jbrowse-plugin-graphgenomeviewer 1.0.0 → 3.0.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (283) hide show
  1. package/LICENSE +674 -0
  2. package/README.md +202 -24
  3. package/dist/chunks/AddTrackWorkflow-Y3OBHM33.js +2 -0
  4. package/dist/chunks/AddTrackWorkflow-Y3OBHM33.js.map +7 -0
  5. package/dist/chunks/GbzBaseSyntenyAdapter-EFIOI2SN.js +8 -0
  6. package/dist/chunks/GbzBaseSyntenyAdapter-EFIOI2SN.js.map +7 -0
  7. package/dist/chunks/GraphGenomeView-UD5WCV3Q.js +14 -0
  8. package/dist/chunks/GraphGenomeView-UD5WCV3Q.js.map +7 -0
  9. package/dist/chunks/MinigraphBubbleAdapter-B75VQK7T.js +2 -0
  10. package/dist/chunks/MinigraphBubbleAdapter-B75VQK7T.js.map +7 -0
  11. package/dist/chunks/RgfaTabixAdapter-IT7I5RR3.js +3 -0
  12. package/dist/chunks/RgfaTabixAdapter-IT7I5RR3.js.map +7 -0
  13. package/dist/chunks/bandage-layout-FIOZ7B3E.js +1660 -0
  14. package/dist/chunks/bandage-layout-FIOZ7B3E.js.map +7 -0
  15. package/dist/chunks/chunk-D7XFR2IV.js +2 -0
  16. package/dist/chunks/chunk-D7XFR2IV.js.map +7 -0
  17. package/dist/chunks/chunk-F4C3BEPV.js +2 -0
  18. package/dist/chunks/chunk-F4C3BEPV.js.map +7 -0
  19. package/dist/chunks/chunk-FCWXYIFC.js +2 -0
  20. package/dist/chunks/chunk-FCWXYIFC.js.map +7 -0
  21. package/dist/chunks/chunk-FY3BTKY4.js +2 -0
  22. package/dist/chunks/chunk-FY3BTKY4.js.map +7 -0
  23. package/dist/chunks/chunk-J4OLMLS5.js +2 -0
  24. package/dist/chunks/chunk-J4OLMLS5.js.map +7 -0
  25. package/dist/chunks/chunk-JCG7RLMB.js +2 -0
  26. package/dist/chunks/chunk-JCG7RLMB.js.map +7 -0
  27. package/dist/chunks/chunk-KWAXLUPQ.js +2 -0
  28. package/dist/chunks/chunk-KWAXLUPQ.js.map +7 -0
  29. package/dist/chunks/chunk-LGKM2PZH.js +2 -0
  30. package/dist/chunks/chunk-LGKM2PZH.js.map +7 -0
  31. package/dist/chunks/chunk-TN6FK5UD.js +2 -0
  32. package/dist/chunks/chunk-TN6FK5UD.js.map +7 -0
  33. package/dist/chunks/chunk-X3X74OGB.js +2 -0
  34. package/dist/chunks/chunk-X3X74OGB.js.map +7 -0
  35. package/dist/chunks/chunk-XEJ47DLD.js +2 -0
  36. package/dist/chunks/chunk-XEJ47DLD.js.map +7 -0
  37. package/dist/chunks/chunk-ZNGDWZ6Z.js +2 -0
  38. package/dist/chunks/chunk-ZNGDWZ6Z.js.map +7 -0
  39. package/dist/chunks/executeDiagonalize-XMPEDHVZ.js +2 -0
  40. package/dist/chunks/executeDiagonalize-XMPEDHVZ.js.map +7 -0
  41. package/dist/jbrowse-plugin-graphgenomeviewer.esm.js +3 -0
  42. package/dist/jbrowse-plugin-graphgenomeviewer.esm.js.map +7 -0
  43. package/package.json +94 -49
  44. package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.test.ts +427 -0
  45. package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts +461 -0
  46. package/src/GbzBaseSyntenyAdapter/configSchema.ts +181 -0
  47. package/src/GbzBaseSyntenyAdapter/index.ts +27 -0
  48. package/src/GbzBaseSyntenyAdapter/test_data/micb-kir3dl1.gbz.db +0 -0
  49. package/src/GbzBaseSyntenyAdapter/test_data/micb-kir3dl1.haplotype-index.db +0 -0
  50. package/src/GetSubgraph.test.ts +193 -0
