@jbrowse/core 4.0.4 → 4.1.1

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 (45) hide show
  1. package/esm/PluginLoader.js +11 -9
  2. package/esm/pluggableElementTypes/RpcMethodType.d.ts +1 -0
  3. package/esm/pluggableElementTypes/RpcMethodType.js +49 -5
  4. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +1 -0
  5. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +5 -2
  6. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +57 -26
  7. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +35 -16
  8. package/esm/pluggableElementTypes/renderers/LayoutSession.js +6 -3
  9. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +4 -1
  10. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.d.ts +2 -1
  11. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +2 -2
  12. package/esm/rpc/methods/CoreRender.js +7 -2
  13. package/esm/ui/FileSelector/FileSelector.d.ts +0 -1
  14. package/esm/ui/FileSelector/FileSelector.js +19 -31
  15. package/esm/ui/FileSelector/LocalFileChooser.js +90 -26
  16. package/esm/ui/FileSelector/SourceTypeSelector.js +18 -33
  17. package/esm/ui/FileSelector/util.d.ts +8 -0
  18. package/esm/ui/FileSelector/util.js +34 -0
  19. package/esm/ui/SnackbarContents.js +4 -4
  20. package/esm/ui/SnackbarModel.d.ts +4 -4
  21. package/esm/ui/SnackbarModel.js +18 -7
  22. package/esm/ui/index.d.ts +1 -1
  23. package/esm/ui/index.js +1 -1
  24. package/esm/util/IntervalTree.d.ts +42 -0
  25. package/esm/util/IntervalTree.js +257 -0
  26. package/esm/util/colord.d.ts +22 -8
  27. package/esm/util/colord.js +227 -10
  28. package/esm/util/crypto.d.ts +7 -0
  29. package/esm/util/crypto.js +536 -0
  30. package/esm/util/fileHandleStore.d.ts +6 -0
  31. package/esm/util/fileHandleStore.js +68 -0
  32. package/esm/util/idMaker.js +9 -1
  33. package/esm/util/index.d.ts +3 -0
  34. package/esm/util/index.js +3 -0
  35. package/esm/util/io/index.js +11 -1
  36. package/esm/util/jexl.js +1 -0
  37. package/esm/util/tracks.d.ts +41 -7
  38. package/esm/util/tracks.js +141 -9
  39. package/esm/util/types/index.d.ts +10 -4
  40. package/esm/util/types/index.js +6 -0
  41. package/esm/util/types/mst.d.ts +17 -0
  42. package/esm/util/types/mst.js +10 -2
  43. package/package.json +350 -15
  44. package/esm/ui/FileSelector/index.d.ts +0 -1
  45. package/esm/ui/FileSelector/index.js +0 -1
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
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  {
2
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  "name": "@jbrowse/core",
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- "version": "4.0.4",
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+ "version": "4.1.1",
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  "type": "module",
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  "description": "JBrowse 2 core libraries used by plugins",
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  "keywords": [
@@ -19,13 +19,7 @@
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  "directory": "packages/core"
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  },
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  "author": "JBrowse Team",
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- "main": "esm/index.js",
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- "types": "esm/index.d.ts",
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  "exports": {
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- ".": {
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- "types": "./esm/index.d.ts",
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- "import": "./esm/index.js"
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- },
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  "./BaseFeatureWidget": {
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  "types": "./esm/BaseFeatureWidget/index.d.ts",
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  "import": "./esm/BaseFeatureWidget/index.js"
@@ -457,6 +451,14 @@
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  "./util/nanoid": {
458
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  "types": "./esm/util/nanoid.d.ts",
459
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  "import": "./esm/util/nanoid.js"
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+ },
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+ "./ReExports/list": {
