jbrowse-plugin-msaview 2.3.5 → 2.3.8
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/README.md +15 -216
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +19 -4
- package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +16 -7
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +4 -2
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +4 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js +8 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js +15 -7
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js +8 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js +3 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map +1 -1
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +7 -2
- package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/TabPanel.js +1 -1
- package/dist/LaunchMsaView/components/TabPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/TranscriptSelector.js +7 -3
- package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -1
- package/dist/MsaViewPanel/afterCreateAutoruns.js +9 -15
- package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
- package/dist/MsaViewPanel/components/ConnectStructureDialog.js +15 -10
- package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -1
- package/dist/MsaViewPanel/components/MsaViewPanel.js +8 -1
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +2 -2
- package/dist/MsaViewPanel/model.js +13 -10
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/pairwiseAlignment.js +6 -6
- package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -1
- package/dist/MsaViewPanel/structureConnection.d.ts +22 -0
- package/dist/MsaViewPanel/structureConnection.js +4 -0
- package/dist/MsaViewPanel/structureConnection.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +24 -24
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +2 -4
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +1 -2
- package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +22 -7
- package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +17 -9
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +8 -3
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +4 -1
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx +9 -1
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.tsx +15 -8
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx +9 -1
- package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts +3 -0
- package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +11 -2
- package/src/LaunchMsaView/components/TabPanel.tsx +1 -1
- package/src/LaunchMsaView/components/TranscriptSelector.tsx +7 -3
- package/src/MsaViewPanel/afterCreateAutoruns.ts +9 -27
- package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +23 -25
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +9 -1
- package/src/MsaViewPanel/model.ts +23 -18
- package/src/MsaViewPanel/pairwiseAlignment.ts +6 -6
- package/src/MsaViewPanel/structureConnection.ts +23 -0
- package/src/version.ts +1 -1
|
@@ -1,15 +1,22 @@
|
|
|
1
1
|
import React, { useState } from 'react';
|
|
2
2
|
import { Button, Dialog, DialogActions, DialogContent, DialogTitle, } from '@mui/material';
|
|
3
|
+
import { makeStyles } from 'tss-react/mui';
|
|
3
4
|
import { BASE_BLAST_URL } from './consts';
|
|
4
5
|
import TextField2 from '../../../components/TextField2';
|
|
6
|
+
const useStyles = makeStyles()({
|
|
7
|
+
urlField: {
|
|
8
|
+
minWidth: 300,
|
|
9
|
+
},
|
|
10
|
+
});
|
|
5
11
|
export default function NCBISettingsDialog({ handleClose, baseUrl, }) {
|
|
12
|
+
const { classes } = useStyles();
|
|
6
13
|
const [tempBaseUrl, setTempBaseUrl] = useState(baseUrl);
|
|
7
14
|
return (React.createElement(Dialog, { open: true, maxWidth: "lg", onClose: () => {
|
|
8
15
|
handleClose();
|
|
9
16
|
} },
|
|
10
17
|
React.createElement(DialogTitle, null, "BLAST Settings"),
|
|
11
18
|
React.createElement(DialogContent, null,
|
|
12
|
-
React.createElement(TextField2, { autoFocus: true, margin: "dense", label: "BLAST Base URL", fullWidth: true, variant: "outlined", value: tempBaseUrl,
|
|
19
|
+