  51. package/src/GetSubgraph.ts +93 -0
  52. package/src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx +167 -0
  53. package/src/GraphAddTrackWorkflow/buildTrackConfig.test.ts +150 -0
  54. package/src/GraphAddTrackWorkflow/buildTrackConfig.ts +114 -0
  55. package/src/GraphAddTrackWorkflow/index.ts +20 -0
  56. package/src/GraphComputeLayout.ts +46 -0
  57. package/src/GraphGenomeView/anchoredNodes.ts +101 -0
  58. package/src/GraphGenomeView/bubbleSpreads.ts +102 -0
  59. package/src/GraphGenomeView/bubbles/bubbleHalos.test.ts +58 -0
  60. package/src/GraphGenomeView/bubbles/bubbleHalos.ts +149 -0
  61. package/src/GraphGenomeView/bubbles/bubbleRoutes.test.ts +141 -0
  62. package/src/GraphGenomeView/bubbles/bubblesFromGraph.test.ts +239 -0
  63. package/src/GraphGenomeView/bubbles/bubblesFromGraph.ts +210 -0
  64. package/src/GraphGenomeView/bubbles/classifyBubble.test.ts +172 -0
  65. package/src/GraphGenomeView/bubbles/classifyBubble.ts +138 -0
  66. package/src/GraphGenomeView/bubbles/popBubble.test.ts +73 -0
  67. package/src/GraphGenomeView/bubbles/popBubble.ts +26 -0
  68. package/src/GraphGenomeView/colorSchemes.ts +36 -0
  69. package/src/GraphGenomeView/components/BubbleHalos.tsx +162 -0
  70. package/src/GraphGenomeView/components/BubbleOverlay.tsx +181 -0
  71. package/src/GraphGenomeView/components/ColorSchemeSelect.tsx +41 -0
  72. package/src/GraphGenomeView/components/GenePins.tsx +107 -0
  73. package/src/GraphGenomeView/components/GraphCanvas.tsx +759 -0
  74. package/src/GraphGenomeView/components/GraphGenomeView.test.tsx +77 -0
  75. package/src/GraphGenomeView/components/GraphGenomeView.tsx +18 -17
  76. package/src/GraphGenomeView/components/GraphLoadStatus.tsx +84 -0
  77. package/src/GraphGenomeView/components/GraphSettingsDialog.tsx +327 -0
  78. package/src/GraphGenomeView/components/GraphStats.tsx +82 -0
  79. package/src/GraphGenomeView/components/GraphToolbar.tsx +84 -0
  80. package/src/GraphGenomeView/components/ImportForm.tsx +124 -0
  81. package/src/GraphGenomeView/components/LabelChip.tsx +65 -0
  82. package/src/GraphGenomeView/components/LayoutSelect.tsx +56 -0
  83. package/src/GraphGenomeView/components/RepeatSelect.tsx +51 -0
  84. package/src/GraphGenomeView/components/SettingsMenu.tsx +82 -0
  85. package/src/GraphGenomeView/components/SubgraphContextSelect.tsx +75 -0
  86. package/src/GraphGenomeView/components/SubgraphHaplotypesField.tsx +86 -0
  87. package/src/GraphGenomeView/components/WalkRowsOverlay.tsx +252 -0
  88. package/src/GraphGenomeView/components/WalkSelect.tsx +51 -0
  89. package/src/GraphGenomeView/components/overlayLabels.test.ts +56 -0
  90. package/src/GraphGenomeView/components/overlayLabels.ts +75 -0
  91. package/src/GraphGenomeView/deletionEdges.test.ts +198 -0
  92. package/src/GraphGenomeView/deletionEdges.ts +217 -0
  93. package/src/GraphGenomeView/genes/geneFeatures.ts +107 -0
  94. package/src/GraphGenomeView/genes/genePins.ts +130 -0
