jbrowse-plugin-protein3d 0.0.3 → 0.0.4
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/dist/AddHighlightModel/GenomeMouseoverHighlight.js +3 -9
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js +4 -3
- package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js.map +1 -1
- package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.d.ts +1 -2
- package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js +4 -3
- package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/util.js +1 -1
- package/dist/AddHighlightModel/util.js.map +1 -1
- package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.d.ts +16 -0
- package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js +43 -0
- package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js.map +1 -0
- package/dist/AlphaFoldConfidenceAdapter/configSchema.d.ts +13 -0
- package/dist/AlphaFoldConfidenceAdapter/configSchema.js +16 -0
- package/dist/AlphaFoldConfidenceAdapter/configSchema.js.map +1 -0
- package/dist/AlphaFoldConfidenceAdapter/index.d.ts +2 -0
- package/dist/AlphaFoldConfidenceAdapter/index.js +11 -0
- package/dist/AlphaFoldConfidenceAdapter/index.js.map +1 -0
- package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.d.ts +30 -0
- package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js +78 -0
- package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js.map +1 -0
- package/dist/AlphaMissensePathogenicityAdapter/configSchema.d.ts +13 -0
- package/dist/AlphaMissensePathogenicityAdapter/configSchema.js +16 -0
- package/dist/AlphaMissensePathogenicityAdapter/configSchema.js.map +1 -0
- package/dist/AlphaMissensePathogenicityAdapter/index.d.ts +2 -0
- package/dist/AlphaMissensePathogenicityAdapter/index.js +11 -0
- package/dist/AlphaMissensePathogenicityAdapter/index.js.map +1 -0
- package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js +161 -11
- package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js.map +1 -1
- package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js +8 -6
- package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js.map +1 -1
- package/dist/LaunchProteinView/components/HelpButton.js +6 -2
- package/dist/LaunchProteinView/components/HelpButton.js.map +1 -1
- package/dist/LaunchProteinView/components/HelpDialog.js +3 -1
- package/dist/LaunchProteinView/components/HelpDialog.js.map +1 -1
- package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js +6 -2
- package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js.map +1 -1
- package/dist/LaunchProteinView/components/MSATable.js +3 -1
- package/dist/LaunchProteinView/components/MSATable.js.map +1 -1
- package/dist/LaunchProteinView/components/TranscriptSelector.js +3 -1
- package/dist/LaunchProteinView/components/TranscriptSelector.js.map +1 -1
- package/dist/LaunchProteinView/components/UserProvidedStructure.js +18 -11
- package/dist/LaunchProteinView/components/UserProvidedStructure.js.map +1 -1
- package/dist/LaunchProteinView/components/calculateProteinSequence.js +5 -3
- package/dist/LaunchProteinView/components/calculateProteinSequence.js.map +1 -1
- package/dist/LaunchProteinView/components/useLocalStructureFileSequence.d.ts +1 -1
- package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js +29 -9
- package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js.map +1 -1
- package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.d.ts +1 -1
- package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js +25 -8
- package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js.map +1 -1
- package/dist/LaunchProteinView/components/util.js +1 -1
- package/dist/LaunchProteinView/index.js +7 -3
- package/dist/LaunchProteinView/index.js.map +1 -1
- package/dist/ProteinView/{loadStructureFromData.d.ts → addStructureFromData.d.ts} +2 -2
- package/dist/ProteinView/{loadStructureFromData.js → addStructureFromData.js} +3 -8
- package/dist/ProteinView/addStructureFromData.js.map +1 -0
- package/dist/ProteinView/{loadStructureFromURL.d.ts → addStructureFromURL.d.ts} +2 -2
- package/dist/ProteinView/{loadStructureFromURL.js → addStructureFromURL.js} +11 -9
- package/dist/ProteinView/addStructureFromURL.js.map +1 -0
- package/dist/ProteinView/clearSelection.js +1 -1
- package/dist/ProteinView/clearSelection.js.map +1 -1
- package/dist/ProteinView/components/ProteinAlignment.d.ts +2 -2
- package/dist/ProteinView/components/ProteinAlignment.js +37 -26
- package/dist/ProteinView/components/ProteinAlignment.js.map +1 -1
- package/dist/ProteinView/components/ProteinAlignmentHelpButton.d.ts +2 -2
- package/dist/ProteinView/components/ProteinAlignmentHelpButton.js +6 -4
- package/dist/ProteinView/components/ProteinAlignmentHelpButton.js.map +1 -1
- package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js +6 -5
- package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js.map +1 -1
- package/dist/ProteinView/components/ProteinView.js +18 -60
- package/dist/ProteinView/components/ProteinView.js.map +1 -1
- package/dist/ProteinView/components/{Header.js → ProteinViewHeader.js} +29 -12
- package/dist/ProteinView/components/ProteinViewHeader.js.map +1 -0
- package/dist/ProteinView/components/SplitString.d.ts +4 -4
- package/dist/ProteinView/components/SplitString.js +3 -3
- package/dist/ProteinView/components/SplitString.js.map +1 -1
- package/dist/ProteinView/genomeToProtein.d.ts +2 -2
- package/dist/ProteinView/genomeToProtein.js +4 -5
- package/dist/ProteinView/genomeToProtein.js.map +1 -1
- package/dist/ProteinView/highlightResidue.js +2 -2
- package/dist/ProteinView/highlightResidue.js.map +1 -1
- package/dist/ProteinView/launchRemotePairwiseAlignment.d.ts +2 -5
- package/dist/ProteinView/launchRemotePairwiseAlignment.js +7 -3
- package/dist/ProteinView/launchRemotePairwiseAlignment.js.map +1 -1
- package/dist/ProteinView/model.d.ts +496 -160
- package/dist/ProteinView/model.js +61 -246
- package/dist/ProteinView/model.js.map +1 -1
- package/dist/ProteinView/proteinToGenomeMapping.d.ts +6 -6
- package/dist/ProteinView/proteinToGenomeMapping.js +29 -28
- package/dist/ProteinView/proteinToGenomeMapping.js.map +1 -1
- package/dist/ProteinView/selectResidue.js +1 -1
- package/dist/ProteinView/selectResidue.js.map +1 -1
- package/dist/ProteinView/structureModel.d.ts +183 -0
- package/dist/ProteinView/structureModel.js +407 -0
- package/dist/ProteinView/structureModel.js.map +1 -0
- package/dist/ProteinView/useProteinView.d.ts +1 -4
- package/dist/ProteinView/useProteinView.js +3 -15
- package/dist/ProteinView/useProteinView.js.map +1 -1
- package/dist/ProteinView/util.d.ts +3 -3
- package/dist/ProteinView/util.js +8 -6
- package/dist/ProteinView/util.js.map +1 -1
- package/dist/UniProtVariationAdapter/UniProtVariationAdapter.d.ts +15 -0
- package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js +55 -0
- package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js.map +1 -0
- package/dist/UniProtVariationAdapter/configSchema.d.ts +17 -0
- package/dist/UniProtVariationAdapter/configSchema.js +20 -0
- package/dist/UniProtVariationAdapter/configSchema.js.map +1 -0
- package/dist/UniProtVariationAdapter/index.d.ts +2 -0
- package/dist/UniProtVariationAdapter/index.js +11 -0
- package/dist/UniProtVariationAdapter/index.js.map +1 -0
- package/dist/genomeToTranscriptMapping.d.ts +2 -2
- package/dist/genomeToTranscriptMapping.js +3 -3
- package/dist/genomeToTranscriptMapping.js.map +1 -1
- package/dist/index.js +6 -0
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-protein3d.umd.production.min.js +1467 -1482
- package/dist/jbrowse-plugin-protein3d.umd.production.min.js.map +4 -4
- package/dist/mappings.d.ts +12 -10
- package/dist/mappings.js +7 -7
- package/dist/mappings.js.map +1 -1
- package/dist/mappings.test.js +7 -5
- package/dist/mappings.test.js.map +1 -1
- package/dist/test_data/gene.d.ts +577 -64
- package/dist/test_data/gene.js +1 -1
- package/dist/test_data/gene.js.map +1 -1
- package/package.json +16 -15
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +4 -17
- package/src/AddHighlightModel/ProteinToGenomeClickHighlight.tsx +17 -14
