jbrowse-plugin-msaview 2.1.0 → 2.2.0
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.
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +3 -3
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +3 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
- package/dist/ExternalLink.d.ts +3 -0
- package/dist/ExternalLink.js +11 -0
- package/dist/ExternalLink.js.map +1 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +28 -33
- package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +1 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js +0 -6
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map +1 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts +1 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js +12 -22
- package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +1 -1
- package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts +2 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js +20 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map +1 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts +24 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map +1 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts +10 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +27 -0
- package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +1 -0
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +5 -5
- package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/NcbiBlastPanel.d.ts → ManualMSALoader/ManualMSALoader.d.ts} +2 -2
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +103 -0
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -0
- package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.js.map +1 -1
- package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts +14 -0
- package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +12 -0
- package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map +1 -0
- package/dist/LaunchMsaView/components/{MSALoader/MSALoader.d.ts → NCBIBlastQuery/NCBIBlastAutomaticPanel.d.ts} +4 -2
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +89 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.d.ts +10 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +55 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.d.ts +5 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js +11 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js.map +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.d.ts +7 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js +30 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.d.ts +5 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js +26 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map +1 -0
- package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.d.ts → NCBIBlastQuery/blastLaunchView.d.ts} +2 -1
- package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.js → NCBIBlastQuery/blastLaunchView.js} +3 -6
- package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +1 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +2 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -0
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +17 -16
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/TranscriptSelector.d.ts +10 -0
- package/dist/LaunchMsaView/components/TranscriptSelector.js +45 -0
- package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -0
- package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/calculateProteinSequence.d.ts → calculateProteinSequence.d.ts} +1 -2
- package/dist/LaunchMsaView/components/calculateProteinSequence.js +39 -0
- package/dist/LaunchMsaView/components/calculateProteinSequence.js.map +1 -0
- package/dist/LaunchMsaView/components/fetchSeq.js.map +1 -0
- package/dist/LaunchMsaView/components/types.js +2 -0
- package/dist/LaunchMsaView/components/types.js.map +1 -0
- package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.d.ts → useFeatureSequence.d.ts} +2 -1
- package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.js → useFeatureSequence.js} +12 -1
- package/dist/LaunchMsaView/components/useFeatureSequence.js.map +1 -0
- package/dist/LaunchMsaView/components/util.js.map +1 -0
- package/dist/LaunchMsaView/util.d.ts +5 -1
- package/dist/LaunchMsaView/util.js +15 -1
- package/dist/LaunchMsaView/util.js.map +1 -1
- package/dist/MsaViewPanel/components/LoadingBLAST.d.ts +2 -1
- package/dist/MsaViewPanel/components/LoadingBLAST.js +6 -6