  95. package/src/GraphGenomeView/genes/genes.test.ts +153 -0
  96. package/src/GraphGenomeView/gfa/gfaConverter.test.ts +394 -0
  97. package/src/GraphGenomeView/gfa/gfaConverter.ts +235 -0
  98. package/src/GraphGenomeView/graphLabels.budget.test.ts +36 -0
  99. package/src/GraphGenomeView/graphLabels.test.ts +548 -0
  100. package/src/GraphGenomeView/graphLabels.ts +640 -0
  101. package/src/GraphGenomeView/index.ts +29 -7
  102. package/src/GraphGenomeView/laneRamp.test.ts +97 -0
  103. package/src/GraphGenomeView/laneRamp.ts +87 -0
  104. package/src/GraphGenomeView/launchKeys.test.ts +63 -0
  105. package/src/GraphGenomeView/layout/anchoredLayout.test.ts +213 -0
  106. package/src/GraphGenomeView/layout/anchoredLayout.ts +80 -0
  107. package/src/GraphGenomeView/layout/bubbleCrossing.test.ts +190 -0
  108. package/src/GraphGenomeView/layout/drawnScale.ts +199 -0
  109. package/src/GraphGenomeView/layout/mergeRuns.test.ts +100 -0
  110. package/src/GraphGenomeView/layout/mergeRuns.ts +203 -0
  111. package/src/GraphGenomeView/layout/orderedLayout.test.ts +212 -0
  112. package/src/GraphGenomeView/layout/orderedLayout.ts +396 -0
  113. package/src/GraphGenomeView/layout/orientToReference.test.ts +110 -0
  114. package/src/GraphGenomeView/layout/orientToReference.ts +79 -0
  115. package/src/GraphGenomeView/layout/placeOffReference.ts +147 -0
  116. package/src/GraphGenomeView/layout/referenceSeeds.test.ts +79 -0
  117. package/src/GraphGenomeView/layout/referenceSeeds.ts +89 -0
  118. package/src/GraphGenomeView/layout/rowSpacing.ts +5 -0
  119. package/src/GraphGenomeView/layout/sampleRowLayout.test.ts +318 -0
  120. package/src/GraphGenomeView/layout/sampleRowLayout.ts +134 -0
  121. package/src/GraphGenomeView/layout/variantMapLayout.test.ts +59 -0
  122. package/src/GraphGenomeView/layout/variantMapLayout.ts +20 -0
  123. package/src/GraphGenomeView/layout/walkRowLayout.ts +54 -0
  124. package/src/GraphGenomeView/layout/walkRows.test.ts +178 -0
  125. package/src/GraphGenomeView/layout/walkRows.ts +177 -0
  126. package/src/GraphGenomeView/layoutModes.ts +131 -0
  127. package/src/GraphGenomeView/model.test.ts +2696 -0
  128. package/src/GraphGenomeView/model.ts +2672 -94
  129. package/src/GraphGenomeView/nodeWidths.ts +67 -0
  130. package/src/GraphGenomeView/pathAnchoring.test.ts +252 -0
  131. package/src/GraphGenomeView/pathAnchoring.ts +164 -0
  132. package/src/GraphGenomeView/pathColors.test.ts +83 -0
  133. package/src/GraphGenomeView/pathColors.ts +122 -0
  134. package/src/GraphGenomeView/referenceSpan.test.ts +84 -0
  135. package/src/GraphGenomeView/referenceSpan.ts +133 -0
  136. package/src/GraphGenomeView/renderPasses.bench.ts +172 -0
  137. package/src/GraphGenomeView/renderPipeline.test.ts +226 -0
  138. package/src/GraphGenomeView/renderer/Canvas2DRenderer.test.ts +205 -0
  139. package/src/GraphGenomeView/renderer/Canvas2DRenderer.ts +246 -0
  140. package/src/GraphGenomeView/renderer/GeometryBuilder.test.ts +723 -0