- package/src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx +18 -17
- package/src/AddHighlightModel/util.ts +1 -1
- package/src/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.ts +63 -0
- package/src/AlphaFoldConfidenceAdapter/configSchema.ts +21 -0
- package/src/AlphaFoldConfidenceAdapter/index.ts +19 -0
- package/src/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.ts +109 -0
- package/src/AlphaMissensePathogenicityAdapter/configSchema.ts +21 -0
- package/src/AlphaMissensePathogenicityAdapter/index.ts +19 -0
- package/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx +172 -10
- package/src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx +8 -6
- package/src/LaunchProteinView/components/HelpButton.tsx +10 -2
- package/src/LaunchProteinView/components/HelpDialog.tsx +6 -1
- package/src/LaunchProteinView/components/LaunchProteinViewDialog.tsx +9 -2
- package/src/LaunchProteinView/components/MSATable.tsx +3 -1
- package/src/LaunchProteinView/components/TranscriptSelector.tsx +9 -7
- package/src/LaunchProteinView/components/UserProvidedStructure.tsx +17 -12
- package/src/LaunchProteinView/components/calculateProteinSequence.ts +6 -4
- package/src/LaunchProteinView/components/useLocalStructureFileSequence.ts +28 -9
- package/src/LaunchProteinView/components/useRemoteStructureFileSequence.ts +23 -8
- package/src/LaunchProteinView/components/util.ts +1 -1
- package/src/LaunchProteinView/index.ts +36 -26
- package/src/ProteinView/{loadStructureFromData.ts → addStructureFromData.ts} +2 -8
- package/src/ProteinView/{loadStructureFromURL.ts → addStructureFromURL.ts} +11 -11
- package/src/ProteinView/clearSelection.ts +1 -1
- package/src/ProteinView/components/ProteinAlignment.tsx +51 -35
- package/src/ProteinView/components/ProteinAlignmentHelpButton.tsx +4 -4
- package/src/ProteinView/components/ProteinAlignmentHelpDialog.tsx +15 -11
- package/src/ProteinView/components/ProteinView.tsx +22 -82
- package/src/ProteinView/components/{Header.tsx → ProteinViewHeader.tsx} +44 -23
- package/src/ProteinView/components/SplitString.tsx +8 -8
- package/src/ProteinView/genomeToProtein.ts +5 -9
- package/src/ProteinView/highlightResidue.ts +2 -2
- package/src/ProteinView/launchRemotePairwiseAlignment.ts +6 -3
- package/src/ProteinView/model.ts +74 -287
- package/src/ProteinView/proteinToGenomeMapping.ts +40 -38
- package/src/ProteinView/selectResidue.ts +1 -1
- package/src/ProteinView/structureModel.ts +512 -0
- package/src/ProteinView/useProteinView.ts +2 -19
- package/src/ProteinView/util.ts +20 -9
- package/src/UniProtVariationAdapter/UniProtVariationAdapter.ts +99 -0
- package/src/UniProtVariationAdapter/configSchema.ts +25 -0
- package/src/UniProtVariationAdapter/index.ts +17 -0
- package/src/__snapshots__/mappings.test.ts.snap +224 -224
- package/src/genomeToTranscriptMapping.ts +9 -9
- package/src/index.ts +6 -0
- package/src/mappings.test.ts +7 -5
- package/src/mappings.ts +25 -23
- package/src/test_data/gene.ts +3 -3
- package/dist/ProteinView/components/Header.js.map +0 -1
- package/dist/ProteinView/loadStructureFromData.js.map +0 -1
- package/dist/ProteinView/loadStructureFromURL.js.map +0 -1
- package/dist/ProteinView/useProteinViewClickBehavior.d.ts +0 -8
- package/dist/ProteinView/useProteinViewClickBehavior.js +0 -34
- package/dist/ProteinView/useProteinViewClickBehavior.js.map +0 -1
- package/dist/ProteinView/useProteinViewHoverBehavior.d.ts +0 -6
- package/dist/ProteinView/useProteinViewHoverBehavior.js +0 -31
- package/dist/ProteinView/useProteinViewHoverBehavior.js.map +0 -1
- package/src/ProteinView/useProteinViewClickBehavior.ts +0 -48
- package/src/ProteinView/useProteinViewHoverBehavior.ts +0 -44
- /package/dist/ProteinView/components/{Header.d.ts → ProteinViewHeader.d.ts} +0 -0
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+
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@@ -17,10 +17,7 @@ export default function AlphaFoldDBSearchStatus({ uniprotId, selectedTranscript,
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|
17
17
|
? `https://www.uniprot.org/uniprotkb/${uniprotId}/entry`
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18
18
|
: undefined;
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|
19
19
|
const [showAllProteinSequences, setShowAllProteinSequences] = useState(false);
|
|
20
|
-
return
|
|
21
|
-
"Searching ",
|
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22
|
-
getDisplayName(selectedTranscript),
|
|
23
|
-
" for UniProt ID")) : (React.createElement(React.Fragment, null,
|
|
20
|
+
return uniprotId ? (React.createElement(React.Fragment, null,
|
|
24
21
|
React.createElement(Typography, null,
|
|
25
22
|
"Found Uniprot ID:",
|
|
26
23
|
' ',
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@@ -30,9 +27,14 @@ export default function AlphaFoldDBSearchStatus({ uniprotId, selectedTranscript,
|
|
|
30
27
|
' ',
|
|
31
28
|
React.createElement("a", { href: url, target: "_blank", rel: "noreferrer" }, url)),
|
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32
29
|
structureSequence ? (React.createElement("div", { style: { margin: 20 } },
|
|
33
|
-
React.createElement(Button, { variant: "contained", color: "primary", onClick: () =>
|
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30
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+
React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
|
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31
|
+
setShowAllProteinSequences(!showAllProteinSequences);
|
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32
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+
} }, showAllProteinSequences
|
|
34
33
|
? 'Hide all isoform protein sequences'
|
|
35
34
|
: 'Show all isoform protein sequences'),
|
|
36
|
-
showAllProteinSequences ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: uniprotId, isoformSequences: isoformSequences })) : null)) : (React.createElement(NotFound, { uniprotId: uniprotId }))))
|
|
35
|
+
showAllProteinSequences ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: uniprotId, isoformSequences: isoformSequences })) : null)) : (React.createElement(NotFound, { uniprotId: uniprotId })))) : (React.createElement(Typography, null,
|
|
36
|
+
"Searching ",
|
|
37
|
+
getDisplayName(selectedTranscript),
|
|
38
|
+
" for UniProt ID"));
|
|
37
39
|
}
|
|
38
40
|
//# sourceMappingURL=AlphaFoldDBSearchStatus.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"AlphaFoldDBSearchStatus.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAGxD,SAAS;AACT,OAAO,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,SAAS,QAAQ,CAAC,EAAE,SAAS,EAAyB;IACpD,OAAO,CACL,oBAAC,UAAU;;QAC4C,GAAG;QACxD,oBAAC,IAAI,IACH,MAAM,EAAC,QAAQ,EACf,IAAI,EAAE,2CAA2C,SAAS,EAAE,2BAGvD,CACI,CACd,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,SAAS,EACT,kBAAkB,EAClB,iBAAiB,EACjB,gBAAgB,GAMjB;IACC,MAAM,GAAG,GAAG,SAAS;QACnB,CAAC,CAAC,wCAAwC,SAAS,kBAAkB;QACrE,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,IAAI,GAAG,SAAS;QACpB,CAAC,CAAC,qCAAqC,SAAS,QAAQ;QACxD,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,CAAC,uBAAuB,EAAE,0BAA0B,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE7E,OAAO,
|
|
1
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+