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+ "types": "./esm/ReExports/list.d.ts",
457
+ "import": "./esm/ReExports/list.js"
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+ },
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+ "./util/fileHandleStore": {
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+ "types": "./esm/util/fileHandleStore.d.ts",
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+ "import": "./esm/util/fileHandleStore.js"
460
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  }
461
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  },
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  "files": [
@@ -468,21 +470,20 @@
468
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  "@emotion/utils": "^1.4.2",
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  "@floating-ui/react": "^0.27.16",
470
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  "@gmod/abortable-promise-cache": "^3.0.4",
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- "@gmod/bgzf-filehandle": "^6.0.10",
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+ "@gmod/bgzf-filehandle": "^6.0.12",
472
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  "@gmod/http-range-fetcher": "^5.0.7",
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  "@jbrowse/jexl": "^3.0.1",
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  "@jbrowse/mobx-state-tree": "^5.5.0",
475
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  "@jbrowse/quick-lru": "^7.3.5",
476
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  "@leeoniya/ufuzzy": "^1.0.19",
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- "@mui/icons-material": "^7.3.6",
478
- "@mui/material": "^7.3.6",
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- "@mui/system": "^7.3.6",
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- "@mui/types": "^7.4.9",
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- "@mui/x-data-grid": "^8.25.0",
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+ "@mui/icons-material": "^7.3.7",
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+ "@mui/material": "^7.3.7",
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+ "@mui/system": "^7.3.7",
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+ "@mui/types": "^7.4.10",
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+ "@mui/x-data-grid": "^8.26.0",
482
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  "@types/file-saver-es": "^2.0.3",
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  "canvas-sequencer-ts": "^3.1.3",
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  "canvas2svg": "^1.0.16",
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- "colord": "^2.9.3",
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  "copy-to-clipboard": "^3.3.3",
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  "deepmerge": "^4.3.1",
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  "detect-node": "^2.1.0",
@@ -491,8 +492,8 @@
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  "fast-deep-equal": "^3.1.3",
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  "file-saver-es": "^2.0.5",
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  "generic-filehandle2": "^2.0.18",
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+ "idb": "^8.0.3",
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  "librpc-web-mod": "^2.1.1",
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- "load-script": "^2.0.0",
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  "mobx": "^6.15.0",
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  "mobx-react": "^9.2.1",
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  "react-draggable": "^4.5.0",
@@ -517,5 +518,339 @@
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  "generate:exports": "node scripts/generateExports.mjs",
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  "build:esm": "tsc -p tsconfig.build.esm.json",
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  "build": "pnpm build:esm"
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+ },
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+ "typesVersions": {
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+ "*": {
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+ "BaseFeatureWidget": [