- package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
- package/dist/MsaViewPanel/components/MsaViewPanel.js +1 -1
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/components/RIDLink.d.ts +2 -1
- package/dist/MsaViewPanel/components/RIDLink.js +6 -9
- package/dist/MsaViewPanel/components/RIDLink.js.map +1 -1
- package/dist/MsaViewPanel/doLaunchBlast.js +18 -20
- package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +3 -4
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/ReadOnlyTextField2.d.ts +4 -0
- package/dist/ReadOnlyTextField2.js +20 -0
- package/dist/ReadOnlyTextField2.js.map +1 -0
- package/dist/index.d.ts +15 -0
- package/dist/index.js +17 -0
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +41 -51
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/fetch.d.ts +1 -1
- package/dist/utils/fetch.js.map +1 -1
- package/dist/utils/ncbiBlast.d.ts +2 -2
- package/dist/utils/ncbiBlast.js +29 -15
- package/dist/utils/ncbiBlast.js.map +1 -1
- package/dist/utils/types.d.ts +20 -0
- package/dist/utils/types.js +2 -0
- package/dist/utils/types.js.map +1 -0
- package/package.json +3 -3
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +3 -3
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +2 -1
- package/src/ExternalLink.tsx +15 -0
- package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +39 -55
- package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts +0 -6
- package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +19 -54
- package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts +22 -0
- package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts +28 -0
- package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +29 -0
- package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +9 -5
- package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +219 -0
- package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +34 -0
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +226 -0
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +111 -0
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.tsx +34 -0
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx +82 -0
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx +75 -0
- package/src/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.ts → NCBIBlastQuery/blastLaunchView.ts} +4 -5
- package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +1 -0
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +27 -37
- package/src/LaunchMsaView/components/TranscriptSelector.tsx +99 -0
- package/src/LaunchMsaView/components/{NewNCBIBlastQuery/calculateProteinSequence.ts → calculateProteinSequence.ts} +12 -22
- package/src/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.ts → useFeatureSequence.ts} +16 -2
- package/src/LaunchMsaView/util.ts +22 -2
- package/src/MsaViewPanel/components/LoadingBLAST.tsx +26 -8
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +5 -1
- package/src/MsaViewPanel/components/RIDLink.tsx +8 -8
- package/src/MsaViewPanel/doLaunchBlast.ts +29 -30
- package/src/MsaViewPanel/model.ts +1 -0
- package/src/ReadOnlyTextField2.tsx +33 -0
- package/src/index.ts +23 -0
- package/src/utils/fetch.ts +2 -2
- package/src/utils/ncbiBlast.ts +40 -30
- package/src/utils/types.ts +14 -0
- package/dist/LaunchMsaView/components/MSALoader/MSALoader.js +0 -94
- package/dist/LaunchMsaView/components/MSALoader/MSALoader.js.map +0 -1
- package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.d.ts +0 -1
- package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js +0 -12
- package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js.map +0 -1
- package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.d.ts +0 -9
- package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js +0 -36
- package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js +0 -85
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js +0 -47
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/fetchSeq.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.d.ts +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js +0 -2
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/types.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map +0 -1
- package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.js.map +0 -1
- package/dist/OpenInNewIcon.d.ts +0 -3
- package/dist/OpenInNewIcon.js +0 -8