{"version":3,"file":"AlphaFoldDBSearchStatus.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAGxD,SAAS;AACT,OAAO,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,SAAS,QAAQ,CAAC,EAAE,SAAS,EAAyB;IACpD,OAAO,CACL,oBAAC,UAAU;;QAC4C,GAAG;QACxD,oBAAC,IAAI,IACH,MAAM,EAAC,QAAQ,EACf,IAAI,EAAE,2CAA2C,SAAS,EAAE,2BAGvD,CACI,CACd,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,SAAS,EACT,kBAAkB,EAClB,iBAAiB,EACjB,gBAAgB,GAMjB;IACC,MAAM,GAAG,GAAG,SAAS;QACnB,CAAC,CAAC,wCAAwC,SAAS,kBAAkB;QACrE,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,IAAI,GAAG,SAAS;QACpB,CAAC,CAAC,qCAAqC,SAAS,QAAQ;QACxD,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,CAAC,uBAAuB,EAAE,0BAA0B,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE7E,OAAO,SAAS,CAAC,CAAC,CAAC,CACjB;QACE,oBAAC,UAAU;;YACS,GAAG;YACrB,2BAAG,IAAI,EAAE,IAAI,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,IAC5C,SAAS,CACR,CACO;QACb,oBAAC,UAAU;;YACS,GAAG;YACrB,2BAAG,IAAI,EAAE,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,IAC3C,GAAG,CACF,CACO;QACZ,iBAAiB,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;YACxB,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;oBACZ,0BAA0B,CAAC,CAAC,uBAAuB,CAAC,CAAA;gBACtD,CAAC,IAEA,uBAAuB;gBACtB,CAAC,CAAC,oCAAoC;gBACtC,CAAC,CAAC,oCAAoC,CACjC;YACR,uBAAuB,CAAC,CAAC,CAAC,CACzB,oBAAC,QAAQ,IACP,iBAAiB,EAAE,iBAAiB,EACpC,aAAa,EAAE,SAAS,EACxB,gBAAgB,EAAE,gBAAgB,GAClC,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,QAAQ,IAAC,SAAS,EAAE,SAAS,GAAI,CACnC,CACA,CACJ,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU;;QACE,cAAc,CAAC,kBAAkB,CAAC;0BAClC,CACd,CAAA;AACH,CAAC"}
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@@ -7,9 +7,13 @@ const HelpDialog = lazy(() => import('./HelpDialog'));
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export default function HelpButton() {
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React.createElement(Help, null)),
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{"version":3,"file":"HelpButton.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/HelpButton.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,QAAQ;AACR,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,SAAS;AACT,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,UAAU;IAChC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvC,OAAO,CACL;QACE,oBAAC,UAAU,
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{"version":3,"file":"HelpButton.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/HelpButton.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,QAAQ;AACR,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,SAAS;AACT,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,UAAU;IAChC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvC,OAAO,CACL;QACE,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;gBACZ,OAAO,CAAC,IAAI,CAAC,CAAA;YACf,CAAC;YAED,oBAAC,IAAI,OAAG,CACG;QACZ,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,UAAU,IACT,WAAW,EAAE,GAAG,EAAE;oBAChB,OAAO,CAAC,KAAK,CAAC,CAAA;gBAChB,CAAC,GACD,CACO,CACZ,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}
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@@ -18,6 +18,8 @@ export default function HelpDialog({ handleClose, }) {
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React.createElement(Typography2, null, "If you run into challenges with this workflow e.g. your transcripts are not being found in mygene.info then you can use the Manual import form, or contact colin.diesh@gmail.com for troubleshooting")),
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{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,OAAO,EACP,UAAU,GAEX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,WAAW,CAAC,EAAE,QAAQ,EAAmB;IAChD,OAAO,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,IAAG,QAAQ,CAAc,CAAA;AAClE,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,QAAQ,EAAC,IAAI,EAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,MAAM;QAC3D,oBAAC,aAAa;YACZ,oBAAC,WAAW;;gBAEV;oBACE,mPAKK;oBACL,uLAIK;oBACL,wPAKK;oBACL,8PAKK;oBACL,+RAKK,CACF,CACO;YACd,oBAAC,WAAW,+MAIE,CACA;QAChB,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,oBAAC,MAAM,
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{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,OAAO,EACP,UAAU,GAEX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,WAAW,CAAC,EAAE,QAAQ,EAAmB;IAChD,OAAO,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,IAAG,QAAQ,CAAc,CAAA;AAClE,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,QAAQ,EAAC,IAAI,EAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,MAAM;QAC3D,oBAAC,aAAa;YACZ,oBAAC,WAAW;;gBAEV;oBACE,mPAKK;oBACL,uLAIK;oBACL,wPAKK;oBACL,8PAKK;oBACL,+RAKK,CACF,CACO;YACd,oBAAC,WAAW,+MAIE,CACA;QAChB,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,KAAK,EAAC,SAAS,YAGR,CACK,CACT,CACV,CAAA;AACH,CAAC"}
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@@ -7,8 +7,12 @@ import UserProvidedStructure from './UserProvidedStructure';
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import TabPanel from './TabPanel';
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export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
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const [choice, setChoice] = useState(0);
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return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", onClose: () =>
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return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", onClose: () => {
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handleClose();
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}, open: true },
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} },
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React.createElement(Tab, { value: 0, label: "Automatic lookup" }),
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@@ -1 +1 @@
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{"version":3,"file":"LaunchProteinViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/LaunchProteinViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAGzC,SAAS;AACT,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,qBAAqB,EAC3B,OAAO,EAAE,GAAG,EAAE,
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{"version":3,"file":"LaunchProteinViewDialog.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/LaunchProteinViewDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAGzC,SAAS;AACT,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,qBAAqB,EAC3B,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,IAAI,IACH,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,SAAS,CAAC,GAAG,CAAC,CAAA;YAChB,CAAC;YAED,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,kBAAkB,GAAG;YAC1C,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,QAAQ,GAAG,CAC3B;QACP,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,iBAAiB,IAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO;QACX,oBAAC,QAAQ,IAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;YAC/B,oBAAC,qBAAqB,IACpB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,GACxB,CACO,CACJ,CACV,CAAA;AACH,CAAC"}
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@@ -42,7 +42,9 @@ export default function MSATable({ structureName, structureSequence, isoformSequ
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...Object.values(removedStars).map(({ feature, seq }) => `>${getTranscriptDisplayName(feature)}\n${seq}`),
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].join('\n');
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{"version":3,"file":"MSATable.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/MSATable.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAW,GAAG,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;QACzB,UAAU,EAAE,KAAK;KAClB;IACD,MAAM,EAAE;QACN,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAC/B,aAAa,EACb,iBAAiB,EACjB,gBAAgB,GAKjB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACjE,MAAM,YAAY,GAAG,MAAM,CAAC,WAAW,CACrC,MAAM,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;QACnD,GAAG;QACH,EAAE,GAAG,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE;KAC7C,CAAC,CACH,CAAA;IACD,MAAM,gCAAgC,GAAG,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,IAAI,CACxE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,iBAAiB,KAAK,GAAG,CAAC,GAAG,CAC5C,CAAA;IACD,MAAM,KAAK,GAAG,GAAG,aAAa,IAAI,EAAE,uBAAuB,CAAA;IAC3D,MAAM,SAAS,GAAG,GAAG,CAAC;QACpB,KAAK,CAAC,MAAM;QACZ,GAAG,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,GAAG,CACjC,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,wBAAwB,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,MAAM,CAC3D;KACF,CAAC,CAAA;IAEF,MAAM,EAAE,GAAG;QACT,GAAG,KAAK,CAAC,MAAM,CAAC,SAAS,CAAC,GAAG,gCAAgC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,iBAAiB,EAAE;QAChG,gCAAgC;YAC9B,CAAC,CAAC,GAAG,wBAAwB,CAAC,gCAAgC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,gCAAgC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE;YAC1I,CAAC,CAAC,SAAS;QACb,GAAG,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC;aAC5B,GAAG,CACF,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CACX,GAAG,wBAAwB,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,GAAG,CAAC,GAAG,EAAE,CAC3E;aACA,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,gCAAgC,EAAE,CAAC,CAAC,CAAC,CAAC;KAChE;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,IAAI,CAAC,CAAA;IAEb,MAAM,EAAE,GAAG;QACT,IAAI,KAAK,KAAK,iBAAiB,EAAE;QACjC,GAAG,MAAM,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC,GAAG,CAChC,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,IAAI,wBAAwB,CAAC,OAAO,CAAC,KAAK,GAAG,EAAE,CACtE;KACF,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACZ,OAAO,CACL;QACE,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EACL,oBAAC,QAAQ,IACP,QAAQ,EAAE,KAAK,CAAC,EAAE,
