react-msaview 9.0.0 → 9.1.0

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 (157) hide show
  1. package/README.md +19 -10
  2. package/bundle/index.js +74 -74
  3. package/bundle/index.js.map +4 -4
  4. package/dist/colorSchemes.js +1 -3
  5. package/dist/colorSchemes.js.map +1 -1
  6. package/dist/columnCounts.d.ts +0 -1
  7. package/dist/columnCounts.js +1 -1
  8. package/dist/columnCounts.js.map +1 -1
  9. package/dist/components/Loading.js +5 -5
  10. package/dist/components/Loading.js.map +1 -1
  11. package/dist/components/MSAViewer.d.ts +1891 -4
  12. package/dist/components/MSAViewer.js +144 -201
  13. package/dist/components/MSAViewer.js.map +1 -1
  14. package/dist/components/ResizeHandles.js +3 -2
  15. package/dist/components/ResizeHandles.js.map +1 -1
  16. package/dist/components/Track.js +2 -1
  17. package/dist/components/Track.js.map +1 -1
  18. package/dist/components/controls.d.ts +11 -0
  19. package/dist/components/controls.js +48 -0
  20. package/dist/components/controls.js.map +1 -0
  21. package/dist/components/dialogs/AnnotationFileDialog.js +5 -16
  22. package/dist/components/dialogs/AnnotationFileDialog.js.map +1 -1
  23. package/dist/components/dialogs/ExportSVGDialog.js +5 -7
  24. package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
  25. package/dist/components/dialogs/HelpDialog.d.ts +6 -0
  26. package/dist/components/dialogs/HelpDialog.js +30 -0
  27. package/dist/components/dialogs/HelpDialog.js.map +1 -0
  28. package/dist/components/header/FileMenu.js +33 -7
  29. package/dist/components/header/FileMenu.js.map +1 -1
  30. package/dist/components/header/Header.js +4 -6
  31. package/dist/components/header/Header.js.map +1 -1
  32. package/dist/components/header/TreeSettingsMenu.d.ts +1 -1
  33. package/dist/components/header/TreeSettingsMenu.js +1 -32
  34. package/dist/components/header/TreeSettingsMenu.js.map +1 -1
  35. package/dist/components/header/ZoomControls.js +28 -44
  36. package/dist/components/header/ZoomControls.js.map +1 -1
  37. package/dist/components/header/settingsMenuItems.d.ts +1 -0
  38. package/dist/components/header/settingsMenuItems.js +44 -0
  39. package/dist/components/header/settingsMenuItems.js.map +1 -1
  40. package/dist/components/import/data/seq2.d.ts +0 -1
  41. package/dist/components/import/data/seq2.js +0 -17
  42. package/dist/components/import/data/seq2.js.map +1 -1
  43. package/dist/components/msa/MSACanvas.js +2 -1
  44. package/dist/components/msa/MSACanvas.js.map +1 -1
  45. package/dist/components/msa/MSACanvasBlock.js +2 -5
  46. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  47. package/dist/components/msa/drawFeatureSpans.d.ts +50 -11
  48. package/dist/components/msa/drawFeatureSpans.js +99 -56
  49. package/dist/components/msa/drawFeatureSpans.js.map +1 -1
  50. package/dist/components/msa/msaRaster.d.ts +14 -1
  51. package/dist/components/msa/msaRaster.js +19 -9
  52. package/dist/components/msa/msaRaster.js.map +1 -1
  53. package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts +9 -0
  54. package/dist/components/msa/renderBoxFeatureCanvasBlock.js +19 -8
  55. package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
  56. package/dist/components/msa/renderHighlights.d.ts +2 -2
  57. package/dist/components/msa/renderHighlights.js +2 -3
  58. package/dist/components/msa/renderHighlights.js.map +1 -1
  59. package/dist/components/msa/renderMSAMouseover.js +2 -1
  60. package/dist/components/msa/renderMSAMouseover.js.map +1 -1
  61. package/dist/components/renderCtx.d.ts +1 -1
  62. package/dist/components/rowpanels/renderFeaturePanel.d.ts +5 -1
  63. package/dist/components/rowpanels/renderFeaturePanel.js +12 -5
  64. package/dist/components/rowpanels/renderFeaturePanel.js.map +1 -1
  65. package/dist/components/tracks/drawTracks.d.ts +1 -53
  66. package/dist/components/tracks/drawTracks.js +5 -5
  67. package/dist/components/tracks/drawTracks.js.map +1 -1
  68. package/dist/components/tree/CladeLabels.d.ts +1 -1
  69. package/dist/components/tree/CladeLabels.js +22 -34
  70. package/dist/components/tree/CladeLabels.js.map +1 -1
  71. package/dist/components/tree/cladeBrackets.d.ts +17 -10
  72. package/dist/components/tree/cladeBrackets.js +33 -3