- package/dist/OpenInNewIcon.js.map +0 -1
- package/src/LaunchMsaView/components/MSALoader/MSALoader.tsx +0 -130
- package/src/LaunchMsaView/components/MSALoader/fetchGeneList.ts +0 -13
- package/src/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.ts +0 -55
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx +0 -171
- package/src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx +0 -1
- package/src/OpenInNewIcon.tsx +0 -14
- /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery → EnsemblGeneTree}/types.js +0 -0
- /package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.d.ts +0 -0
- /package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.js +0 -0
- /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/fetchSeq.d.ts → fetchSeq.d.ts} +0 -0
- /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/fetchSeq.js → fetchSeq.js} +0 -0
- /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/types.d.ts → types.d.ts} +0 -0
- /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/util.d.ts → util.d.ts} +0 -0
- /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/util.js → util.js} +0 -0
- /package/src/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.ts +0 -0
- /package/src/LaunchMsaView/components/{NewNCBIBlastQuery/fetchSeq.ts → fetchSeq.ts} +0 -0
- /package/src/LaunchMsaView/components/{NewNCBIBlastQuery/types.ts → types.ts} +0 -0
- /package/src/LaunchMsaView/components/{NewNCBIBlastQuery/util.ts → util.ts} +0 -0
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import { Feature } from '@jbrowse/core/util';
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import type { Feature } from '@jbrowse/core/util';
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export function getId(val) {
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LaunchMsaView/util.ts"],"names":[],"mappings":"
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LaunchMsaView/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,oBAAoB,CAAA;AAIxC,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAA;IACpD,OAAO,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC;QACnD,CAAC,CAAC,CAAC,OAAO,CAAC;QACX,CAAC,CAAC,oEAAoE;YACpE,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CACrB,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC,CACzD,CAAA;AACP,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,OAAgB;IAClD,MAAM,MAAM,GAAG,GAAG,CAChB,OAAO;SACJ,GAAG,CAAC,aAAa,CAAC;QACnB,EAAE,MAAM,CACN,CAAC,CAAC,EAAE,CAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAwB,EAAE,WAAW,EAAE,KAAK,KAAK,CACpE;SACA,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CACjD,CAAA;IACD,OAAO;QACL,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC;QAC3B,GAAG,EAAE,MAAM,GAAG,CAAC;KAChB,CAAA;AACH,CAAC;AACD,MAAM,UAAU,KAAK,CAAC,GAAa;IACjC,OAAO,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,IAAI,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,GAAa;IACpD,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACjE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAa;IAC9C,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC;YACE,GAAG,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC;YACvC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;SAC1C;aACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,IAAI,CAAC,GAAG,CAAC,CAAA;AAClB,CAAC"}
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@@ -1,6 +1,7 @@
|
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1
1
|
import React from 'react';
|
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2
2
|
import { JBrowsePluginMsaViewModel } from '../model';
|
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3
|
-
declare const LoadingBLAST: ({ model, }: {
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|
+
declare const LoadingBLAST: ({ model, baseUrl, }: {
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model: JBrowsePluginMsaViewModel;
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+
baseUrl: string;
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}) => React.JSX.Element;
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export default LoadingBLAST;
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@@ -12,23 +12,23 @@ const useStyles = makeStyles()(theme => ({
|
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background: theme.palette.background.paper,
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},
