jbrowse-plugin-msaview 2.2.2 → 2.2.4
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.
- package/CHANGELOG.md +1 -1
- package/README.md +229 -0
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +23 -18
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +23 -13
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
- package/dist/AddHighlightModel/index.js +8 -1
- package/dist/AddHighlightModel/index.js.map +1 -1
- package/dist/AddHighlightModel/util.d.ts +2 -2
- package/dist/BgzipFastaMsaAdapter/configSchema.d.ts +2 -2
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +5 -11
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +1 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +5 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +1 -1
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +16 -16
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +38 -46
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
- package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts +4 -3
- package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +4 -3
- package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.d.ts +9 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +76 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +35 -13
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +6 -12
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +6 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +15 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +12 -34
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/consts.d.ts +1 -0
- package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js +1 -0
- package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js.map +1 -1
- package/dist/LaunchMsaView/components/TabPanel.d.ts +2 -2
- package/dist/LaunchMsaView/components/TranscriptSelector.d.ts +2 -2
- package/dist/LaunchMsaView/components/TranscriptSelector.js +3 -6
- package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -1
- package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +6 -4
- package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +1 -1
- package/dist/LaunchMsaView/components/useTranscriptSelection.d.ts +16 -0
- package/dist/LaunchMsaView/components/useTranscriptSelection.js +31 -0
- package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +1 -0
- package/dist/LaunchMsaView/components/util.d.ts +3 -1
- package/dist/LaunchMsaView/components/util.js +12 -2
- package/dist/LaunchMsaView/components/util.js.map +1 -1
- package/dist/LaunchMsaView/util.d.ts +2 -0
- package/dist/LaunchMsaView/util.js +16 -4
- package/dist/LaunchMsaView/util.js.map +1 -1
- package/dist/LaunchMsaViewExtensionPoint/index.d.ts +2 -0
- package/dist/LaunchMsaViewExtensionPoint/index.js +31 -0
- package/dist/LaunchMsaViewExtensionPoint/index.js.map +1 -0
- package/dist/MsaViewPanel/components/ConnectStructureDialog.d.ts +7 -0
- package/dist/MsaViewPanel/components/ConnectStructureDialog.js +56 -0
- package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -0
- package/dist/MsaViewPanel/components/MsaViewPanel.js +4 -2
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/doLaunchBlast.d.ts +1 -0
- package/dist/MsaViewPanel/doLaunchBlast.js +65 -19
- package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
- package/dist/MsaViewPanel/genomeToMSA.d.ts +6 -0
- package/dist/MsaViewPanel/genomeToMSA.js +38 -8
- package/dist/MsaViewPanel/genomeToMSA.js.map +1 -1
- package/dist/MsaViewPanel/genomeToMSA.test.d.ts +1 -0
- package/dist/MsaViewPanel/genomeToMSA.test.js +244 -0
- package/dist/MsaViewPanel/genomeToMSA.test.js.map +1 -0
- package/dist/MsaViewPanel/model.d.ts +727 -226
- package/dist/MsaViewPanel/model.js +496 -52
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts +10 -2
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.js +26 -27
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map +1 -1
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.d.ts +1 -0
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js +240 -0
- package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js.map +1 -0
- package/dist/MsaViewPanel/msaDataStore.d.ts +14 -0
- package/dist/MsaViewPanel/msaDataStore.js +197 -0
- package/dist/MsaViewPanel/msaDataStore.js.map +1 -0
- package/dist/MsaViewPanel/pairwiseAlignment.d.ts +27 -0
- package/dist/MsaViewPanel/pairwiseAlignment.js +776 -0
- package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -0
- package/dist/MsaViewPanel/pairwiseAlignment.test.d.ts +1 -0
- package/dist/MsaViewPanel/pairwiseAlignment.test.js +112 -0
- package/dist/MsaViewPanel/pairwiseAlignment.test.js.map +1 -0
- package/dist/MsaViewPanel/structureConnection.d.ts +27 -0
- package/dist/MsaViewPanel/structureConnection.js +46 -0
- package/dist/MsaViewPanel/structureConnection.js.map +1 -0
- package/dist/MsaViewPanel/structureConnection.test.d.ts +1 -0
- package/dist/MsaViewPanel/structureConnection.test.js +122 -0
- package/dist/MsaViewPanel/structureConnection.test.js.map +1 -0
- package/dist/MsaViewPanel/types.d.ts +13 -0
- package/dist/MsaViewPanel/types.js +2 -0
- package/dist/MsaViewPanel/types.js.map +1 -0
- package/dist/MsaViewPanel/util.d.ts +7 -0
- package/dist/MsaViewPanel/util.js +10 -0