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+ "esm/BaseFeatureWidget/index.d.ts"
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+ ],
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+ "BaseFeatureWidget/BaseFeatureDetail": [
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+ "esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts"
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+ ],
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+ "BaseFeatureWidget/BaseFeatureDetail/Attributes": [
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+ "esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts"
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+ ],
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+ "BaseFeatureWidget/BaseFeatureDetail/BaseCard": [
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+ "esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts"
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+ ],
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+ "BaseFeatureWidget/BaseFeatureDetail/FeatureDetails": [
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+ "esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts"
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+ ],
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+ "BaseFeatureWidget/BaseFeatureDetail/SimpleField": [
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+ "esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts"
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+ ],
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+ "Plugin": [
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+ "esm/Plugin.d.ts"
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+ ],
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+ "PluginLoader": [
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+ "esm/PluginLoader.d.ts"
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+ ],
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+ "PluginManager": [
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+ "esm/PluginManager.d.ts"
550
+ ],
551
+ "TextSearch/BaseResults": [
552
+ "esm/TextSearch/BaseResults.d.ts"
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+ ],
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+ "TextSearch/TextSearchManager": [
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+ "esm/TextSearch/TextSearchManager.d.ts"
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+ ],
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+ "assemblyManager": [
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+ "esm/assemblyManager/index.d.ts"
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+ ],
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+ "assemblyManager/assembly": [
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+ "esm/assemblyManager/assembly.d.ts"
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+ ],
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+ "assemblyManager/assemblyConfigSchema": [
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+ "esm/assemblyManager/assemblyConfigSchema.d.ts"
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+ ],
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+ "configuration": [
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+ "esm/configuration/index.d.ts"
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+ ],
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+ "data_adapters/BaseAdapter": [
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+ "esm/data_adapters/BaseAdapter/index.d.ts"
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+ ],
572
+ "data_adapters/BaseAdapter/BaseOptions": [
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+ "esm/data_adapters/BaseAdapter/BaseOptions.d.ts"
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+ ],
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+ "data_adapters/BaseAdapter/stats": [
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+ "esm/data_adapters/BaseAdapter/stats.d.ts"
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+ ],
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+ "data_adapters/dataAdapterCache": [
579
+ "esm/data_adapters/dataAdapterCache.d.ts"
580
+ ],
581
+ "pluggableElementTypes": [
582
+ "esm/pluggableElementTypes/index.d.ts"
583
+ ],
584
+ "pluggableElementTypes/AdapterType": [
585