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}));
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function RIDError({ rid, error }) {
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+
function RIDError({ baseUrl, rid, error, }) {
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return (React.createElement("div", null,
|
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rid ? React.createElement(RIDLink, { rid: rid }) : null,
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rid ? React.createElement(RIDLink, { rid: rid, baseUrl: baseUrl }) : null,
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React.createElement(ErrorMessage, { error: error })));
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}
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function RIDProgress({ rid, progress }) {
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+
function RIDProgress({ baseUrl, rid, progress, }) {
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const { classes } = useStyles();
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return (React.createElement("div", { className: classes.loading },
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rid ? React.createElement(RIDLink, { rid: rid }) : null,
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rid ? React.createElement(RIDLink, { baseUrl: baseUrl, rid: rid }) : null,
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React.createElement(Typography, null, progress)));
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}
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-
const LoadingBLAST = observer(function LoadingBLAST2({ model, }) {
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+
const LoadingBLAST = observer(function LoadingBLAST2({ model, baseUrl, }) {
|
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|
const { progress, rid, error, processing } = model;
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const { classes } = useStyles();
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return (React.createElement("div", { className: classes.margin },
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React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
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error ? (React.createElement(RIDError, { rid: rid, error: error })) :
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error ? (React.createElement(RIDError, { baseUrl: baseUrl, rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { baseUrl: baseUrl, rid: rid, progress: progress })) : null,
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React.createElement(Typography, null, processing || 'Initializing BLAST query')));
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});
|
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export default LoadingBLAST;
|
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@@ -1 +1 @@
|
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1
|
-
{"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAG1C,OAAO,OAAO,MAAM,WAAW,CAAA;AAE/B,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,EAAE;KACZ;IACD,OAAO,EAAE;QACP,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;KAC3C;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,QAAQ,CAAC,
|
|
1
|
+
{"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAG1C,OAAO,OAAO,MAAM,WAAW,CAAA;AAE/B,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,EAAE;KACZ;IACD,OAAO,EAAE;QACP,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;KAC3C;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,QAAQ,CAAC,EAChB,OAAO,EACP,GAAG,EACH,KAAK,GAKN;IACC,OAAO,CACL;QACG,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,GAAG,EAAE,GAAG,EAAE,OAAO,EAAE,OAAO,GAAI,CAAC,CAAC,CAAC,IAAI;QACrD,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EACnB,OAAO,EACP,GAAG,EACH,QAAQ,GAKT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,OAAO;QAC5B,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,GAAI,CAAC,CAAC,CAAC,IAAI;QACrD,oBAAC,UAAU,QAAE,QAAQ,CAAc,CAC/B,CACP,CAAA;AACH,CAAC;AAED,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAClD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM;QAC5B,oBAAC,eAAe,IAAC,OAAO,EAAC,oBAAoB,EAAC,OAAO,EAAC,IAAI,GAAG;QAC5D,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,QAAQ,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,GAAI,CACvD,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAChE,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,UAAU,QAAE,UAAU,IAAI,0BAA0B,CAAc,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
