jbrowse-plugin-msaview 2.3.5 → 2.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (148) hide show
  1. package/README.md +15 -216
  2. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +4 -15
  3. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
  4. package/dist/AddHighlightModel/MsaToGenomeHighlight.js +5 -8
  5. package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
  6. package/dist/AddHighlightModel/util.d.ts +3 -0
  7. package/dist/AddHighlightModel/util.js +3 -0
  8. package/dist/AddHighlightModel/util.js.map +1 -1
  9. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +3 -8
  10. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
  11. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +26 -14
  12. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
  13. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +16 -7
  14. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -1
  15. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +6 -7
  16. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
  17. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +4 -4
  18. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
  19. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js +8 -1
  20. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map +1 -1
  21. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js +15 -7
  22. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map +1 -1
  23. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js +8 -1
  24. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map +1 -1
  25. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +4 -4
  26. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +2 -2
  27. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
  28. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +4 -0
  29. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +2 -0
  30. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -1
  31. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js +3 -0
  32. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map +1 -1
  33. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +17 -23
  34. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  35. package/dist/LaunchMsaView/components/PreLoadedMSA/types.d.ts +1 -0
  36. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js +4 -1
  37. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map +1 -1
  38. package/dist/LaunchMsaView/components/TabPanel.js +1 -1
  39. package/dist/LaunchMsaView/components/TabPanel.js.map +1 -1
  40. package/dist/LaunchMsaView/components/TranscriptSelector.js +7 -3
  41. package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -1
  42. package/dist/LaunchMsaView/components/types.d.ts +0 -3
  43. package/dist/LaunchMsaView/components/useFeatureSequence.d.ts +4 -4
  44. package/dist/LaunchMsaView/components/useFeatureSequence.js +2 -4
  45. package/dist/LaunchMsaView/components/useFeatureSequence.js.map +1 -1
  46. package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts +4 -5
  47. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +11 -30
  48. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +1 -1
  49. package/dist/MsaViewPanel/afterCreateAutoruns.js +10 -25
  50. package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
  51. package/dist/MsaViewPanel/components/ConnectStructureDialog.js +15 -10
  52. package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -1
  53. package/dist/MsaViewPanel/components/LoadingBLAST.js +2 -3
  54. package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
  55. package/dist/MsaViewPanel/components/MsaViewPanel.js +8 -1
  56. package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
  57. package/dist/MsaViewPanel/model.d.ts +6 -13
  58. package/dist/MsaViewPanel/model.js +15 -26
  59. package/dist/MsaViewPanel/model.js.map +1 -1
  60. package/dist/MsaViewPanel/msaDataStore.d.ts +0 -1
  61. package/dist/MsaViewPanel/msaDataStore.js +0 -9
  62. package/dist/MsaViewPanel/msaDataStore.js.map +1 -1
  63. package/dist/MsaViewPanel/pairwiseAlignment.js +6 -6
  64. package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -1
  65. package/dist/MsaViewPanel/structureConnection.d.ts +28 -4
  66. package/dist/MsaViewPanel/structureConnection.js +10 -6
  67. package/dist/MsaViewPanel/structureConnection.js.map +1 -1
  68. package/dist/MsaViewPanel/structureConnection.test.js +1 -19
  69. package/dist/MsaViewPanel/structureConnection.test.js.map +1 -1
  70. package/dist/jbrowse-plugin-msaview.umd.production.min.js +25 -27
  71. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  72. package/dist/utils/blastCache.d.ts +7 -13
  73. package/dist/utils/blastCache.js +0 -12
  74. package/dist/utils/blastCache.js.map +1 -1
  75. package/dist/utils/msa.d.ts +2 -1
  76. package/dist/utils/msa.js +0 -3
  77. package/dist/utils/msa.js.map +1 -1
  78. package/dist/utils/ncbiBlast.d.ts +3 -2
  79. package/dist/utils/ncbiBlast.js +1 -1
  80. package/dist/utils/ncbiBlast.js.map +1 -1
  81. package/dist/utils/taxonomyNames.js +9 -4
  82. package/dist/utils/taxonomyNames.js.map +1 -1
  83. package/dist/version.d.ts +1 -1
  84. package/dist/version.js +1 -1
  85. package/package.json +19 -19
  86. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +7 -22
  87. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +10 -10
  88. package/src/AddHighlightModel/util.ts +6 -0
  89. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +3 -16
  90. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +30 -19