  141. package/src/GraphGenomeView/renderer/GeometryBuilder.ts +882 -0
  142. package/src/GraphGenomeView/renderer/GraphRenderer.ts +13 -0
  143. package/src/GraphGenomeView/renderer/colorBits.ts +43 -0
  144. package/src/GraphGenomeView/renderer/recordingCanvas.ts +64 -0
  145. package/src/GraphGenomeView/renderer/types.ts +84 -0
  146. package/src/GraphGenomeView/renderer/walkFade.test.ts +100 -0
  147. package/src/GraphGenomeView/repeats/repeatFeatures.test.ts +114 -0
  148. package/src/GraphGenomeView/repeats/repeatFeatures.ts +202 -0
  149. package/src/GraphGenomeView/repeats/test_data/abca7_trgt_walks.json +575 -0
  150. package/src/GraphGenomeView/repeats/walkCalls.test.ts +127 -0
  151. package/src/GraphGenomeView/repeats/walkCalls.ts +132 -0
  152. package/src/GraphGenomeView/stress.test.ts +214 -0
  153. package/src/GraphGenomeView/subgraphLoad.test.ts +245 -0
  154. package/src/GraphGenomeView/types.ts +141 -0
  155. package/src/GraphGenomeView/util/SpatialIndex.test.ts +73 -0
  156. package/src/GraphGenomeView/util/SpatialIndex.ts +312 -0
  157. package/src/GraphGenomeView/util/edgeCurves.test.ts +93 -0
  158. package/src/GraphGenomeView/util/edgeCurves.ts +94 -0
  159. package/src/GraphGenomeView/util/geometry.test.ts +447 -0
  160. package/src/GraphGenomeView/util/geometry.ts +656 -0
  161. package/src/GraphGenomeView/util/hitDetection.test.ts +307 -0
  162. package/src/GraphGenomeView/util/hitDetection.ts +330 -0
  163. package/src/GraphGenomeView/util/wheelZoom.test.ts +40 -0
  164. package/src/GraphGenomeView/util/wheelZoom.ts +26 -0
  165. package/src/GraphGenomeView/walkHighlight.test.ts +54 -0
  166. package/src/GraphGenomeView/walkHighlight.ts +56 -0
  167. package/src/LaunchGraphGenomeView.ts +46 -0
  168. package/src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.test.ts +139 -0
  169. package/src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.ts +86 -0
  170. package/src/MinigraphBubbleAdapter/bubbleLine.ts +92 -0
  171. package/src/MinigraphBubbleAdapter/configSchema.ts +109 -0
  172. package/src/MinigraphBubbleAdapter/index.ts +22 -0
  173. package/src/MinigraphBubbleAdapter/test_data/hprc_bubbles_mhc.bed.gz +0 -0
  174. package/src/MinigraphBubbleAdapter/test_data/hprc_bubbles_mhc.bed.gz.tbi +0 -0
  175. package/src/RgfaTabixAdapter/RgfaTabixAdapter.test.ts +285 -0
  176. package/src/RgfaTabixAdapter/RgfaTabixAdapter.ts +194 -0
  177. package/src/RgfaTabixAdapter/bubbleTier.test.ts +84 -0
  178. package/src/RgfaTabixAdapter/configSchema.ts +142 -0
  179. package/src/RgfaTabixAdapter/index.ts +24 -0
  180. package/src/RgfaTabixAdapter/rgfaBed.test.ts +158 -0
  181. package/src/RgfaTabixAdapter/rgfaBed.ts +156 -0
  182. package/src/RgfaTabixAdapter/test_data/bubble_tier_chrY.links.bed.gz +0 -0
  183. package/src/RgfaTabixAdapter/test_data/bubble_tier_chrY.links.bed.gz.tbi +0 -0
  184. package/src/RgfaTabixAdapter/test_data/bubble_tier_chrY.segs.bed.gz +0 -0
  185. package/src/RgfaTabixAdapter/test_data/bubble_tier_chrY.segs.bed.gz.tbi +0 -0