|
|
@@ -4,7 +4,7 @@ import { MSAView } from 'react-msaview';
|
|
|
4
4
|
import LoadingBLAST from './LoadingBLAST';
|
|
5
5
|
const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
|
|
6
6
|
const { blastParams } = model;
|
|
7
|
-
return (React.createElement("div", null, blastParams ? React.createElement(LoadingBLAST, { model: model }) : React.createElement(MSAView, { model: model })));
|
|
7
|
+
return (React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : (React.createElement(MSAView, { model: model }))));
|
|
8
8
|
});
|
|
9
9
|
export default MsaViewPanel;
|
|
10
10
|
//# sourceMappingURL=MsaViewPanel.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAGvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CACL,iCACG,WAAW,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,
|
|
1
|
+
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAGvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CACL,iCACG,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,GAAI,CAC7D,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
|
|
@@ -1,16 +1,13 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import {
|
|
3
|
-
import
|
|
4
|
-
|
|
5
|
-
function RIDLink({ rid }) {
|
|
2
|
+
import { Typography } from '@mui/material';
|
|
3
|
+
import ExternalLink from '../../ExternalLink';
|
|
4
|
+
function RIDLink({ baseUrl, rid }) {
|
|
6
5
|
return (React.createElement(Typography, null,
|
|
7
6
|
"RID ",
|
|
8
7
|
rid,
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9
|
-
|
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10
|
-
React.createElement(
|
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11
|
-
|
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12
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-
React.createElement(OpenInNewIcon, null),
|
|
13
|
-
")")));
|
|
8
|
+
" (",
|
|
9
|
+
React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${rid}` }, "see status"),
|
|
10
|
+
")"));
|
|
14
11
|
}
|
|
15
12
|
export default RIDLink;
|
|
16
13
|
//# sourceMappingURL=RIDLink.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"RIDLink.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/RIDLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"RIDLink.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/RIDLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,YAAY,MAAM,oBAAoB,CAAA;AAE7C,SAAS,OAAO,CAAC,EAAE,OAAO,EAAE,GAAG,EAAoC;IACjE,OAAO,CACL,oBAAC,UAAU;;QACJ,GAAG;;QACR,oBAAC,YAAY,IAAC,IAAI,EAAE,GAAG,OAAO,gBAAgB,GAAG,EAAE,iBAEpC;YAEJ,CACd,CAAA;AACH,CAAC;AAED,eAAe,OAAO,CAAA"}
|
|
@@ -1,13 +1,13 @@
|
|
|
1
|
-
import { makeId, strip
|
|
1
|
+
import { makeId, strip } from '../LaunchMsaView/components/util';
|
|
2
2
|
import { launchMSA } from '../utils/msa';
|
|
3
3
|
import { queryBlast } from '../utils/ncbiBlast';
|
|
4
4
|
export async function doLaunchBlast({ self, }) {
|
|
5
|
-
const { blastDatabase, blastProgram, msaAlgorithm, proteinSequence } = self.blastParams;
|
|
6
|
-
const query = proteinSequence.replaceAll('*', '').replaceAll('&', '');
|
|
5
|
+
const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, } = self.blastParams;
|
|
7
6
|
const { hits } = await queryBlast({
|
|
8
|
-
query,
|
|
7
|
+
query: proteinSequence.replaceAll('*', '').replaceAll('&', ''),
|
|
9
8
|
blastDatabase,
|
|
10
9
|
blastProgram,
|
|
10
|
+
baseUrl,
|
|
11
11
|
onProgress: arg => {
|
|
12
12
|
self.setProgress(arg);
|
|
13
13
|
},
|
|
@@ -15,26 +15,24 @@ export async function doLaunchBlast({ self, }) {
|
|
|
15
15
|
self.setRid(rid);
|
|
16
16
|
},
|
|
17
17
|
});
|
|
18
|
-
|
|
19
|
-
`>QUERY\n${query}`,
|
|
20
|
-
...hits
|
|
21
|
-
.map(h => [
|
|
22
|
-
makeId(h.description[0] ?? {
|
|
23
|
-
accession: 'unknown',
|
|
24
|
-
id: 'unknown',
|
|
25
|
-
sciname: 'unknown',
|
|
26
|
-
}),
|
|
27
|
-
strip(h.hsps[0]?.hseq ?? ''),
|
|
28
|
-
])
|
|
29
|
-
.map(([id, seq]) => `>${id}\n${seq}`),
|
|
30
|
-
].join('\n');
|
|
31
|
-
const data = await launchMSA({
|
|
18
|
+
return launchMSA({
|
|
32
19
|
algorithm: msaAlgorithm,
|
|
33
|
-
sequence
|
|
20
|
+
sequence: [
|
|
21
|
+
`>QUERY\n${proteinSequence.replaceAll('*', '').replaceAll('&', '')}`,
|
|
22
|
+
...hits
|
|
23
|
+
.map(h => [
|
|
24
|
+
makeId(h.description[0] ?? {
|