  73. package/dist/components/tree/cladeBrackets.js.map +1 -1
  74. package/dist/components/tree/renderTreeCanvas.js +2 -8
  75. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  76. package/dist/components/tree/renderTreeOverview.js +4 -11
  77. package/dist/components/tree/renderTreeOverview.js.map +1 -1
  78. package/dist/element.js +3 -6
  79. package/dist/element.js.map +1 -1
  80. package/dist/exportLayout.d.ts +39 -0
  81. package/dist/exportLayout.js +78 -0
  82. package/dist/exportLayout.js.map +1 -0
  83. package/dist/headlessRenderEnv.d.ts +12 -39
  84. package/dist/headlessRenderEnv.js +18 -12
  85. package/dist/headlessRenderEnv.js.map +1 -1
  86. package/dist/hierarchy.d.ts +5 -8
  87. package/dist/hierarchy.js +5 -79
  88. package/dist/hierarchy.js.map +1 -1
  89. package/dist/index.d.ts +3 -1
  90. package/dist/index.js +4 -1
  91. package/dist/index.js.map +1 -1
  92. package/dist/measureTextCanvas.d.ts +7 -0
  93. package/dist/measureTextCanvas.js +8 -6
  94. package/dist/measureTextCanvas.js.map +1 -1
  95. package/dist/model/treeModel.d.ts +0 -5
  96. package/dist/model/treeModel.js +0 -7
  97. package/dist/model/treeModel.js.map +1 -1
  98. package/dist/model.d.ts +38 -44
  99. package/dist/model.js +153 -112
  100. package/dist/model.js.map +1 -1
  101. package/dist/renderToSvg.d.ts +2 -7
  102. package/dist/renderToSvg.js +32 -120
  103. package/dist/renderToSvg.js.map +1 -1
  104. package/dist/svgTestUtil.d.ts +12 -20
  105. package/dist/types.d.ts +0 -1
  106. package/dist/version.d.ts +1 -1
  107. package/dist/version.js +1 -1
  108. package/dist/viewerSnapshot.d.ts +169 -0
  109. package/dist/viewerSnapshot.js +100 -0
  110. package/dist/viewerSnapshot.js.map +1 -0
  111. package/package.json +3 -3
  112. package/src/colorSchemes.ts +1 -4
  113. package/src/columnCounts.ts +1 -1
  114. package/src/components/Loading.tsx +19 -12
  115. package/src/components/MSAViewer.tsx +275 -251
  116. package/src/components/ResizeHandles.tsx +9 -2
  117. package/src/components/Track.tsx +2 -1
  118. package/src/components/controls.ts +61 -0
  119. package/src/components/dialogs/AnnotationFileDialog.tsx +5 -21
  120. package/src/components/dialogs/ExportSVGDialog.tsx +8 -19
  121. package/src/components/dialogs/HelpDialog.tsx +79 -0
  122. package/src/components/header/FileMenu.tsx +33 -7
  123. package/src/components/header/Header.tsx +4 -6
  124. package/src/components/header/TreeSettingsMenu.tsx +2 -32
  125. package/src/components/header/ZoomControls.tsx +30 -66
  126. package/src/components/header/settingsMenuItems.ts +59 -0
  127. package/src/components/import/data/seq2.ts +0 -18
  128. package/src/components/msa/MSACanvas.tsx +2 -1
  129. package/src/components/msa/MSACanvasBlock.tsx +2 -6
  130. package/src/components/msa/drawFeatureSpans.ts +160 -79
  131. package/src/components/msa/msaRaster.ts +27 -9
  132. package/src/components/msa/renderBoxFeatureCanvasBlock.ts +39 -24
  133. package/src/components/msa/renderHighlights.ts +2 -3
  134. package/src/components/msa/renderMSAMouseover.ts +5 -1
  135. package/src/components/renderCtx.ts +0 -1
  136. package/src/components/rowpanels/renderFeaturePanel.ts +26 -7
  137. package/src/components/tracks/drawTracks.ts +5 -5
  138. package/src/components/tree/CladeLabels.tsx +30 -54
  139. package/src/components/tree/cladeBrackets.ts +50 -3
  140. package/src/components/tree/renderTreeCanvas.ts +2 -13
  141. package/src/components/tree/renderTreeOverview.ts +7 -14
  142. package/src/element.ts +3 -7
  143. package/src/exportLayout.ts +134 -0
  144. package/src/headlessRenderEnv.ts +24 -11
  145. package/src/hierarchy.ts +5 -88
  146. package/src/index.ts +5 -5
  147. package/src/measureTextCanvas.ts +8 -6
  148. package/src/model/treeModel.ts +0 -7
  149. package/src/model.ts +170 -122
  150. package/src/renderToSvg.tsx +55 -194
  151. package/src/types.ts +0 -1
  152. package/src/version.ts +1 -1
  153. package/src/viewerSnapshot.ts +147 -0
  154. package/dist/components/header/ZoomMenu.d.ts +0 -6
  155. package/dist/components/header/ZoomMenu.js +0 -37
  156. package/dist/components/header/ZoomMenu.js.map +0 -1
  157. package/src/components/header/ZoomMenu.tsx +0 -48
package/README.md CHANGED
@@ -8,11 +8,16 @@ many color schemes, and SVG export.
8
8
 