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+
{"version":3,"file":"MSATable.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/MSATable.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAW,GAAG,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;QACzB,UAAU,EAAE,KAAK;KAClB;IACD,MAAM,EAAE;QACN,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAC/B,aAAa,EACb,iBAAiB,EACjB,gBAAgB,GAKjB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACjE,MAAM,YAAY,GAAG,MAAM,CAAC,WAAW,CACrC,MAAM,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;QACnD,GAAG;QACH,EAAE,GAAG,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE;KAC7C,CAAC,CACH,CAAA;IACD,MAAM,gCAAgC,GAAG,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,IAAI,CACxE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,iBAAiB,KAAK,GAAG,CAAC,GAAG,CAC5C,CAAA;IACD,MAAM,KAAK,GAAG,GAAG,aAAa,IAAI,EAAE,uBAAuB,CAAA;IAC3D,MAAM,SAAS,GAAG,GAAG,CAAC;QACpB,KAAK,CAAC,MAAM;QACZ,GAAG,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,GAAG,CACjC,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,wBAAwB,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,MAAM,CAC3D;KACF,CAAC,CAAA;IAEF,MAAM,EAAE,GAAG;QACT,GAAG,KAAK,CAAC,MAAM,CAAC,SAAS,CAAC,GAAG,gCAAgC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,iBAAiB,EAAE;QAChG,gCAAgC;YAC9B,CAAC,CAAC,GAAG,wBAAwB,CAAC,gCAAgC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,gCAAgC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE;YAC1I,CAAC,CAAC,SAAS;QACb,GAAG,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC;aAC5B,GAAG,CACF,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CACX,GAAG,wBAAwB,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,GAAG,CAAC,GAAG,EAAE,CAC3E;aACA,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,gCAAgC,EAAE,CAAC,CAAC,CAAC,CAAC;KAChE;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,IAAI,CAAC,CAAA;IAEb,MAAM,EAAE,GAAG;QACT,IAAI,KAAK,KAAK,iBAAiB,EAAE;QACjC,GAAG,MAAM,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC,GAAG,CAChC,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,IAAI,wBAAwB,CAAC,OAAO,CAAC,KAAK,GAAG,EAAE,CACtE;KACF,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACZ,OAAO,CACL;QACE,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EACL,oBAAC,QAAQ,IACP,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,oBAAoB,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;gBAC5C,CAAC,EACD,OAAO,EAAE,iBAAiB,GAC1B,EAEJ,KAAK,EAAC,uBAAuB,GAC7B;QACF,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,iBAAiB,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,EAClC,UAAU,EAAE;gBACV,QAAQ,EAAE,IAAI;gBACd,OAAO,EAAE;oBACP,KAAK,EAAE,OAAO,CAAC,YAAY;iBAC5B;aACF,GACD,CACD,CACJ,CAAA;AACH,CAAC"}
|
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@@ -7,7 +7,9 @@ function TextField2({ children, ...rest }) {
|
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7
7
|
React.createElement(TextField, { ...rest }, children)));
|
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8
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}
|
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9
|
export default function TranscriptSelector({ val, setVal, isoforms, isoformSequences, structureSequence, feature, }) {
|
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|
-
return (React.createElement(TextField2, { value: val, onChange: event =>
|
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+
return (React.createElement(TextField2, { value: val, onChange: event => {
|
|
11
|
+
setVal(event.target.value);
|
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12
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+
}, label: "Choose transcript isoform", select: true },
|
|
11
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|
isoforms
|
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12
14
|
.filter(f => !!isoformSequences[f.id()])
|
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13
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|
.filter(f => isoformSequences[f.id()].seq.replaceAll('*', '') ===
|
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAkB,MAAM,eAAe,CAAA;AAGnE,SAAS;AACT,OAAO,EAAE,kBAAkB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAErE,SAAS,UAAU,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAkB;IACvD,OAAO,CACL;QACE,oBAAC,SAAS,OAAK,IAAI,IAAG,QAAQ,CAAa,CACvC,CACP,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,GAAG,EACH,MAAM,EACN,QAAQ,EACR,gBAAgB,EAChB,iBAAiB,EACjB,OAAO,GAQR;IACC,OAAO,CACL,oBAAC,UAAU,IACT,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,
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1
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+
{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAkB,MAAM,eAAe,CAAA;AAGnE,SAAS;AACT,OAAO,EAAE,kBAAkB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAErE,SAAS,UAAU,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAkB;IACvD,OAAO,CACL;QACE,oBAAC,SAAS,OAAK,IAAI,IAAG,QAAQ,CAAa,CACvC,CACP,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,GAAG,EACH,MAAM,EACN,QAAQ,EACR,gBAAgB,EAChB,iBAAiB,EACjB,OAAO,GAQR;IACC,OAAO,CACL,oBAAC,UAAU,IACT,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,EACD,KAAK,EAAC,2BAA2B,EACjC,MAAM;QAEL,QAAQ;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aACvC,MAAM,CACL,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;YACjD,iBAAiB,CACpB;aACA,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE;YACjC,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,CAAC,CAAC;;YAC3D,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;+CAE5B,CACZ,CAAC;QACH,QAAQ;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aACvC,MAAM,CACL,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;YACjD,iBAAiB,CACpB;aACA,IAAI,CACH,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;YACpC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM,CACvC;aACA,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE;YACjC,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,CAAC,CAAC;;YAC3D,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;kBAC5B,CACZ,CAAC;QACH,QAAQ;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aACtC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,QAAQ;YAC3C,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,CAAC,CAAC;yBAEnD,CACZ,CAAC,CACO,CACd,CAAA;AACH,CAAC"}
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@@ -50,12 +50,11 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
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50
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view,
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});
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52
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|
const protein = isoformSequences?.[userSelection ?? ''];
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53
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const {
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54
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-
const {
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55
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-
const structureName = file?.name ??
