jbrowse-plugin-msaview 2.3.8 → 2.4.1
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.
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +4 -15
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +11 -13
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
- package/dist/AddHighlightModel/util.d.ts +6 -0
- package/dist/AddHighlightModel/util.js +6 -0
- package/dist/AddHighlightModel/util.js.map +1 -1
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts +2 -0
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +8 -4
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +3 -8
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +7 -10
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +2 -5
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +0 -3
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +4 -4
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +2 -2
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +4 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +2 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +10 -21
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/types.d.ts +1 -0
- package/dist/LaunchMsaView/components/PreLoadedMSA/types.js +4 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map +1 -1
- package/dist/LaunchMsaView/components/types.d.ts +0 -3
- package/dist/LaunchMsaView/components/useFeatureSequence.d.ts +4 -4
- package/dist/LaunchMsaView/components/useFeatureSequence.js +2 -4
- package/dist/LaunchMsaView/components/useFeatureSequence.js.map +1 -1
- package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts +4 -5
- package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +11 -30
- package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +1 -1
- package/dist/MsaViewPanel/afterCreateAutoruns.js +13 -17
- package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
- package/dist/MsaViewPanel/components/ConnectStructureDialog.js +2 -2
- package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -1
- package/dist/MsaViewPanel/components/LoadingBLAST.js +2 -3
- package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +9 -11
- package/dist/MsaViewPanel/model.js +22 -23
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/msaDataStore.d.ts +0 -1
- package/dist/MsaViewPanel/msaDataStore.js +0 -9
- package/dist/MsaViewPanel/msaDataStore.js.map +1 -1
- package/dist/MsaViewPanel/structureConnection.d.ts +6 -4
- package/dist/MsaViewPanel/structureConnection.js +6 -6
- package/dist/MsaViewPanel/structureConnection.js.map +1 -1
- package/dist/MsaViewPanel/structureConnection.test.js +1 -19
- package/dist/MsaViewPanel/structureConnection.test.js.map +1 -1
- package/dist/MsaViewPanel/util.d.ts +11 -0
- package/dist/MsaViewPanel/util.js +11 -3
- package/dist/MsaViewPanel/util.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +25 -27
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/blastCache.d.ts +7 -13
- package/dist/utils/blastCache.js +0 -12
- package/dist/utils/blastCache.js.map +1 -1
- package/dist/utils/msa.d.ts +2 -1
- package/dist/utils/msa.js +0 -3
- package/dist/utils/msa.js.map +1 -1
- package/dist/utils/ncbiBlast.d.ts +3 -2
- package/dist/utils/ncbiBlast.js +7 -7
- package/dist/utils/ncbiBlast.js.map +1 -1
- package/dist/utils/taxonomyNames.js +9 -7
- package/dist/utils/taxonomyNames.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +22 -20
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +8 -25
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +16 -16
- package/src/AddHighlightModel/util.ts +11 -0
- package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +10 -4
- package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +3 -16
- package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +8 -12
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +6 -15
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +0 -9
- package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +6 -6
- package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +7 -0
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +12 -27
- package/src/LaunchMsaView/components/PreLoadedMSA/types.ts +6 -0
- package/src/LaunchMsaView/components/types.ts +0 -3
- package/src/LaunchMsaView/components/useFeatureSequence.ts +1 -7
- package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +10 -37
- package/src/MsaViewPanel/afterCreateAutoruns.ts +15 -17
- package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +2 -2
- package/src/MsaViewPanel/components/LoadingBLAST.tsx +4 -3
- package/src/MsaViewPanel/model.ts +33 -33
- package/src/MsaViewPanel/msaDataStore.ts +0 -9
- package/src/MsaViewPanel/structureConnection.test.ts +0 -21
- package/src/MsaViewPanel/structureConnection.ts +7 -7
- package/src/MsaViewPanel/util.ts +27 -2
- package/src/utils/blastCache.ts +14 -37
- package/src/utils/msa.ts +5 -6
- package/src/utils/ncbiBlast.ts +18 -11
- package/src/utils/taxonomyNames.ts +13 -6
- package/src/version.ts +1 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts +0 -8
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +0 -70
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts +0 -13
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js +0 -12
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts +0 -6
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js +0 -25
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts +0 -2
- package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js +0 -20
- package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts +0 -24
- package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js +0 -2
- package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts +0 -10
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +0 -11
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts +0 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js +0 -2
- package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map +0 -1
- package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +0 -123
- package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts +0 -30
- package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +0 -47
- package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts +0 -22
- package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts +0 -28
- package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +0 -17
- package/src/LaunchMsaView/components/EnsemblGeneTree/util.ts +0 -6
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-
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{"version":3,"file":"structureConnection.test.js","sourceRoot":"","sources":["../../src/MsaViewPanel/structureConnection.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EACL,wBAAwB,EACxB,wBAAwB,GACzB,MAAM,uBAAuB,CAAA;AAE9B,QAAQ,CAAC,0BAA0B,EAAE,GAAG,EAAE;IACxC,IAAI,CAAC,yDAAyD,EAAE,GAAG,EAAE;QACnE,MAAM,GAAG,GAAG,QAAQ,CAAA;QACpB,wCAAwC;QACxC,yDAAyD;QACzD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,SAAS;QAC1D,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,SAAS;QAC1D,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,SAAS;QAC1D,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,SAAS;IAC5D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oCAAoC,EAAE,GAAG,EAAE;QAC9C,MAAM,GAAG,GAAG,QAAQ,CAAA;QACpB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA,CAAC,MAAM;QAC/D,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA,CAAC,MAAM;IACjE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GAAG,KAAK,CAAA;QACjB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACzD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IAC5D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oCAAoC,EAAE,GAAG,EAAE;QAC9C,MAAM,GAAG,GAAG,OAAO,CAAA;QACnB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;IACvD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,qCAAqC,EAAE,GAAG,EAAE;QAC/C,MAAM,GAAG,GAAG,OAAO,CAAA;QACnB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,CAAC,wBAAwB,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IACzD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,0BAA0B,EAAE,GAAG,EAAE;QACpC,MAAM,GAAG,GAAG,KAAK,CAAA;QACjB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IAC1D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,0BAA0B,EAAE,GAAG,EAAE;IACxC,IAAI,CAAC,iCAAiC,EAAE,GAAG,EAAE;QAC3C,MAAM,GAAG,GAAG,QAAQ,CAAA;QACpB,8BAA8B;QAC9B,gCAAgC;QAChC,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;IACvD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uDAAuD,EAAE,GAAG,EAAE;QACjE,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IAC5D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oCAAoC,EAAE,GAAG,EAAE;QAC9C,MAAM,GAAG,GAAG,OAAO,CAAA;QACnB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QACrD,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;IACvD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,CAAC,wBAAwB,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IACzD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,0BAA0B,EAAE,GAAG,EAAE;QACpC,MAAM,GAAG,GAAG,KAAK,CAAA;QACjB,MAAM,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAA;IAC1D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,oEAAoE,EAAE,GAAG,EAAE;IAClF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,GAAG,GAAG,YAAY,CAAA;QACxB,oFAAoF;QACpF,KAAK,IAAI,CAAC,GA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