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
189
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
190
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
191
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
192
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
193
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
194
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
195
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
196
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
197
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
198
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
199
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
200
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
201
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
202
- }>>, {
98
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
99
+ treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
203
100
  locationType: "UriLocation";
204
101
  uri: string;
205
102
  internetAccountId: string | undefined;
@@ -218,51 +115,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
218
115
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
219
116
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
220
117
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
221
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
222
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
223
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
224
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
225
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
226
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
227
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
228
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
229
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
230
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
231
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
232
- }, {}> | ({
233
- locationType: "UriLocation";
234
- uri: string;
235
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
236
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
237
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
238
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
239
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
240
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
241
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
242
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
243
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
244
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
245
- 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<{
246
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
247
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
248
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
249
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
250
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
251
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
252
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
253
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
254
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
255
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
256
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
257
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
258
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
259
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
260
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
261
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
262
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
263
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
264
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
265
- }>>, {
118
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
119
+ gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
266
120
  locationType: "UriLocation";
267
121
  uri: string;
268
122
  internetAccountId: string | undefined;
@@ -281,30 +135,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
281
135
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
282
136
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
283
137
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
284
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
285
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
286
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
287
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
288
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
289
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
290
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
291
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
292
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
293
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
294
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
295
- }, {}> | ({
296
- locationType: "UriLocation";
297
- uri: string;
298
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
299
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
300
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
301
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
302
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
303
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
304
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
305
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
306
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
307
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
138
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
308
139
  currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
309
140
  collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
310
141
  showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -327,7 +158,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
327
158
  }>, [undefined]>;
328
159
  featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
329
160
  relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
330
- } & {
161
+ highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
162
+ }, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "connectedStructures" | "dataStoreId" | "mafRegion"> & {
331
163
  connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
332
164
  connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
333
165
  blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
@@ -365,11 +197,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
365
197
  } & {
366
198
  setColorSchemeName(name: string): void;
367
199
  setBgColor(arg: boolean): void;
200
+ setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
368
201
  } & {
369
202
  headerHeight: number;
370
203
  status: {
371
204
  msg: string;
372
205
  url?: string;
206
+ onCancel?: () => void;
373
207
  } | undefined;
374
208
  highResScaleFactor: number;
375
209
  loadingMSA: boolean;
@@ -386,7 +220,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
386
220
  descendantNames: string[];
387
221
  } | undefined;
388
222
  highlightedColumns: number[] | undefined;
389
- nref: number;
390
223
  minimapHeight: number;
391
224
  conservationTrackHeight: number;
392
225
  marginLeft: number;
@@ -399,10 +232,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
399
232
  setLoadingMSA(arg: boolean): void;
400
233
  setLoadingTree(arg: boolean): void;
401
234
  setWidth(arg: number): void;
235
+ setHighResScaleFactor(arg: number): void;
402
236
  setHeight(height: number): void;
403
237
  setError(error?: unknown): void;
404
238
  setMousePos(col?: number, row?: number): void;
405
- setHoveredTreeNode(nodeId?: string): void;
406
239
  setHighlightedColumns(columns?: number[]): void;
407
240
  setShowDomains(arg: boolean): void;
408
241
  setSubFeatureRows(arg: boolean): void;
@@ -434,16 +267,28 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
434
267
  } & {
435
268
  extraViewMenuItems(): never[];
436
269
  readonly colorScheme: Record<string, string>;
437
- readonly header: Record<string, unknown>;
270
+ readonly header: Record<string, unknown> | {
271
+ info: string;
272
+ version: string | undefined;
273
+ } | {
274
+ General: Record<string, string[]>;
275
+ Accessions: {
276
+ [k: string]: string | undefined;
277
+ };
278
+ Dbxref: {
279
+ [k: string]: string;
280
+ };
281
+ };
438
282
  readonly alignmentNames: string[];
439
283
  readonly noTree: boolean;
440
284
  readonly noDomains: boolean;
441
285
  menuItems(): never[];
442
286
  readonly treeMetadata: any;
443
- readonly MSA: import("react-msaview").MSAParserType | null;
287
+ readonly MSA: import("msa-parsers").MSAParserType | null;
444
288
  readonly numColumns: number;
445
289
  readonly tree: import("react-msaview").NodeWithIds;
446
290
  readonly rowNames: string[];
291
+ readonly rowNamesSet: Map<string, number>;
447
292
  readonly mouseOverRowName: string | undefined;
448
293
  readonly hoveredInsertion: {
449
294
  rowName: string;
@@ -462,9 +307,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
462
307
  readonly rows: [string, string][];
463
308
  readonly numRows: number;
464
309
  readonly rowMap: Map<string, string>;
465
- readonly columns: {
466
- [k: string]: string;
467
- };
310
+ readonly columns: Map<string, string>;
468
311
  readonly columns2d: string[];
469
312
  readonly fontSize: number;
470
313
  readonly colStats: Record<string, number>[];
@@ -479,22 +322,27 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
479
322
  readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
480
323
  readonly totalHeight: number;
481
324
  readonly leaves: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>[];