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56
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-
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57
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-
|
|
58
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-
const structureSequence = structureSequence1 ?? structureSequence2;
|
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53
|
+
const { sequences: structureSequences1, error: error3 } = useLocalStructureFileSequence({ file });
|
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54
|
+
const { sequences: structureSequences2, error: error4 } = useRemoteStructureFileSequence({ url: structureURL });
|
|
55
|
+
const structureName = file?.name ?? structureURL.slice(structureURL.lastIndexOf('/') + 1);
|
|
56
|
+
const structureSequences = structureSequences1 ?? structureSequences2;
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57
|
+
const structureSequence = structureSequences?.[0];
|
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59
58
|
useEffect(() => {
|
|
60
59
|
if (isoformSequences !== undefined) {
|
|
61
60
|
const ret = options.find(f => isoformSequences[f.id()]?.seq.replaceAll('*', '') ==
|
|
@@ -73,19 +72,23 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
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73
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"Open your structure file ",
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74
73
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React.createElement(HelpButton, null)),
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React.createElement(FormControl, { component: "fieldset" },
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76
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-
React.createElement(RadioGroup, { value: choice, onChange: event =>
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75
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+
React.createElement(RadioGroup, { value: choice, onChange: event => {
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76
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+
setChoice(event.target.value);
|
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+
} },
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React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
|
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React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }),
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React.createElement(FormControlLabel, { value: "pdb", control: React.createElement(Radio, null), label: "PDB ID" }))),
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choice === 'url' ? (React.createElement("div", null,
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React.createElement(Typography, null, "Open a PDB/mmCIF/etc. file from remote URL"),
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82
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-
React.createElement(TextField, { label: "URL", value: structureURL, onChange: event =>
|
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83
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+
React.createElement(TextField, { label: "URL", value: structureURL, onChange: event => {
|
|
84
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+
setStructureURL(event.target.value);
|
|
85
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+
} }))) : null,
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86
|
choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
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|
React.createElement(Typography, null, "Open a PDB/mmCIF/etc. file from your local drive"),
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React.createElement(Button, { variant: "outlined", component: "label" },
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"Choose File",
|
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React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
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-
const file = target
|
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91
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+
const file = target.files?.[0];
|
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92
|
if (file) {
|
|
90
93
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setFile(file);
|
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94
|
}
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@@ -98,12 +101,16 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
|
|
|
98
101
|
React.createElement("div", { style: { margin: 20 } }, isoformSequences ? (structureSequence ? (React.createElement(React.Fragment, null,
|
|
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102
|
React.createElement(TranscriptSelector, { val: userSelection ?? '', setVal: setUserSelection, structureSequence: structureSequence, isoforms: options, feature: feature, isoformSequences: isoformSequences }),
|
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100
103
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React.createElement("div", { style: { margin: 10 } },
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101
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-
React.createElement(Button, { variant: "contained", color: "primary", onClick: () =>
|
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104
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+
React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
|
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105
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+
setShowAllProteinSequences(!showAllProteinSequences);
|
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+
} }, showAllProteinSequences
|
|
102
107
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? 'Hide all isoform protein sequences'
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108
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: 'Show all isoform protein sequences'),
|
|
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109
|
showAllProteinSequences ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: structureName, isoformSequences: isoformSequences })) : null))) : null) : (React.createElement(LoadingEllipses, { title: "Loading protein sequences", variant: "h6" })))),
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React.createElement(DialogActions, null,
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-
React.createElement(Button, { variant: "contained", color: "secondary", onClick: () =>
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+
React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
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+
handleClose();
|
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+
} }, "Cancel"),
|
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|
React.createElement(Button, { variant: "contained", color: "primary", disabled: !(structureURL || file) || !protein || !selectedTranscript, onClick: () => {
|
|
108
115
|
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
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109
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|
;
|