+ "esm/pluggableElementTypes/AdapterType.d.ts"
586
+ ],
587
+ "pluggableElementTypes/ConnectionType": [
588
+ "esm/pluggableElementTypes/ConnectionType.d.ts"
589
+ ],
590
+ "pluggableElementTypes/DisplayType": [
591
+ "esm/pluggableElementTypes/DisplayType.d.ts"
592
+ ],
593
+ "pluggableElementTypes/GlyphType": [
594
+ "esm/pluggableElementTypes/GlyphType.d.ts"
595
+ ],
596
+ "pluggableElementTypes/InternetAccountType": [
597
+ "esm/pluggableElementTypes/InternetAccountType.d.ts"
598
+ ],
599
+ "pluggableElementTypes/RpcMethodType": [
600
+ "esm/pluggableElementTypes/RpcMethodType.d.ts"
601
+ ],
602
+ "pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions": [
603
+ "esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts"
604
+ ],
605
+ "pluggableElementTypes/TextSearchAdapterType": [
606
+ "esm/pluggableElementTypes/TextSearchAdapterType.d.ts"
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+ ],
608
+ "pluggableElementTypes/TrackType": [
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+ "esm/pluggableElementTypes/TrackType.d.ts"
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+ ],
611
+ "pluggableElementTypes/ViewType": [
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+ "esm/pluggableElementTypes/ViewType.d.ts"
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+ ],
614
+ "pluggableElementTypes/WidgetType": [
615
+ "esm/pluggableElementTypes/WidgetType.d.ts"
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+ ],
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+ "pluggableElementTypes/models": [
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+ "esm/pluggableElementTypes/models/index.d.ts"
619
+ ],
620
+ "pluggableElementTypes/models/BaseViewModel": [
621
+ "esm/pluggableElementTypes/models/BaseViewModel.d.ts"
622
+ ],
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+ "pluggableElementTypes/models/baseConnectionConfig": [
624
+ "esm/pluggableElementTypes/models/baseConnectionConfig.d.ts"
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+ ],
626
+ "pluggableElementTypes/renderers/BoxRendererType": [
627
+ "esm/pluggableElementTypes/renderers/BoxRendererType.d.ts"
628
+ ],
629
+ "pluggableElementTypes/renderers/CircularChordRendererType": [
630
+ "esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts"
631
+ ],
632
+ "pluggableElementTypes/renderers/FeatureRendererType": [
633
+ "esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts"
634
+ ],
635
+ "pluggableElementTypes/renderers/LayoutSession": [
636
+ "esm/pluggableElementTypes/renderers/LayoutSession.d.ts"
637
+ ],
638
+ "pluggableElementTypes/renderers/RendererType": [
639
+ "esm/pluggableElementTypes/renderers/RendererType.d.ts"
640
+ ],
641
+ "pluggableElementTypes/renderers/ServerSideRendererType": [
642
+ "esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts"
643
+ ],
644
+ "pluggableElementTypes/renderers/util": [
645
+ "esm/pluggableElementTypes/renderers/util.d.ts"
646
+ ],
647
+ "pluggableElementTypes/renderers/util/serializableFilterChain": [
648
+ "esm/pluggableElementTypes/renderers/util/serializableFilterChain.d.ts"
649
+ ],
650
+ "rpc/RpcManager": [
651
+ "esm/rpc/RpcManager.d.ts"
652
+ ],
653
+ "rpc/coreRpcMethods": [
654
+ "esm/rpc/coreRpcMethods.d.ts"
655
+ ],
656
+ "rpc/methods/util": [
657
+ "esm/rpc/methods/util.d.ts"
658
+ ],
659
+ "ui": [
660
+ "esm/ui/index.d.ts"
661
+ ],
662
+ "ui/AppLogo": [
663
+ "esm/ui/AppLogo.d.ts"
664
+ ],
665
+ "ui/BaseTooltip": [
666
+ "esm/ui/BaseTooltip.d.ts"
667
+ ],
668
+ "ui/CascadingMenuButton": [
669
+ "esm/ui/CascadingMenuButton.d.ts"
670
+ ],
671
+ "ui/ColorPicker": [
672
+ "esm/ui/ColorPicker.d.ts"
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+ ],
674
+ "ui/ConfirmDialog": [
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+ "esm/ui/ConfirmDialog.d.ts"
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+ ],
677
+ "ui/DataGridFlexContainer": [
678
+ "esm/ui/DataGridFlexContainer.d.ts"
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+ ],
680
+ "ui/Dialog": [
681
+ "esm/ui/Dialog.d.ts"
682
+ ],
683
+ "ui/DraggableDialog": [
684
+ "esm/ui/DraggableDialog.d.ts"
685
+ ],
686
+ "ui/DropDownMenu": [
687
+ "esm/ui/DropDownMenu.d.ts"
688
+ ],
689
+ "ui/EditableTypography": [
690
+ "esm/ui/EditableTypography.d.ts"
691
+ ],
692
+ "ui/ErrorBoundary": [
693
+ "esm/ui/ErrorBoundary.d.ts"