|
25
|
+
accession: 'unknown',
|
|
26
|
+
id: 'unknown',
|
|
27
|
+
sciname: 'unknown',
|
|
28
|
+
}),
|
|
29
|
+
strip(h.hsps[0]?.hseq ?? ''),
|
|
30
|
+
])
|
|
31
|
+
.map(([id, seq]) => `>${id}\n${seq}`),
|
|
32
|
+
].join('\n'),
|
|
34
33
|
onProgress: arg => {
|
|
35
34
|
self.setProgress(arg);
|
|
36
35
|
},
|
|
37
36
|
});
|
|
38
|
-
return data;
|
|
39
37
|
}
|
|
40
38
|
//# sourceMappingURL=doLaunchBlast.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"doLaunchBlast.js","sourceRoot":"","sources":["../../src/MsaViewPanel/doLaunchBlast.ts"],"names":[],"mappings":"AACA,OAAO,
|
|
1
|
+
{"version":3,"file":"doLaunchBlast.js","sourceRoot":"","sources":["../../src/MsaViewPanel/doLaunchBlast.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,kCAAkC,CAAA;AAChE,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,EAClC,IAAI,GAGL;IACC,MAAM,EACJ,OAAO,EACP,aAAa,EACb,YAAY,EACZ,YAAY,EACZ,eAAe,GAChB,GAAG,IAAI,CAAC,WAAY,CAAA;IACrB,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,UAAU,CAAC;QAChC,KAAK,EAAE,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;QAC9D,aAAa;QACb,YAAY;QACZ,OAAO;QACP,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;QACD,KAAK,EAAE,GAAG,CAAC,EAAE;YACX,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;KACF,CAAC,CAAA;IAEF,OAAO,SAAS,CAAC;QACf,SAAS,EAAE,YAAY;QACvB,QAAQ,EAAE;YACR,WAAW,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE;YACpE,GAAG,IAAI;iBACJ,GAAG,CACF,CAAC,CAAC,EAAE,CACF;gBACE,MAAM,CACJ,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI;oBAClB,SAAS,EAAE,SAAS;oBACpB,EAAE,EAAE,SAAS;oBACb,OAAO,EAAE,SAAS;iBACnB,CACF;gBACD,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,IAAI,EAAE,CAAC;aACpB,CACb;iBACA,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;SACxC,CAAC,IAAI,CAAC,IAAI,CAAC;QACZ,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -9,6 +9,7 @@ export interface IRegion {
|
|
|
9
9
|
end: number;
|
|
10
10
|
}
|
|
11
11
|
export interface BlastParams {
|
|
12
|
+
baseUrl: string;
|
|
12
13
|
blastDatabase: string;
|
|
13
14
|
msaAlgorithm: string;
|
|
14
15
|
blastProgram: string;
|
|
@@ -39,13 +40,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
39
40
|
} & {
|
|
40
41
|
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
41
42
|
showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
43
|
+
hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
42
44
|
allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
43
45
|
contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
44
46
|
subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
45
47
|
type: import("mobx-state-tree").ISimpleType<"MsaView">;
|
|
46
48
|
drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
47
|
-
hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
48
|
-
drawTreeText: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
49
49
|
height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
50
50
|
rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
51
51
|
scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
@@ -573,12 +573,11 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
|
|
|
573
573
|
colorSchemeName: string;
|
|
574
574
|
id: string;
|
|
575
575
|
showDomains: boolean;
|
|
576
|
+
hideGaps: boolean;
|
|
576
577
|
allowedGappyness: number;
|
|
577
578
|
contrastLettering: boolean;
|
|
578
579
|
subFeatureRows: boolean;
|
|
579
580
|
drawMsaLetters: boolean;
|
|
580
|
-
hideGaps: boolean;
|
|
581
|
-
drawTreeText: boolean;
|
|
582
581
|
rowHeight: number;
|
|
583
582
|
scrollY: number;
|
|
584
583
|
scrollX: number;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/MsaViewPanel/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,4BAA4B,EAAE,MAAM,YAAY,CAAA;AACzD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/MsaViewPanel/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,4BAA4B,EAAE,MAAM,YAAY,CAAA;AACzD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAyB/D;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB;IACvC,OAAO,KAAK;SACT,OAAO,CACN,aAAa,EACb,SAAS,EAAE,EACX,KAAK,CAAC,KAAK,CAAC,SAAS,EAAE;QACrB;;WAEG;QACH,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,gBAAgB,EAAE,KAAK,CAAC,MAAM,EAAE;QAChC;;WAEG;QACH,mBAAmB,EAAE,KAAK,CAAC,KAAK,CAC9B,KAAK,CAAC,KAAK,CAAC;YACV,OAAO,EAAE,KAAK,CAAC,MAAM;YACrB,KAAK,EAAE,KAAK,CAAC,MAAM;YACnB,GAAG,EAAE,KAAK,CAAC,MAAM;SAClB,CAAC,CACH;QACD;;WAEG;QACH,WAAW,EAAE,KAAK,CAAC,MAAM,EAA2B;QAEpD;;WAEG