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"UserProvidedStructure.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/UserProvidedStructure.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,WAAW,EACX,IAAI,EACJ,KAAK,EACL,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAGL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAGhE,SAAS;AACT,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,QAAQ,CAAA;AAEf,aAAa;AACb,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,QAAQ;AACR,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AACrE,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,8BAA8B,MAAM,kCAAkC,CAAA;AAE7E,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC3B,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAC,CAAA;AAIH,SAAS,QAAQ;IACf,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE;;QAE6C,GAAG;QAC9E,oBAAC,IAAI,IAAC,MAAM,EAAC,QAAQ,EAAC,IAAI,EAAC,wCAAwC,gBAE5D;4MAIH,CACP,CAAA;AACH,CAAC;AAED,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAC/C,OAAO,EACP,KAAK,EACL,WAAW,GAKZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAQ,CAAA;IACxC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACtC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5C,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC9C,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACpD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC5D,MAAM,CAAC,uBAAuB,EAAE,0BAA0B,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE7E,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAAQ,CAAA;IAC5C,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAC,CAAA;IAC5E,MAAM,EAAE,gBAAgB,EAAE,KAAK,EAAE,GAAG,0BAA0B,CAAC;QAC7D,OAAO;QACP,IAAI;KACL,CAAC,CAAA;IACF,MAAM,OAAO,GAAG,gBAAgB,EAAE,CAAC,aAAa,IAAI,EAAE,CAAC,CAAA;IACvD,MAAM,EAAE,
|
|
1
|
+
{"version":3,"file":"UserProvidedStructure.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/UserProvidedStructure.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,WAAW,EACX,IAAI,EACJ,KAAK,EACL,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAGL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAGhE,SAAS;AACT,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,QAAQ,CAAA;AAEf,aAAa;AACb,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,QAAQ;AACR,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AACrE,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,8BAA8B,MAAM,kCAAkC,CAAA;AAE7E,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC3B,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAC,CAAA;AAIH,SAAS,QAAQ;IACf,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE;;QAE6C,GAAG;QAC9E,oBAAC,IAAI,IAAC,MAAM,EAAC,QAAQ,EAAC,IAAI,EAAC,wCAAwC,gBAE5D;4MAIH,CACP,CAAA;AACH,CAAC;AAED,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAC/C,OAAO,EACP,KAAK,EACL,WAAW,GAKZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAQ,CAAA;IACxC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACtC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5C,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC9C,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACpD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC5D,MAAM,CAAC,uBAAuB,EAAE,0BAA0B,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE7E,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAAQ,CAAA;IAC5C,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAC,CAAA;IAC5E,MAAM,EAAE,gBAAgB,EAAE,KAAK,EAAE,GAAG,0BAA0B,CAAC;QAC7D,OAAO;QACP,IAAI;KACL,CAAC,CAAA;IACF,MAAM,OAAO,GAAG,gBAAgB,EAAE,CAAC,aAAa,IAAI,EAAE,CAAC,CAAA;IACvD,MAAM,EAAE,SAAS,EAAE,mBAAmB,EAAE,KAAK,EAAE,MAAM,EAAE,GACrD,6BAA6B,CAAC,EAAE,IAAI,EAAE,CAAC,CAAA;IAEzC,MAAM,EAAE,SAAS,EAAE,mBAAmB,EAAE,KAAK,EAAE,MAAM,EAAE,GACrD,8BAA8B,CAAC,EAAE,GAAG,EAAE,YAAY,EAAE,CAAC,CAAA;IACvD,MAAM,aAAa,GACjB,IAAI,EAAE,IAAI,IAAI,YAAY,CAAC,KAAK,CAAC,YAAY,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;IACrE,MAAM,kBAAkB,GAAG,mBAAmB,IAAI,mBAAmB,CAAA;IACrE,MAAM,iBAAiB,GAAG,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAA;IAEjD,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,gBAAgB,KAAK,SAAS,EAAE,CAAC;YACnC,MAAM,GAAG,GACP,OAAO,CAAC,IAAI,CACV,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;gBACjD,iBAAiB,CACpB,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;YACpD,gBAAgB,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAA;QAC7B,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,iBAAiB,EAAE,gBAAgB,CAAC,CAAC,CAAA;IAElD,MAAM,CAAC,GAAG,KAAK,IAAI,MAAM,IAAI,MAAM,IAAI,MAAM,CAAA;IAC7C,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,QAAQ,OAAG;YAEZ,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE;gBACzC,oBAAC,UAAU;;oBACgB,oBAAC,UAAU,OAAG,CAC5B;gBAEb,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;oBAC/B,oBAAC,UAAU,IACT,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE;4BAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBAC/B,CAAC;wBAED,oBAAC,gBAAgB,IAAC,KAAK,EAAC,KAAK,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,KAAK,GAAG;wBAChE,oBAAC,gBAAgB,IAAC,KAAK,EAAC,MAAM,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,MAAM,GAAG;wBAClE,oBAAC,gBAAgB,IACf,KAAK,EAAC,KAAK,EACX,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,QAAQ,GACd,CACS,CACD;gBACb,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB;oBACE,oBAAC,UAAU,qDAEE;oBACb,oBAAC,SAAS,IACR,KAAK,EAAC,KAAK,EACX,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;4BAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBACrC,CAAC,GACD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE;oBAC5B,oBAAC,UAAU,2DAEE;oBACb,oBAAC,MAAM,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAC,OAAO;;wBAE1C,+BACE,IAAI,EAAC,MAAM,EACX,MAAM,QACN,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE;gCACvB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;gCAC9B,IAAI,IAAI,EAAE,CAAC;oCACT,OAAO,CAAC,IAAI,CAAC,CAAA;gCACf,CAAC;4BACH,CAAC,GACD,CACK,CACL,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB,oBAAC,SAAS,IACR,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,KAAK,CAAA;wBAC5B,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACX,eAAe,CAAC,mCAAmC,CAAC,MAAM,CAAC,CAAA;oBAC7D,CAAC,EACD,KAAK,EAAC,QAAQ,GACd,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,IACvB,gBAAgB,CAAC,CAAC,CAAC,CAClB,iBAAiB,CAAC,CAAC,CAAC,CAClB;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|
|
@@ -8,7 +8,7 @@ export function calculateProteinSequence({ cds, sequence, codonTable, }) {
|
|
|
8
8
|
let protein = '';
|
|
9
9
|
for (let i = 0; i < str.length; i += 3) {
|
|
10
10
|
// use & symbol for undefined codon, or partial slice
|
|
11
|
-
protein += codonTable[str.slice(i, i + 3)]
|
|
11
|
+
protein += codonTable[str.slice(i, i + 3)] ?? '&';
|
|
12
12
|
}
|
|
13
13
|
return protein;
|
|
14
14
|
}
|
|
@@ -52,8 +52,10 @@ export async function fetchProteinSeq({ feature, view, }) {
|
|
|
52
52
|
const refName = feature.get('refName');
|
|
53
53
|
const session = getSession(view);
|
|
54
54
|
const { assemblyManager, rpcManager } = session;
|
|
55
|
-
const
|
|
56
|
-
const assembly =
|
|
55
|
+
const assemblyName = view?.assemblyNames?.[0];
|
|
56
|
+
const assembly = assemblyName
|
|
57
|
+
? await assemblyManager.waitForAssembly(assemblyName)
|
|
58
|
+
: undefined;
|
|
57
59
|
if (!assembly) {
|
|
58
60
|
throw new Error('assembly not found');
|
|
59
61
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAEL,iBAAiB,EACjB,kBAAkB,EAClB,UAAU,EACV,MAAM,GACP,MAAM,oBAAoB,CAAA;AAQ3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAc;IAClD,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AACtC,CAAC;AAED,sDAAsD;AACtD,SAAS,SAAS,CAAC,IAAU;IAC3B,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACpC,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAY;IACjC,OAAO,IAAI,CAAC,MAAM,CAChB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,
|
|
1
|
+