325
+ readonly maxBranchLength: number;
326
+ readonly maxDepthToLeaf: number;
482
327
  readonly allBranchesLength0: boolean;
483
328
  readonly showBranchLenEffective: boolean;
484
329
  } & {
485
330
  readonly totalWidth: number;
486
331
  } & {
487
- readonly dataInitialized: boolean | "" | undefined;
332
+ readonly dataInitialized: boolean;
488
333
  readonly blocksX: number[];
489
334
  readonly blocksY: number[];
490
335
  } & {
491
336
  readonly blocks2d: (readonly [number, number])[];
492
337
  readonly isLoading: boolean;
493
338
  readonly maxScrollX: number;
339
+ readonly maxScrollY: number;
494
340
  readonly showMsaLetters: boolean;
495
341
  readonly showTreeText: boolean;
496
342
  } & {
497
343
  setDrawMsaLetters(arg: boolean): void;
344
+ setScrollZoom(arg: boolean): void;
345
+ setHoveredTreeNode(nodeId?: string): void;
498
346
  calculateNeighborJoiningTreeFromMSA(): void;
499
347
  resetZoom(): void;
500
348
  zoomOutHorizontal(): void;
@@ -503,8 +351,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
503
351
  zoomOutVertical(): void;
504
352
  zoomIn(): void;
505
353
  zoomOut(): void;
354
+ zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
506
355
  doScrollY(deltaY: number): void;
507
- setInterProAnnotations(data: Record<string, import("react-msaview").InterProScanResults>): void;
356
+ setDomains(data?: Record<string, import("react-msaview").InterProScanResults>): void;
508
357
  applyGFFText(gffText: string): void;
509
358
  doScrollX(deltaX: number): void;
510
359
  setScrollX(n: number): void;
@@ -512,8 +361,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
512
361
  setStatus(status?: {
513
362
  msg: string;
514
363
  url?: string;
364
+ onCancel?: () => void;
515
365
  }): void;
516
366
  } & {
367
+ readonly labelWidthMap: Map<string, number>;
517
368
  readonly labelsWidth: number;
518
369
  readonly secondaryStructureConsensus: string | undefined;
519
370
  readonly seqConsensus: string | undefined;
@@ -521,7 +372,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
521
372
  readonly tracks: import("react-msaview").BasicTrack[];
522
373
  readonly turnedOnTracks: import("react-msaview").BasicTrack[];
523
374
  readonly showHorizontalScrollbar: boolean;
524
- readonly rowNamesSet: Map<string, number>;
525
375
  visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
526
376
  visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
527
377
  visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
@@ -529,12 +379,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
529
379
  seqPosToGlobalCol(rowName: string, seqPos: number): number;
530
380
  seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
531
381
  } & {
532
- readonly hoveredCell: {
533
- rowName: string;
534
- col: number;
535
- base: string | undefined;
536
- seqPos: number | undefined;
537
- } | undefined;
538
382
  readonly msaAreaHeight: number;
539
383
  readonly totalTrackAreaHeight: number;
540
384
  readonly tidyInterProAnnotationTypes: Map<string, {
@@ -595,9 +439,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
595
439
  theme: import("@mui/material").Theme;
596
440
  includeMinimap?: boolean;
597
441
  includeTracks?: boolean;
598
- exportType: string;
442
+ exportType: "entire" | "viewport";
599
443
  }): Promise<void>;
600
- incrementRef(): void;
601
444
  initFilter(arg: string): void;
602
445
  setFilter(arg: string, flag: boolean): void;
603
446
  fit(): void;
@@ -610,6 +453,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
610
453
  error: unknown;
611
454
  loadingStoredData: boolean;
612
455
  isStoringData: boolean;
456
+ domainsRequested: boolean;
613
457
  } & {
614
458
  /**
615
459
  * #method
@@ -641,15 +485,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
641
485
  proteinView: ProteinView;
642
486
  })[];
643
487
  } & {
644
- /**
645
- * #getter
646
- */
647
- readonly structureHoverCol: number | undefined;
648
- } & {
649
- /**
650
- * #getter
651
- */
652
- readonly mouseCol2: number | undefined;
653
488
  /**
654
489
  * #getter
655
490
  */
@@ -703,6 +538,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
703
538
  * #action
704
539
  */
705
540
  setIsStoringData(arg: boolean): void;
541
+ /**
542
+ * #action
543
+ */
544
+ setDomainsRequested(arg: boolean): void;
706
545
  /**
707
546
  * #action
708
547
  */
@@ -741,11 +580,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
741
580
  })[];
742
581
  } & {
743
582
  afterCreate(): void;
744
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
745
- id: string;
746
- displayName: string | undefined;
747
- minimized: boolean;
748
- } & import("@jbrowse/mobx-state-tree").NonEmptyObject & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
583
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
584
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
585
+ displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
586
+ minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
587
+ }> & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
749
588
  drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
750
589
  labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
751
590
  treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -753,10 +592,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
753
592
  showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
754
593
  drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
755
594
  drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
756
- } & {
595
+ }, "bgColor" | "colorSchemeName" | "msaFormat"> & {
757
596
  bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
758
597
  colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
759
- } & {
598
+ msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
599
+ }, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
760
600
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
761
601
  showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
762
602
  hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -764,32 +604,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
764
604
  subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
765
605
  type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
766
606
  drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
607
+ scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
767
608
  height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
768
609
  rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
769
610
  scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
770
611
  scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
771
612
  colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
772
- 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<{
773
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
774
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
775
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
776
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
777
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
778
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
779
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
780
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
781
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
782
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
783
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
784
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
785
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
786
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
787
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
788
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
789
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
790
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
791
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
792
- }>>, {
613
+ treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
793
614
  locationType: "UriLocation";
794
615
  uri: string;
795
616
  internetAccountId: string | undefined;
@@ -808,51 +629,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
808
629
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
809
630
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
810
631
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
811
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
812
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
813
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
814
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
815
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
816
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
817
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
818
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
819
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
820
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
821
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
822
- }, {}> | ({
823
- locationType: "UriLocation";
824
- uri: string;
825
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
826
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
827
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
828
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
829
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
830
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
831
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
832
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
833
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
834
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
835
- 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<{