  186. package/src/RgfaTabixAdapter/test_data/pggb_ecoli.links.bed.gz +0 -0
  187. package/src/RgfaTabixAdapter/test_data/pggb_ecoli.links.bed.gz.tbi +0 -0
  188. package/src/RgfaTabixAdapter/test_data/pggb_ecoli.segs.bed.gz +0 -0
  189. package/src/RgfaTabixAdapter/test_data/pggb_ecoli.segs.bed.gz.tbi +0 -0
  190. package/src/RgfaTabixAdapter/test_data/rgfa_ecoli.links.bed.gz +0 -0
  191. package/src/RgfaTabixAdapter/test_data/rgfa_ecoli.links.bed.gz.tbi +0 -0
  192. package/src/RgfaTabixAdapter/test_data/rgfa_ecoli.segs.bed.gz +0 -0
  193. package/src/RgfaTabixAdapter/test_data/rgfa_ecoli.segs.bed.gz.tbi +0 -0
  194. package/src/alleleProjection/projectAlleles.test.ts +75 -0
  195. package/src/alleleProjection/projectAlleles.ts +190 -0
  196. package/src/bandage/README.md +121 -0
  197. package/src/bandage/bandage-layout.d.ts +14 -0
  198. package/src/bandage/bandage-layout.js +0 -0
  199. package/src/bandage/native/CMakeLists.txt +45 -0
  200. package/src/bandage/native/include/graph.h +188 -0
  201. package/src/bandage/native/include/graphlayout.h +74 -0
  202. package/src/bandage/native/include/settings.h +86 -0
  203. package/src/bandage/native/include/types.h +56 -0
  204. package/src/bandage/native/src/bindings.cpp +164 -0
  205. package/src/bandage/native/src/graphlayout.cpp +621 -0
  206. package/src/bandage/resizableDecode.test.ts +58 -0
  207. package/src/gfa-core/gfaParser.bench.ts +55 -0
  208. package/src/gfa-core/gfaParser.test.ts +168 -0
  209. package/src/gfa-core/gfaParser.ts +237 -0
  210. package/src/gfa-core/index.ts +10 -0
  211. package/src/hoverSync/GraphNodeHighlight.tsx +62 -0
  212. package/src/hoverSync/graphViewHighlights.test.ts +158 -0
  213. package/src/hoverSync/graphViewHighlights.ts +119 -0
  214. package/src/hoverSync/index.test.tsx +36 -0
  215. package/src/hoverSync/index.tsx +19 -0
  216. package/src/hoverSync/lgvHover.test.ts +202 -0
  217. package/src/hoverSync/lgvHover.ts +136 -0
  218. package/src/index.ts +46 -15
  219. package/src/launchFromGraph/contributors.test.ts +197 -0
  220. package/src/launchFromGraph/contributors.ts +0 -0
  221. package/src/launchFromGraph/graphMenuItems.ts +211 -0
  222. package/src/launchFromGraph/launchFromGraph.test.ts +489 -0
  223. package/src/launchFromGraph/launchFromGraph.ts +265 -0
  224. package/src/launchFromGraph/launchTracks.test.ts +72 -0
  225. package/src/launchFromGraph/launchTracks.ts +50 -0
  226. package/src/launchFromGraph/linearViewTarget.test.ts +82 -0
  227. package/src/launchFromGraph/linearViewTarget.ts +75 -0
  228. package/src/launchFromGraph/syntenyTracks.ts +47 -0
  229. package/src/launchSubgraph/index.ts +152 -0
  230. package/src/launchSubgraph/launchSubgraph.test.ts +264 -0
  231. package/src/launchSubgraph/launchSubgraphView.ts +128 -0
  232. package/src/launchSubgraph/linearViewMenuItems.test.ts +176 -0
  233. package/src/launchSubgraph/linearViewMenuItems.ts +107 -0
  234. package/src/launchSubgraph/multiWayLaunch.test.ts +289 -0