;QACH,eAAe,EAAE,KAAK;KACvB,CAAC,CACH;SAEA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf;;WAEG;QACH,GAAG,EAAE,SAA+B;QACpC;;WAEG;QACH,QAAQ,EAAE,EAAE;QACZ;;WAEG;QACH,KAAK,EAAE,SAAoB;KAC5B,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,gBAAgB,CAAC,OAAe,EAAE,QAAgB;YAChD,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;YACjD,MAAM,GAAG,GAAG,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;YACpB,IAAI,GAAG,IAAI,QAAQ,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;gBACjC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACT,IAAI,CAAC,GAAG,CAAC,CAAA;gBACT,OAAO,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;oBAC9B,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACtB,CAAC,EAAE,CAAA;oBACL,CAAC;gBACH,CAAC;gBACD,OAAO,CAAC,CAAA;YACV,CAAC;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,kBAAkB;YACpB,OAAO,IAAI,CAAC,gBAAgB;gBAC1B,CAAC,CAAC,4BAA4B,CAAC,IAAI,CAAC,gBAAgB,CAAC;gBACrD,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,SAAS;YACX,OAAO,WAAW,CAAC,EAAE,KAAK,EAAE,IAAiC,EAAE,CAAC,CAAA;QAClE,CAAC;QACD;;WAEG;QACH,IAAI,SAAS;YACX,OAAO,SAAS,CAAA;QAClB,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,UAAU;YACZ,OAAO,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,IAAI,aAAa;YACf,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAClC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC,eAAe,CAAa,CAAA;QACnE,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,QAAQ,CAAC,CAAU;YACjB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,WAAW,CAAC,GAAW;YACrB,IAAI,CAAC,QAAQ,GAAG,GAAG,CAAA;QACrB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAW;YAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,sBAAsB,CAAC,CAAY;YACjC,IAAI,CAAC,mBAAmB,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;QACD;;WAEG;QACH,wBAAwB,CAAC,CAAU;YACjC,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,wBAAwB;YACtB,IAAI,CAAC,mBAAmB,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,CAAC;QACD;;WAEG;QACH,cAAc,CAAC,IAAkB;YAC/B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAA;QACzB,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;;WAGG;QACH,kBAAkB;YAChB,OAAO;gBACL;oBACE,KAAK,EAAE,8BAA8B;oBACrC,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC,kBAAkB,CAAC,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;oBAChD,CAAC;iBACF;aACF,CAAA;QACH,CAAC;QACD;;WAEG;QACH,IAAI,UAAU;YACZ,OAAO,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,IAAI,aAAa;YACf,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAClC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC,eAAe,CAAa,CAAA;QACnE,CAAC;KACF,CAAC,CAAC;SAEF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;gBACjB,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;oBACrB,IAAI,CAAC;wBACH,IAAI,CAAC,WAAW,CAAC,kBAAkB,CAAC,CAAA;wBACpC,MAAM,IAAI,GAAG,MAAM,aAAa,CAAC;4BAC/B,IAAI,EAAE,IAAiC;yBACxC,CAAC,CAAA;wBACF,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;wBAClB,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;wBAC9B,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;oBACtB,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAClB,CAAC;4BAAS,CAAC;wBACT,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;oBACtB,CAAC;gBACH,CAAC;YACH,CAAC,CAAC,CACH,CAAA;YAED,sEAAsE;YACtE,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;gBACxC,MAAM,EAAE,GACN,QAAQ,KAAK,SAAS;oBACpB,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,CAAA;gBAC7D,MAAM,EAAE,GACN,aAAa,KAAK,SAAS;oBACzB,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC,CAAA;gBAClE,IAAI,CAAC,sBAAsB,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACxD,CAAC,CAAC,CACH,CAAA;YAED,qCAAqC;YACrC,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,EAAE,aAAa,EAAE,eAAe,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;gBAC9D,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;gBAC5C,MAAM,EAAE,GACN,aAAa,KAAK,SAAS;oBACzB,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC,CAAA;gBAElE,IAAI,CAAC,EAAE,IAAI,CAAC,aAAa,EAAE,CAAC;oBAC1B,OAAM;gBACR,CAAC;gBAED,IAAI,eAAe,EAAE,CAAC;oBACpB,aAAa,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;gBACzB,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,GACL,eAAe;yBACZ,GAAG,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC;wBACrC,EAAE,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,OAAO,CAAA;oBACnD,aAAa,CAAC,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;gBACrC,CAAC;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { makeStyles } from 'tss-react/mui';