  91. package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +17 -9
  92. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +14 -18
  93. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +4 -10
  94. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx +9 -1
  95. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.tsx +15 -8
  96. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx +9 -1
  97. package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +6 -6
  98. package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +7 -0
  99. package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts +3 -0
  100. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +23 -29
  101. package/src/LaunchMsaView/components/PreLoadedMSA/types.ts +6 -0
  102. package/src/LaunchMsaView/components/TabPanel.tsx +1 -1
  103. package/src/LaunchMsaView/components/TranscriptSelector.tsx +7 -3
  104. package/src/LaunchMsaView/components/types.ts +0 -3
  105. package/src/LaunchMsaView/components/useFeatureSequence.ts +1 -7
  106. package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +10 -37
  107. package/src/MsaViewPanel/afterCreateAutoruns.ts +13 -39
  108. package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +23 -25
  109. package/src/MsaViewPanel/components/LoadingBLAST.tsx +4 -3
  110. package/src/MsaViewPanel/components/MsaViewPanel.tsx +9 -1
  111. package/src/MsaViewPanel/model.ts +31 -39
  112. package/src/MsaViewPanel/msaDataStore.ts +0 -9
  113. package/src/MsaViewPanel/pairwiseAlignment.ts +6 -6
  114. package/src/MsaViewPanel/structureConnection.test.ts +0 -21
  115. package/src/MsaViewPanel/structureConnection.ts +30 -7
  116. package/src/utils/blastCache.ts +14 -37
  117. package/src/utils/msa.ts +5 -6
  118. package/src/utils/ncbiBlast.ts +9 -5
  119. package/src/utils/taxonomyNames.ts +13 -4
  120. package/src/version.ts +1 -1
  121. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts +0 -8
  122. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +0 -70
  123. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +0 -1
  124. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts +0 -13
  125. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js +0 -12
  126. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map +0 -1
  127. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts +0 -6
  128. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js +0 -25
  129. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +0 -1
  130. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts +0 -2
  131. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js +0 -20
  132. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map +0 -1
  133. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts +0 -24
  134. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js +0 -2
  135. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map +0 -1
  136. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts +0 -10
  137. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +0 -11
  138. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +0 -1
  139. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts +0 -1
  140. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js +0 -2
  141. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map +0 -1
  142. package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +0 -123
  143. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts +0 -30
  144. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +0 -47
  145. package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts +0 -22
  146. package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts +0 -28
  147. package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +0 -17
  148. package/src/LaunchMsaView/components/EnsemblGeneTree/util.ts +0 -6
@@ -1 +1 @@
1
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@@ -1,3 +1,31 @@
1
+ export interface ProteinViewStructure {
2
+ url?: string;
3
+ connectedViewId?: string;
4
+ uniprotId?: string;
5
+ structureSequences?: string[];
6
+ hoverGenomeHighlights?: {
7
+ start: number;
8
+ end: number;
9
+ }[];
10
+ hoverPosition?: {
11
+ structureSeqPos?: number;
12
+ };
13
+ clearHighlightFromExternal?: () => void;
14
+ highlightFromExternal?: (pos: number) => void;
15
+ }
16
+ export interface ProteinView {
17
+ type: 'ProteinView';
18
+ id: string;
19
+ displayName?: string;
20
+ structures: ProteinViewStructure[];
21
+ }
22
+ export declare function isProteinView(view: unknown): view is ProteinView;
23
+ /**
24
+ * Extract all ProteinView instances from a session's views array.
25
+ */
26
+ export declare function getProteinViews(views: {
27
+ type: string;
28
+ }[]): ProteinView[];
1
29
  /**
2
30
  * Represents a connection between the MSA view and a protein structure
3
31
  */
@@ -21,7 +49,3 @@ export declare function gappedToUngappedPosition(sequence: string, gappedPositio
21
49
  * Helper to convert ungapped position to gapped MSA column for a specific row
22
50
  */
23
51
  export declare function ungappedToGappedPosition(sequence: string, ungappedPosition: number): number | undefined;
24
- /**
25
- * Convert Map to plain object for MST frozen storage
26
- */
27
- export declare function mapToRecord(map: Map<number, number>): Record<number, number>;
@@ -1,3 +1,13 @@
1
+ export function isProteinView(view) {
2
+ const v = view;
3
+ return v.type === 'ProteinView' && Array.isArray(v.structures);
4
+ }
5
+ /**
6
+ * Extract all ProteinView instances from a session's views array.