  235. package/src/launchSubgraph/subgraphMenuItems.ts +73 -0
  236. package/src/launchSubgraph/subgraphTracks.test.ts +165 -0
  237. package/src/launchSubgraph/subgraphTracks.ts +151 -0
  238. package/src/launchSubgraph/testEnv.ts +258 -0
  239. package/src/loadBandage.ts +22 -0
  240. package/src/panSNTabix.test.ts +72 -0
  241. package/src/panSNTabix.ts +149 -0
  242. package/src/pansn.ts +106 -0
  243. package/src/pluginName.ts +3 -0
  244. package/src/synteny/ComparativeAdapterBase.ts +77 -0
  245. package/src/synteny/SyntenyFeature.ts +116 -0
  246. package/src/synteny/clipFeatureToRegion.test.ts +329 -0
  247. package/src/synteny/clipFeatureToRegion.ts +167 -0
  248. package/src/version.ts +1 -0
  249. package/dist/GraphGenomeView/components/FeatureDialog.d.ts +0 -5
  250. package/dist/GraphGenomeView/components/FeatureDialog.js +0 -18
  251. package/dist/GraphGenomeView/components/FeatureDialog.js.map +0 -1
  252. package/dist/GraphGenomeView/components/GraphGenomeView.d.ts +0 -6
  253. package/dist/GraphGenomeView/components/GraphGenomeView.js +0 -17
  254. package/dist/GraphGenomeView/components/GraphGenomeView.js.map +0 -1
  255. package/dist/GraphGenomeView/components/GraphPanel.d.ts +0 -6
  256. package/dist/GraphGenomeView/components/GraphPanel.js +0 -17
  257. package/dist/GraphGenomeView/components/GraphPanel.js.map +0 -1
  258. package/dist/GraphGenomeView/components/Header.d.ts +0 -6
  259. package/dist/GraphGenomeView/components/Header.js +0 -59
  260. package/dist/GraphGenomeView/components/Header.js.map +0 -1
  261. package/dist/GraphGenomeView/components/SettingsDialog.d.ts +0 -7
  262. package/dist/GraphGenomeView/components/SettingsDialog.js +0 -24
  263. package/dist/GraphGenomeView/components/SettingsDialog.js.map +0 -1
  264. package/dist/GraphGenomeView/index.d.ts +0 -2
  265. package/dist/GraphGenomeView/index.js +0 -15
  266. package/dist/GraphGenomeView/index.js.map +0 -1
  267. package/dist/GraphGenomeView/model.d.ts +0 -80
  268. package/dist/GraphGenomeView/model.js +0 -96
  269. package/dist/GraphGenomeView/model.js.map +0 -1
  270. package/dist/GraphGenomeView/util.d.ts +0 -1
  271. package/dist/GraphGenomeView/util.js +0 -8
  272. package/dist/GraphGenomeView/util.js.map +0 -1
  273. package/dist/index.d.ts +0 -8
  274. package/dist/index.js +0 -24
  275. package/dist/index.js.map +0 -1
  276. package/dist/jbrowse-plugin-graphgenomeviewer.umd.production.min.js +0 -67
  277. package/dist/jbrowse-plugin-graphgenomeviewer.umd.production.min.js.map +0 -7
  278. package/src/GraphGenomeView/components/FeatureDialog.tsx +0 -51
  279. package/src/GraphGenomeView/components/GraphPanel.tsx +0 -37
  280. package/src/GraphGenomeView/components/Header.tsx +0 -90
  281. package/src/GraphGenomeView/components/SettingsDialog.tsx +0 -71
  282. package/src/GraphGenomeView/util.ts +0 -7
  283. package/src/declare.d.ts +0 -1

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the package file manually.