9
9
  ## Install
10
10
 
11
- The viewer shares mobx, mobx-state-tree and MUI with `@jbrowse/core` and needs
12
- one copy of each, so the install line pins those majors to what your
13
- `@jbrowse/core` depends on. The
14
- [usage & embedding guide](../../USAGE.md#zero-config-component-recommended) has
15
- the install line.
11
+ ```sh
12
+ npm install react-msaview @jbrowse/core@next mobx@7 mobx-react@10 \
13
+ @jbrowse/mobx-state-tree@6 @mui/material@9 @mui/icons-material@9 \
14
+ @emotion/react @emotion/styled react react-dom
15
+ ```
16
+
17
+ The line pins the mobx, mobx-state-tree and MUI majors the viewer shares with
18
+ `@jbrowse/core`, so the app gets one copy of each. The
19
+ [usage guide](https://github.com/GMOD/JBrowseMSA/blob/main/USAGE.md#troubleshooting)
20
+ lists the errors a second copy throws.
16
21
 
17
22
  ## Quick start
18
23
 
@@ -33,15 +38,19 @@ export default function App() {
33
38
 
34
39
  `MSAViewer` creates the model, measures width, and applies the theme for you.
35
40
  For full control, use the `MSAModelF` / `MSAView` model-based API described in
36
- the [usage & embedding guide](../../USAGE.md).
41
+ the
42
+ [usage & embedding guide](https://github.com/GMOD/JBrowseMSA/blob/main/USAGE.md).
37
43
 
38
44
  ## Docs & links
39
45
 
40
- - [Usage & embedding guide](../../USAGE.md): props, model API, UMD bundle, R
46
+ - [Usage & embedding guide](https://github.com/GMOD/JBrowseMSA/blob/main/USAGE.md):
47
+ props, model API, UMD bundle, R
41
48
  - [Live examples](https://gmod.org/JBrowseMSA/examples): runnable snippets
42
- - [Model API reference](apidocs/MsaView.md)
49
+ - [Model API reference](https://github.com/GMOD/JBrowseMSA/blob/main/packages/lib/apidocs/MsaView.md)
43
50
  - [Main repository](https://github.com/GMOD/JBrowseMSA)
44
- - [CLI](../cli/): domain and exon GFFs, plus headless SVG export
45
- - [msa-parsers](../msa-parsers/): standalone parsing library
51
+ - [CLI](https://github.com/GMOD/JBrowseMSA/tree/main/packages/cli): domain and
52
+ exon GFFs, plus headless SVG export
53
+ - [msa-parsers](https://github.com/GMOD/JBrowseMSA/tree/main/packages/msa-parsers):
54
+ standalone parsing library
46
55
  - [ProteinBrowser](https://github.com/GMOD/proteinbrowser): protein analysis
47
56
  suite built on this viewer