{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAEL,iBAAiB,EACjB,kBAAkB,EAClB,UAAU,EACV,MAAM,GACP,MAAM,oBAAoB,CAAA;AAQ3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAc;IAClD,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AACtC,CAAC;AAED,sDAAsD;AACtD,SAAS,SAAS,CAAC,IAAU;IAC3B,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACpC,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAY;IACjC,OAAO,IAAI,CAAC,MAAM,CAChB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,CACzE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,EACjC,OAAO,EACP,GAAG,GAIJ;IACC,mBAAmB;IACnB,MAAM,CAAC,GAAG,OAAO,CAAC,MAAM,EAMvB,CAAA;IACD,MAAM,GAAG,GAAG,MAAM,CAChB,CAAC,CAAC,WAAW;SACV,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;SACjC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK;QAC1B,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK;KACvB,CAAC,CAAC;SACF,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC,CACjC,CAAA;IAED,OAAO,wBAAwB,CAAC;QAC9B,GAAG,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG;QACrD,QAAQ,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG;QAC7C,UAAU,EAAE,kBAAkB,CAAC,iBAAiB,CAAC;KAClD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,EACpC,OAAO,EACP,IAAI,GAIL;IACC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACtC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAChC,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,YAAY,GAAG,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IAC7C,MAAM,QAAQ,GAAG,YAAY;QAC3B,CAAC,CAAC,MAAM,eAAe,CAAC,eAAe,CAAC,YAAY,CAAC;QACrD,CAAC,CAAC,SAAS,CAAA;IACb,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;IACvC,CAAC;IACD,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,MAAM,KAAK,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QAChE,aAAa,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACzD,SAAS;QACT,OAAO,EAAE;YACP;gBACE,KAAK;gBACL,GAAG;gBACH,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,OAAO,CAAC;gBAC9C,YAAY;aACb;SACF;KACF,CAAC,CAAA;IAEF,MAAM,CAAC,IAAI,CAAC,GAAG,KAAkB,CAAA;IACjC,MAAM,GAAG,GAAG,IAAI,EAAE,GAAG,CAAC,KAAK,CAAuB,CAAA;IAClD,OAAO,GAAG,CAAC,CAAC,CAAC,kBAAkB,CAAC,EAAE,GAAG,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AAC/D,CAAC"}
|
|
@@ -1,23 +1,38 @@
|
|
|
1
1
|
import { useEffect, useState } from 'react';
|
|
2
2
|
import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
|
|
3
3
|
import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
|
|
4
|
-
import {
|
|
4
|
+
import { addStructureFromData } from '../../ProteinView/addStructureFromData';
|
|
5
5
|
async function structureFileSequenceFetcher(file, format) {
|
|
6
6
|
const ret = document.createElement('div');
|
|
7
7
|
const p = await createPluginUI({
|
|
8
8
|
target: ret,
|
|
9
9
|
render: renderReact18,
|
|
10
10
|
});
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
11
|
+
try {
|
|
12
|
+
const { model } = await addStructureFromData({
|
|
13
|
+
data: await file.text(),
|
|
14
|
+
plugin: p,
|
|
15
|
+
format,
|
|
16
|
+
});
|
|
17
|
+
return model.obj?.data.sequence.sequences.map(s => {
|
|
18
|
+
let seq = '';
|
|
19
|
+
const arr = s.sequence.label.toArray();
|
|
20
|
+
// eslint-disable-next-line unicorn/no-for-loop,@typescript-eslint/prefer-for-of
|
|
21
|
+
for (let i = 0; i < arr.length; i++) {
|
|
22
|
+
seq += arr[i];
|
|
23
|
+
}
|
|
24
|
+
return seq;
|
|
25
|
+
});
|
|
26
|
+
}
|
|
27
|
+
finally {
|
|
28
|
+
p.unmount();
|
|
29
|
+
ret.remove();
|
|
30
|
+
}
|
|
16
31
|
}
|
|
17
32
|
export default function useLocalStructureFileSequence({ file, }) {
|
|
18
33
|
const [error, setError] = useState();
|
|
19
34
|
const [isLoading, setLoading] = useState(false);
|
|
20
|
-
const [
|
|
35
|
+
const [sequences, setSequences] = useState();
|
|
21
36
|
useEffect(() => {
|
|
22
37
|
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
23
38
|
;
|
|
@@ -27,7 +42,12 @@ export default function useLocalStructureFileSequence({ file, }) {
|
|
|
27
42
|
setLoading(true);
|
|
28
43
|
const ext = file.name.slice(file.name.lastIndexOf('.') + 1) || 'pdb';
|
|
29
44
|
const seq = await structureFileSequenceFetcher(file, (ext === 'cif' ? 'mmcif' : ext));
|
|
30
|
-
|
|
45
|
+
if (seq) {
|
|
46
|
+
setSequences(seq);
|
|
47
|
+
}
|
|
48
|
+
else {
|
|
49
|
+
throw new Error('no sequences detected in file');
|
|
50
|
+
}
|
|
31
51
|
}
|
|
32
52
|
}
|
|
33
53
|
catch (e) {
|
|
@@ -39,6 +59,6 @@ export default function useLocalStructureFileSequence({ file, }) {
|
|
|
39
59
|
}
|
|
40
60
|
})();
|
|
41
61
|
}, [file]);
|
|
42
|
-
return { error, isLoading,
|
|
62
|
+
return { error, isLoading, sequences };
|
|
43
63
|
}
|
|
44
64
|
//# sourceMappingURL=useLocalStructureFileSequence.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"useLocalStructureFileSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/useLocalStructureFileSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"useLocalStructureFileSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/useLocalStructureFileSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,oBAAoB,EAAE,MAAM,wCAAwC,CAAA;AAE7E,KAAK,UAAU,4BAA4B,CACzC,IAAU,EACV,MAAuB;IAEvB,MAAM,GAAG,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;IACzC,MAAM,CAAC,GAAG,MAAM,cAAc,CAAC;QAC7B,MAAM,EAAE,GAAG;QACX,MAAM,EAAE,aAAa;KACtB,CAAC,CAAA;IAEF,IAAI,CAAC;QACH,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,oBAAoB,CAAC;YAC3C,IAAI,EAAE,MAAM,IAAI,CAAC,IAAI,EAAE;YACvB,MAAM,EAAE,CAAC;YACT,MAAM;SACP,CAAC,CAAA;QACF,OAAO,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAChD,IAAI,GAAG,GAAG,EAAE,CAAA;YACZ,MAAM,GAAG,GAAG,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;YACtC,gFAAgF;YAChF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACpC,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;YAChB,CAAC;YACD,OAAO,GAAG,CAAA;QACZ,CAAC,CAAC,CAAA;IACJ,CAAC;YAAS,CAAC;QACT,CAAC,CAAC,OAAO,EAAE,CAAA;QACX,GAAG,CAAC,MAAM,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,6BAA6B,CAAC,EACpD,IAAI,GAGL;IACC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAY,CAAA;IACtD,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,IAAI,EAAE,CAAC;oBACT,UAAU,CAAC,IAAI,CAAC,CAAA;oBAEhB,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,KAAK,CAAA;oBACpE,MAAM,GAAG,GAAG,MAAM,4BAA4B,CAC5C,IAAI,EACJ,CAAC,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAoB,CACnD,CAAA;oBACD,IAAI,GAAG,EAAE,CAAC;wBACR,YAAY,CAAC,GAAG,CAAC,CAAA;oBACnB,CAAC;yBAAM,CAAC;wBACN,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;oBAClD,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;oBAAS,CAAC;gBACT,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAA;IACV,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,CAAA;AACxC,CAAC"}
|
|
@@ -1,22 +1,34 @@
|
|
|
1
1
|
import { useEffect, useState } from 'react';
|
|
2
2
|
import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
|
|
3
3
|
import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
|
|
4
|
-
import {
|
|
4
|
+
import { addStructureFromURL } from '../../ProteinView/addStructureFromURL';
|
|
5
5
|
async function structureFileSequenceFetcher(url) {
|
|
6
6
|
const ret = document.createElement('div');
|
|
7
7
|
const p = await createPluginUI({
|
|
8
8
|
target: ret,
|
|
9
9
|
render: renderReact18,
|
|
10
10
|
});
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
11
|
+
try {
|
|
12
|
+
const { model } = await addStructureFromURL({ url, plugin: p });
|
|
13
|
+
return model.obj?.data.sequence.sequences.map(s => {
|
|
14
|
+
let seq = '';
|
|
15
|
+
const arr = s.sequence.label.toArray();
|
|
16
|
+
// eslint-disable-next-line unicorn/no-for-loop,@typescript-eslint/prefer-for-of