|
|
3
|
+
import TextField2 from './TextField2';
|
|
4
|
+
const useStyles = makeStyles()({
|
|
5
|
+
textAreaFont: {
|
|
6
|
+
fontFamily: 'Courier New',
|
|
7
|
+
},
|
|
8
|
+
});
|
|
9
|
+
export default function ReadOnlyTextField2({ value }) {
|
|
10
|
+
const { classes } = useStyles();
|
|
11
|
+
return (React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: value, slotProps: {
|
|
12
|
+
input: {
|
|
13
|
+
readOnly: true,
|
|
14
|
+
classes: {
|
|
15
|
+
input: classes.textAreaFont,
|
|
16
|
+
},
|
|
17
|
+
},
|
|
18
|
+
} }));
|
|
19
|
+
}
|
|
20
|
+
//# sourceMappingURL=ReadOnlyTextField2.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ReadOnlyTextField2.js","sourceRoot":"","sources":["../src/ReadOnlyTextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAAqB;IACrE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE;YACT,KAAK,EAAE;gBACL,QAAQ,EAAE,IAAI;gBACd,OAAO,EAAE;oBACP,KAAK,EAAE,OAAO,CAAC,YAAY;iBAC5B;aACF;SACF,GACD,CACH,CAAA;AACH,CAAC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -5,4 +5,19 @@ export default class MsaViewPlugin extends Plugin {
|
|
|
5
5
|
version: any;
|
|
6
6
|
install(pluginManager: PluginManager): void;
|
|
7
7
|
configure(pluginManager: PluginManager): void;
|
|
8
|
+
rootConfigurationSchema: {
|
|
9
|
+
msa: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
10
|
+
datasets: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
11
|
+
name: {
|
|
12
|
+
type: string;
|
|
13
|
+
defaultValue: string;
|
|
14
|
+
};
|
|
15
|
+
adapter: {
|
|
16
|
+
type: string;
|
|
17
|
+
description: string;
|
|
18
|
+
defaultValue: {};
|
|
19
|
+
};
|
|
20
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
|
|
21
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
22
|
+
};
|
|
8
23
|
}
|
package/dist/index.js
CHANGED
|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
import Plugin from '@jbrowse/core/Plugin';
|
|
2
|
+
import { ConfigurationSchema } from '@jbrowse/core/configuration';
|
|
2
3
|
import { isAbstractMenuManager } from '@jbrowse/core/util';
|
|
3
4
|
import GridOn from '@mui/icons-material/GridOn';
|
|
5
|
+
import { types } from 'mobx-state-tree';
|
|
4
6
|
import { version } from '../package.json';
|
|
5
7
|
import AddHighlightModelF from './AddHighlightModel';
|
|
6
8
|
import LaunchMsaViewF from './LaunchMsaView';
|
|
@@ -10,6 +12,21 @@ export default class MsaViewPlugin extends Plugin {
|
|
|
10
12
|
super(...arguments);
|
|
11
13
|
this.name = 'MsaViewPlugin';
|
|
12
14
|
this.version = version;
|
|
15
|
+
this.rootConfigurationSchema = {
|
|
16
|
+
msa: ConfigurationSchema('MSA', {
|
|
17
|
+
datasets: types.maybe(types.array(ConfigurationSchema('MSAEntry', {
|
|
18
|
+
name: {
|
|
19
|
+
type: 'string',
|
|
20
|
+
defaultValue: '',
|
|
21
|
+
},
|
|
22
|
+
adapter: {
|
|
23
|
+
type: 'frozen',
|
|
24
|
+
description: 'This can be a data adapter config for a IndexedFasta for example, which has a special way of being interpreted',
|
|
25
|
+
defaultValue: {},
|
|
26
|
+
},
|
|
27
|
+
}))),
|
|
28
|
+
}),
|
|
29
|
+
};
|
|
13
30
|
}
|
|
14
31
|
install(pluginManager) {
|
|
15
32
|
MsaViewF(pluginManager);
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,EAAwB,qBAAqB,EAAE,MAAM,oBAAoB,CAAA;AAChF,OAAO,MAAM,MAAM,4BAA4B,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAwB,qBAAqB,EAAE,MAAM,oBAAoB,CAAA;AAChF,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,QAAQ,MAAM,gBAAgB,CAAA;AAErC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,MAAM;IAAjD;;QACE,SAAI,GAAG,eAAe,CAAA;QACtB,YAAO,GAAG,OAAO,CAAA;QAoBjB,4BAAuB,GAAG;YACxB,GAAG,EAAE,mBAAmB,CAAC,KAAK,EAAE;gBAC9B,QAAQ,EAAE,KAAK,CAAC,KAAK,CACnB,KAAK,CAAC,KAAK,CACT,mBAAmB,CAAC,UAAU,EAAE;oBAC9B,IAAI,EAAE;wBACJ,IAAI,EAAE,QAAQ;wBACd,YAAY,EAAE,EAAE;qBACjB;oBACD,OAAO,EAAE;wBACP,IAAI,EAAE,QAAQ;wBACd,WAAW,EACT,gHAAgH;wBAClH,YAAY,EAAE,EAAE;qBACjB;iBACF,CAAC,CACH,CACF;aACF,CAAC;SACH,CAAA;IACH,CAAC;IAtCC,OAAO,CAAC,aAA4B;QAClC,QAAQ,CAAC,aAAa,CAAC,CAAA;QACvB,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,aAA4B;QACpC,IAAI,qBAAqB,CAAC,aAAa,CAAC,SAAS,CAAC,EAAE,CAAC;YACnD,aAAa,CAAC,SAAS,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,KAAK,EAAE,kCAAkC;gBACzC,IAAI,EAAE,MAAM;gBACZ,OAAO,EAAE,CAAC,OAA6B,EAAE,EAAE;oBACzC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;gBAChC,CAAC;aACF,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;CAsBF"}
|