7
+ */
8
+ export function getProteinViews(views) {
9
+ return views.filter(isProteinView);
10
+ }
1
11
  /**
2
12
  * Helper to convert gapped MSA column to ungapped position for a specific row
3
13
  */
@@ -33,10 +43,4 @@ export function ungappedToGappedPosition(sequence, ungappedPosition) {
33
43
  }
34
44
  return undefined;
35
45
  }
36
- /**
37
- * Convert Map to plain object for MST frozen storage
38
- */
39
- export function mapToRecord(map) {
40
- return Object.fromEntries(map);
41
- }
42
46
  //# sourceMappingURL=structureConnection.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"structureConnection.js","sourceRoot":"","sources":["../../src/MsaViewPanel/structureConnection.ts"],"names":[],"mappings":"AAgBA;;GAEG;AACH,MAAM,UAAU,wBAAwB,CACtC,QAAgB,EAChB,cAAsB;IAEtB,IAAI,cAAc,GAAG,CAAC,IAAI,cAAc,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAC;QAC5D,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,QAAQ,GAAG,CAAC,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,EAAE,CAAC,EAAE,EAAE,CAAC;QACxC,IAAI,QAAQ,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACxB,QAAQ,EAAE,CAAA;QACZ,CAAC;IACH,CAAC;IAED,oDAAoD;IACpD,IAAI,QAAQ,CAAC,cAAc,CAAC,KAAK,GAAG,EAAE,CAAC;QACrC,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,wBAAwB,CACtC,QAAgB,EAChB,gBAAwB;IAExB,IAAI,QAAQ,GAAG,CAAC,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,OAAO,KAAK,GAAG,EAAE,CAAC;YACpB,IAAI,QAAQ,KAAK,gBAAgB,EAAE,CAAC;gBAClC,OAAO,CAAC,CAAA;YACV,CAAC;YACD,QAAQ,EAAE,CAAA;QACZ,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,GAAwB;IAClD,OAAO,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;AAChC,CAAC"}
1
+ {"version":3,"file":"structureConnection.js","sourceRoot":"","sources":["../../src/MsaViewPanel/structureConnection.ts"],"names":[],"mappings":"AAkBA,MAAM,UAAU,aAAa,CAAC,IAAa;IACzC,MAAM,CAAC,GAAG,IAA+B,CAAA;IACzC,OAAO,CAAC,CAAC,IAAI,KAAK,aAAa,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAA;AAChE,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,eAAe,CAAC,KAAyB;IACvD,OAAQ,KAAmB,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;AACnD,CAAC;AAkBD;;GAEG;AACH,MAAM,UAAU,wBAAwB,CACtC,QAAgB,EAChB,cAAsB;IAEtB,IAAI,cAAc,GAAG,CAAC,IAAI,cAAc,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAC;QAC5D,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,QAAQ,GAAG,CAAC,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,EAAE,CAAC,EAAE,EAAE,CAAC;QACxC,IAAI,QAAQ,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACxB,QAAQ,EAAE,CAAA;QACZ,CAAC;IACH,CAAC;IAED,oDAAoD;IACpD,IAAI,QAAQ,CAAC,cAAc,CAAC,KAAK,GAAG,EAAE,CAAC;QACrC,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,wBAAwB,CACtC,QAAgB,EAChB,gBAAwB;IAExB,IAAI,QAAQ,GAAG,CAAC,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,OAAO,KAAK,GAAG,EAAE,CAAC;YACpB,IAAI,QAAQ,KAAK,gBAAgB,EAAE,CAAC;gBAClC,OAAO,CAAC,CAAA;YACV,CAAC;YACD,QAAQ,EAAE,CAAA;QACZ,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC"}
@@ -1,5 +1,5 @@
1
1
  import { describe, expect, test } from 'vitest';
2
- import { gappedToUngappedPosition, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
2
+ import { gappedToUngappedPosition, ungappedToGappedPosition, } from './structureConnection';
3
3
  describe('gappedToUngappedPosition', () => {
4
4
  test('returns correct ungapped position for non-gap character', () => {
5
5
  const seq = 'M-KA-A';
@@ -101,22 +101,4 @@ describe('gappedToUngappedPosition and ungappedToGappedPosition are inverses', (
101
101
  }
102
102
  });
103
103
  });
104
- describe('mapToRecord', () => {
105
- test('converts Map to Record', () => {
106
- const map = new Map([
107
- [0, 5],
108
- [1, 10],
109
- [2, 15],
110
- ]);
111
- const record = mapToRecord(map);
112
- expect(record[0]).toBe(5);
113
- expect(record[1]).toBe(10);
114
- expect(record[2]).toBe(15);
115
- });
116
- test('handles empty Map', () => {
117
- const map = new Map();
118
- const record = mapToRecord(map);
119
- expect(Object.keys(record)).toHaveLength(0);
120
- });
121
- });
122
104
  //# sourceMappingURL=structureConnection.test.js.map
@@ -1 +1 @@
1
- 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