- package/dist/MsaViewPanel/util.js.map +1 -1
- package/dist/index.d.ts +5 -5
- package/dist/index.js +3 -1
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +39 -90
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/blastCache.d.ts +34 -0
- package/dist/utils/blastCache.js +58 -0
- package/dist/utils/blastCache.js.map +1 -0
- package/dist/utils/fetch.d.ts +1 -1
- package/dist/utils/fetch.js +1 -1
- package/dist/utils/fetch.js.map +1 -1
- package/dist/utils/ncbiBlast.d.ts +1 -5
- package/dist/utils/taxonomyNames.d.ts +5 -0
- package/dist/utils/taxonomyNames.js +79 -0
- package/dist/utils/taxonomyNames.js.map +1 -0
- package/dist/utils/types.d.ts +8 -5
- package/package.json +50 -54
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +37 -21
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +38 -17
- package/src/AddHighlightModel/index.tsx +9 -4
- package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +13 -13
- package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +6 -0
- package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +30 -23
- package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +64 -51
- package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +9 -6
- package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +146 -0
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +53 -22
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +8 -13
- package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +25 -0
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +27 -47
- package/src/LaunchMsaView/components/PreLoadedMSA/consts.ts +1 -0
- package/src/LaunchMsaView/components/TabPanel.tsx +2 -2
- package/src/LaunchMsaView/components/TranscriptSelector.tsx +13 -20
- package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +5 -5
- package/src/LaunchMsaView/components/useTranscriptSelection.ts +48 -0
- package/src/LaunchMsaView/components/util.ts +17 -2
- package/src/LaunchMsaView/index.ts +1 -1
- package/src/LaunchMsaView/util.ts +25 -6
- package/src/LaunchMsaViewExtensionPoint/index.ts +74 -0
- package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +156 -0
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +6 -1
- package/src/MsaViewPanel/doLaunchBlast.ts +83 -23
- package/src/MsaViewPanel/genomeToMSA.test.ts +281 -0
- package/src/MsaViewPanel/genomeToMSA.ts +43 -10
- package/src/MsaViewPanel/model.ts +617 -58
- package/src/MsaViewPanel/msaCoordToGenomeCoord.test.ts +256 -0
- package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +42 -30
- package/src/MsaViewPanel/msaDataStore.ts +236 -0
- package/src/MsaViewPanel/pairwiseAlignment.test.ts +140 -0
- package/src/MsaViewPanel/pairwiseAlignment.ts +818 -0
- package/src/MsaViewPanel/structureConnection.test.ts +143 -0
- package/src/MsaViewPanel/structureConnection.ts +72 -0
- package/src/MsaViewPanel/types.ts +14 -0
- package/src/MsaViewPanel/util.ts +11 -0
- package/src/index.ts +3 -1
- package/src/utils/blastCache.ts +114 -0
- package/src/utils/fetch.ts +1 -1
- package/src/utils/taxonomyNames.ts +111 -0
- package/src/utils/types.ts +9 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.d.ts +0 -5
- package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.js +0 -16
- package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.js.map +0 -1
- package/dist/out.js +0 -55367
- package/src/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.ts +0 -25
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import { getId } from '../../util'
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import type { Feature } from '@jbrowse/core/util'
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// Function to find a valid transcript ID that exists in the MSA list
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export function findValidTranscriptId({
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transcriptsList,
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validMsaList,
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}: {
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transcriptsList: Feature[]
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validMsaList?: string[]
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}) {
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if (!validMsaList || validMsaList.length === 0) {
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return null
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}
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// Try to find a transcript ID that exists in the MSA list
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for (const transcript of transcriptsList) {
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const id = getId(transcript)
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if (id && validMsaList.includes(id)) {
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return id
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}
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}
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return null
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}
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