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+ ],
695
+ "ui/ErrorMessage": [
696
+ "esm/ui/ErrorMessage.d.ts"
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+ ],
698
+ "ui/ErrorMessageStackTraceDialog": [
699
+ "esm/ui/ErrorMessageStackTraceDialog.d.ts"
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+ ],
701
+ "ui/Icons": [
702
+ "esm/ui/Icons.d.ts"
703
+ ],
704
+ "ui/LoadingEllipses": [
705
+ "esm/ui/LoadingEllipses.d.ts"
706
+ ],
707
+ "ui/Logo": [
708
+ "esm/ui/Logo.d.ts"
709
+ ],
710
+ "ui/Menu": [
711
+ "esm/ui/Menu.d.ts"
712
+ ],
713
+ "ui/ResizeHandle": [
714
+ "esm/ui/ResizeHandle.d.ts"
715
+ ],
716
+ "ui/SanitizedHTML": [
717
+ "esm/ui/SanitizedHTML.d.ts"
718
+ ],
719
+ "ui/Snackbar": [
720
+ "esm/ui/Snackbar.d.ts"
721
+ ],
722
+ "ui/SnackbarModel": [
723
+ "esm/ui/SnackbarModel.d.ts"
724
+ ],
725
+ "ui/colors": [
726
+ "esm/ui/colors.d.ts"
727
+ ],
728
+ "ui/theme": [
729
+ "esm/ui/theme.d.ts"
730
+ ],
731
+ "util": [
732
+ "esm/util/index.d.ts"
733
+ ],
734
+ "util/Base1DUtils": [
735
+ "esm/util/Base1DUtils.d.ts"
736
+ ],
737
+ "util/Base1DViewModel": [
738
+ "esm/util/Base1DViewModel.d.ts"
739
+ ],
740
+ "util/QuickLRU": [
741
+ "esm/util/QuickLRU/index.d.ts"
742
+ ],
743
+ "util/TimeTraveller": [
744
+ "esm/util/TimeTraveller.d.ts"
745
+ ],
746
+ "util/aborting": [
747
+ "esm/util/aborting.d.ts"
748
+ ],
749
+ "util/analytics": [
750
+ "esm/util/analytics.d.ts"
751
+ ],
752
+ "util/blockTypes": [
753
+ "esm/util/blockTypes.d.ts"
754
+ ],
755
+ "util/calculateDynamicBlocks": [
756
+ "esm/util/calculateDynamicBlocks.d.ts"
757
+ ],
758
+ "util/calculateStaticBlocks": [
759
+ "esm/util/calculateStaticBlocks.d.ts"
760
+ ],
761
+ "util/color": [
762
+ "esm/util/color/index.d.ts"
763
+ ],
764
+ "util/colord": [
765
+ "esm/util/colord.d.ts"
766
+ ],
767
+ "util/compositeMap": [
768
+ "esm/util/compositeMap.d.ts"
769
+ ],
770
+ "util/convertCodingSequenceToPeptides": [
771
+ "esm/util/convertCodingSequenceToPeptides.d.ts"
772
+ ],
773
+ "util/flatbush": [
774
+ "esm/util/flatbush/index.d.ts"
775
+ ],
776
+ "util/formatFastaStrings": [
777
+ "esm/util/formatFastaStrings.d.ts"
778
+ ],
779
+ "util/io": [
780
+ "esm/util/io/index.d.ts"
781
+ ],
782
+ "util/io/RemoteFileWithRangeCache": [
783
+ "esm/util/io/RemoteFileWithRangeCache.d.ts"
784
+ ],
785
+ "util/jexlStrings": [
786
+ "esm/util/jexlStrings.d.ts"
787
+ ],
788
+ "util/layouts": [
789
+ "esm/util/layouts/index.d.ts"
790
+ ],
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+ "util/layouts/BaseLayout": [
792
+ "esm/util/layouts/BaseLayout.d.ts"
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+ ],
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+ "util/layouts/GranularRectLayout": [
795
+ "esm/util/layouts/GranularRectLayout.d.ts"
796
+ ],
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+ "util/librpc": [
798
+ "esm/util/librpc.d.ts"
799
+ ],
800
+ "util/mst-reflection": [
801
+ "esm/util/mst-reflection.d.ts"
802
+ ],
803
+ "util/offscreenCanvasPonyfill": [
804
+ "esm/util/offscreenCanvasPonyfill.d.ts"
805
+ ],
806
+ "util/offscreenCanvasUtils": [
807
+ "esm/util/offscreenCanvasUtils.d.ts"
808
+ ],
809
+ "util/parseLineByLine": [
810
+ "esm/util/parseLineByLine.d.ts"
811
+ ],
812
+ "util/range": [
813
+ "esm/util/range.d.ts"
814
+ ],
815
+ "util/rxjs": [
816
+ "esm/util/rxjs.d.ts"
817
+ ],
818
+ "util/simpleFeature": [
819
+ "esm/util/simpleFeature.d.ts"
820
+ ],
821
+ "util/stats": [
822
+ "esm/util/stats.d.ts"
823
+ ],
824
+ "util/stopToken": [
825
+ "esm/util/stopToken.d.ts"
826
+ ],
827
+ "util/tracks": [
828
+ "esm/util/tracks.d.ts"
829
+ ],
830
+ "util/tss-react": [
831
+ "esm/util/tss-react/index.d.ts"
832
+ ],
833
+ "util/types": [
834
+ "esm/util/types/index.d.ts"
835
+ ],
836
+ "util/types/mst": [
837
+ "esm/util/types/mst.d.ts"
838
+ ],
839
+ "util/useMeasure": [
840
+ "esm/util/useMeasure.d.ts"
841
+ ],
842
+ "ui/ReturnToImportFormDialog": [
843
+ "esm/ui/ReturnToImportFormDialog.d.ts"
844
+ ],
845
+ "util/nanoid": [
846
+ "esm/util/nanoid.d.ts"
847
+ ],
848
+ "ReExports/list": [
849
+ "esm/ReExports/list.d.ts"
850
+ ],
851
+ "util/fileHandleStore": [
852
+ "esm/util/fileHandleStore.d.ts"
853
+ ]
854
+ }
520
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  }
521
856
  }
@@ -1 +0,0 @@
1
- export { default } from './FileSelector.tsx';
@@ -1 +0,0 @@
1
- export { default } from "./FileSelector.js";