|
|
17
|
+
for (let i = 0; i < arr.length; i++) {
|
|
18
|
+
seq += arr[i];
|
|
19
|
+
}
|
|
20
|
+
return seq;
|
|
21
|
+
});
|
|
22
|
+
}
|
|
23
|
+
finally {
|
|
24
|
+
p.unmount();
|
|
25
|
+
ret.remove();
|
|
26
|
+
}
|
|
15
27
|
}
|
|
16
28
|
export default function useRemoteStructureFileSequence({ url, }) {
|
|
17
29
|
const [error, setError] = useState();
|
|
18
30
|
const [isLoading, setLoading] = useState(false);
|
|
19
|
-
const [
|
|
31
|
+
const [sequences, setSequences] = useState();
|
|
20
32
|
useEffect(() => {
|
|
21
33
|
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
22
34
|
;
|
|
@@ -25,7 +37,12 @@ export default function useRemoteStructureFileSequence({ url, }) {
|
|
|
25
37
|
if (url) {
|
|
26
38
|
setLoading(true);
|
|
27
39
|
const seq = await structureFileSequenceFetcher(url);
|
|
28
|
-
|
|
40
|
+
if (seq) {
|
|
41
|
+
setSequences(seq);
|
|
42
|
+
}
|
|
43
|
+
else {
|
|
44
|
+
throw new Error('no sequences detected in file');
|
|
45
|
+
}
|
|
29
46
|
}
|
|
30
47
|
}
|
|
31
48
|
catch (e) {
|
|
@@ -37,6 +54,6 @@ export default function useRemoteStructureFileSequence({ url, }) {
|
|
|
37
54
|
}
|
|
38
55
|
})();
|
|
39
56
|
}, [url]);
|
|
40
|
-
return { error, isLoading,
|
|
57
|
+
return { error, isLoading, sequences };
|
|
41
58
|
}
|
|
42
59
|
//# sourceMappingURL=useRemoteStructureFileSequence.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"useRemoteStructureFileSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/useRemoteStructureFileSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"useRemoteStructureFileSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/useRemoteStructureFileSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,mBAAmB,EAAE,MAAM,uCAAuC,CAAA;AAE3E,KAAK,UAAU,4BAA4B,CAAC,GAAW;IACrD,MAAM,GAAG,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;IACzC,MAAM,CAAC,GAAG,MAAM,cAAc,CAAC;QAC7B,MAAM,EAAE,GAAG;QACX,MAAM,EAAE,aAAa;KACtB,CAAC,CAAA;IACF,IAAI,CAAC;QACH,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,mBAAmB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAA;QAC/D,OAAO,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAChD,IAAI,GAAG,GAAG,EAAE,CAAA;YACZ,MAAM,GAAG,GAAG,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;YACtC,gFAAgF;YAChF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACpC,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;YAChB,CAAC;YACD,OAAO,GAAG,CAAA;QACZ,CAAC,CAAC,CAAA;IACJ,CAAC;YAAS,CAAC;QACT,CAAC,CAAC,OAAO,EAAE,CAAA;QACX,GAAG,CAAC,MAAM,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,8BAA8B,CAAC,EACrD,GAAG,GAGJ;IACC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAY,CAAA;IACtD,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,GAAG,EAAE,CAAC;oBACR,UAAU,CAAC,IAAI,CAAC,CAAA;oBAChB,MAAM,GAAG,GAAG,MAAM,4BAA4B,CAAC,GAAG,CAAC,CAAA;oBACnD,IAAI,GAAG,EAAE,CAAC;wBACR,YAAY,CAAC,GAAG,CAAC,CAAA;oBACnB,CAAC;yBAAM,CAAC;wBACN,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;oBAClD,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;oBAAS,CAAC;gBACT,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;IACT,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,CAAA;AACxC,CAAC"}
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@@ -7,7 +7,7 @@ function isDisplay(elt) {
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7
7
|
return elt.name === 'LinearBasicDisplay';
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8
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}
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9
9
|
function extendStateModel(stateModel) {
|
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10
|
-
return stateModel.views(self => {
|
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10
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+
return stateModel.views((self) => {
|
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|
const superContextMenuItems = self.contextMenuItems;
|
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return {
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contextMenuItems() {
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@@ -18,12 +18,16 @@ function extendStateModel(stateModel) {
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...(feature
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19
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? [
|
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{
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-
label: 'Launch
|
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+
label: 'Launch protein view',
|
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|
icon: AddIcon,
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|
onClick: () => {
|
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24
|
getSession(track).queueDialog(handleClose => [
|
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LaunchProteinViewDialog,
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-
{
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+
{
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model: track,
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+
handleClose,
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+
feature,
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+
},
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27
31
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]);
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32
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},
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},
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchProteinView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAE,kBAAkB,
|
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1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchProteinView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAE,kBAAkB,EAAW,MAAM,oBAAoB,CAAA;AAE5E,QAAQ;AACR,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,SAAS;AACT,OAAO,uBAAuB,MAAM,sCAAsC,CAAA;AAG1E,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CACrB,CAAC,IAGA,EAAE,EAAE;QACH,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,qBAAqB;gCAC5B,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,uBAAuB;wCACvB;4CACE,KAAK,EAAE,KAAK;4CACZ,WAAW;4CACX,OAAO;yCACR;qCACF,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B,EAC7B,CAAC,GAAyB,EAAE,EAAE;QAC5B,IAAI,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,GAAG,CAAC,UAAU,GAAG,gBAAgB,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QACnD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CACF,CAAA;AACH,CAAC"}
|
|
@@ -4,7 +4,7 @@ import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-st
|
|
|
4
4
|
export interface LoadStructureOptions {
|
|
5
5
|
representationParams?: StructureRepresentationPresetProvider.CommonParams;
|
|
6
6
|
}
|
|
7
|
-
export declare function
|
|
7
|
+
export declare function addStructureFromData({ data, format, options, plugin, }: {
|
|
8
8
|
data: string;
|
|
9
9
|
format?: BuiltInTrajectoryFormat;
|
|
10
10
|
options?: LoadStructureOptions & {
|
|
@@ -13,5 +13,5 @@ export declare function loadStructureFromData({ data, format, options, plugin, }
|
|
|
13
13
|
};
|
|
14
14
|
plugin: PluginContext;
|
|
15
15
|
}): Promise<{
|
|
16
|
-
|
|
16
|
+
model: import("molstar/lib/mol-state").StateObjectSelector<import("molstar/lib/mol-plugin-state/objects").PluginStateObject.Molecule.Model, import("molstar/lib/mol-state").StateTransformer<import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, any>>;
|
|
17
17
|
}>;
|