836
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
837
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
838
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
839
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
840
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
841
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
842
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
843
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
844
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
845
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
846
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
847
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
848
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
849
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
850
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
851
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
852
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
853
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
854
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
855
- }>>, {
632
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
633
+ msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
856
634
  locationType: "UriLocation";
857
635
  uri: string;
858
636
  internetAccountId: string | undefined;
@@ -871,51 +649,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
871
649
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
872
650
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
873
651
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
874
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
875
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
876
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
877
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
878
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
879
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
880
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
881
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
882
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
883
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
884
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
885
- }, {}> | ({
886
- locationType: "UriLocation";
887
- uri: string;
888
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
889
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
890
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
891
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
892
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
893
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
894
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
895
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
896
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
897
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
898
- 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<{
899
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
900
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
901
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
902
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
903
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
904
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
905
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
906
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
907
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
908
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
909
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
910
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
911
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
912
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
913
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
914
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
915
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
916
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
917
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
918
- }>>, {
652
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
653
+ treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
919
654
  locationType: "UriLocation";
920
655
  uri: string;
921
656
  internetAccountId: string | undefined;
@@ -934,51 +669,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
934
669
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
935
670
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
936
671
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
937
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
938
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
939
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
940
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
941
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
942
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
943
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
944
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
945
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
946
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
947
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
948
- }, {}> | ({
949
- locationType: "UriLocation";
950
- uri: string;
951
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
952
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
953
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
954
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
955
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
956
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
957
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
958
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
959
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
960
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
961
- 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<{
962
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
963
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
964
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
965
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
966
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
967
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
968
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
969
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
970
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
971
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
972
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
973
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
974
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
975
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
976
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
977
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
978
- }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
979
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
980
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
981
- }>>, {
672
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
673
+ gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
982
674
  locationType: "UriLocation";
983
675
  uri: string;
984
676
  internetAccountId: string | undefined;
@@ -997,30 +689,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
997
689
  }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
998
690
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
999
691
  localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1000
- }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1001
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
1002
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1003
- blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1004
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1005
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
1006
- name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1007
- handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1008
- }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
1009
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1010
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1011
- }, {}> | ({
1012
- locationType: "UriLocation";
1013
- uri: string;
1014
- } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
1015
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
1016
- uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1017
- baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1018
- internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1019
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
1020
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1021
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1022
- }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1023
- }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
692
+ }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1024
693
  currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
1025
694
  collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1026
695
  showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1043,6 +712,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1043
712
  }>, [undefined]>;
1044
713
  featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
1045
714
  relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
715
+ highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
1046
716
  }>, symbol> & import("@jbrowse/mobx-state-tree")._NotCustomized>;
1047
717
  export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
1048
718
  export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;