React.createElement(TextField2, { autoFocus: true, margin: "dense", label: "BLAST Base URL", fullWidth: true, variant: "outlined", value: tempBaseUrl, className: classes.urlField, onChange: e => {
|
|
13
20
|
setTempBaseUrl(e.target.value);
|
|
14
21
|
} }),
|
|
15
22
|
React.createElement(Button, { variant: "contained", onClick: () => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"NCBISettingsDialog.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,GACZ,MAAM,eAAe,CAAA;
|
|
1
|
+
{"version":3,"file":"NCBISettingsDialog.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,GACZ,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAEvD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,WAAW,EACX,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;IACvD,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC;QAED,oBAAC,WAAW,yBAA6B;QACzC,oBAAC,aAAa;YACZ,oBAAC,UAAU,IACT,SAAS,QACT,MAAM,EAAC,OAAO,EACd,KAAK,EAAC,gBAAgB,EACtB,SAAS,QACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,WAAW,EAClB,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,QAAQ,EAAE,CAAC,CAAC,EAAE;oBACZ,cAAc,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAChC,CAAC,GACD;YACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,cAAc,CAAC,cAAc,CAAC,CAAA;gBAChC,CAAC,YAGM,CACK;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,CAAC,WAAW,CAAC,CAAA;gBAC1B,CAAC,WAGM,CACK,CACT,CACV,CAAA;AACH,CAAC"}
|
|
@@ -4,6 +4,9 @@ const swrConfig = {
|
|
|
4
4
|
revalidateOnFocus: false,
|
|
5
5
|
revalidateOnReconnect: false,
|
|
6
6
|
revalidateIfStale: false,
|
|
7
|
+
refreshWhenHidden: false,
|
|
8
|
+
refreshWhenOffline: false,
|
|
9
|
+
shouldRetryOnError: false,
|
|
7
10
|
};
|
|
8
11
|
export function useCachedBlastResults(geneIds) {
|
|
9
12
|
const { data: results, error, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"useCachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,KAAK,CAAA;AAExB,OAAO,EACL,qBAAqB,EACrB,kBAAkB,EAClB,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAElC,MAAM,SAAS,GAAG;IAChB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;
|
|
1
|
+
{"version":3,"file":"useCachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,KAAK,CAAA;AAExB,OAAO,EACL,qBAAqB,EACrB,kBAAkB,EAClB,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAElC,MAAM,SAAS,GAAG;IAChB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;IACxB,iBAAiB,EAAE,KAAK;IACxB,kBAAkB,EAAE,KAAK;IACzB,kBAAkB,EAAE,KAAK;CAC1B,CAAA;AAED,MAAM,UAAU,qBAAqB,CAAC,OAAiB;IACrD,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,KAAK,EACL,MAAM,GACP,GAAG,MAAM,CACR,gBAAgB,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EACnC,KAAK,IAAI,EAAE;QACT,MAAM,MAAM,GAAG,MAAM,mBAAmB,EAAE,CAAA;QAC1C,OAAO,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;IACnE,CAAC,EACD,SAAS,CACV,CAAA;IAED,MAAM,YAAY,GAAG,KAAK,EAAE,EAAU,EAAE,EAAE;QACxC,MAAM,kBAAkB,CAAC,EAAE,CAAC,CAAA;QAC5B,MAAM,MAAM,CACV,OAAO,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC,IAAI,EAAE,EAC5D,KAAK,CACN,CAAA;IACH,CAAC,CAAA;IAED,MAAM,cAAc,GAAG,KAAK,IAAI,EAAE;QAChC,MAAM,qBAAqB,EAAE,CAAA;QAC7B,MAAM,MAAM,CAAC,EAAE,EAAE,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,OAAO;QACL,OAAO,EAAE,OAAO,IAAI,EAAE;QACtB,KAAK;QACL,SAAS,EAAE,CAAC,OAAO,IAAI,CAAC,KAAK;QAC7B,YAAY;QACZ,cAAc;KACf,CAAA;AACH,CAAC"}
|
|
@@ -17,6 +17,9 @@ const useStyles = makeStyles()({
|
|
|
17
17
|
dialogContent: {
|
|
18
18
|
width: '80em',
|
|
19
19
|
},
|
|
20
|
+
selectedContainer: {
|
|
21
|
+
marginTop: 50,
|
|
22
|
+
},
|
|
20
23
|
});
|
|
21
24
|
const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
|
|
22
25
|
const session = getSession(model);
|
|
@@ -55,7 +58,7 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
|
|
|
55
58
|
React.createElement(TextField2, { select: true, label: "Select MSA dataset", value: selectedDatasetId, onChange: event => {
|
|
56
59
|
setSelectedDatasetId(event.target.value);
|
|
57
60
|
} }, datasets?.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))),
|
|
58
|
-
selectedDataset ? (React.createElement("div", {
|
|
61
|
+
selectedDataset ? (React.createElement("div", { className: classes.selectedContainer },
|
|
59
62
|
!msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for (${selectedId})` })) : null,
|
|
60
63
|
msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
|
|
61
64
|
msaList ? (React.createElement("div", null,
|
|
@@ -86,7 +89,9 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
|
|
|
86
89
|
setViewError(e);
|
|
87
90
|
}
|
|
88
91
|
} }, "Submit"),
|
|
89
|
-
React.createElement(Button, { color: "secondary", variant: "contained", onClick:
|
|
92
|
+
React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
|
|
93
|
+
handleClose();
|
|
94
|
+
} }, "Cancel"))));
|
|
90
95
|
});
|
|
91
96
|
export default PreLoadedMSA;
|
|
92
97
|
//# sourceMappingURL=PreLoadedMSADataPanel.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAC/E,OAAO,EAAE,iBAAiB,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,MAAM,MAAM,KAAK,CAAA;AACxB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,UAAU,CAAA;AACnC,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AAMnE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EACtC,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAW,CAAA;IAErD,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;IAC3B,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAE/C,CAAA;IACb,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CACxD,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,CACzB,CAAA;IACD,MAAM,eAAe,GAAG,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,iBAAiB,CAAC,CAAA;IAC9E,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,iBAAiB,CAAC,CAAC,CAAC,GAAG,iBAAiB,WAAW,CAAC,CAAC,CAAC,eAAe,EACrE,GAAG,EAAE,CACH,eAAe;QACb,CAAC,CAAC,YAAY,CAAC;YACX,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,EACJ,OAAO,EAAE,WAAW,EACpB,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,GAC5B,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC,CAAA;IAEhE,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,UAAU,IAAI,iBAAiB;QAC7B,CAAC,CAAC,GAAG,iBAAiB,IAAI,UAAU,IAAI,OAAO,EAAE,MAAM,MAAM;QAC7D,CAAC,CAAC,UAAU,EACd,GAAG,EAAE,CACH,UAAU,IAAI,eAAe,IAAI,OAAO;QACtC,CAAC,CAAC,QAAQ,CAAC;YACP,KAAK,EAAE,UAAU;YACjB,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,CAAC,GACL,iBAAiB,IAAI,iBAAiB,IAAI,oBAAoB,IAAI,SAAS,CAAA;IAC7E,IAAI,CAAC,EAAE,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAClB,CAAC;IACD,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;YAEtC,oBAAC,UAAU,IACT,MAAM,QACN,KAAK,EAAC,oBAAoB,EAC1B,KAAK,EAAE,iBAAiB,EACxB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,oBAAoB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC,IAEA,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClB,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,CAAC,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,SAAS,IAC3C,CAAC,CAAC,IAAI,CACE,CACZ,CAAC,CACS;YAEZ,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,
|
|
1
|
+
{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAC/E,OAAO,EAAE,iBAAiB,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,MAAM,MAAM,KAAK,CAAA;AACxB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,UAAU,CAAA;AACnC,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AAMnE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,iBAAiB,EAAE;QACjB,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EACtC,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAW,CAAA;IAErD,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;IAC3B,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAE/C,CAAA;IACb,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CACxD,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,CACzB,CAAA;IACD,MAAM,eAAe,GAAG,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,iBAAiB,CAAC,CAAA;IAC9E,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,iBAAiB,CAAC,CAAC,CAAC,GAAG,iBAAiB,WAAW,CAAC,CAAC,CAAC,eAAe,EACrE,GAAG,EAAE,CACH,eAAe;QACb,CAAC,CAAC,YAAY,CAAC;YACX,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,EACJ,OAAO,EAAE,WAAW,EACpB,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,GAC5B,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC,CAAA;IAEhE,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,UAAU,IAAI,iBAAiB;QAC7B,CAAC,CAAC,GAAG,iBAAiB,IAAI,UAAU,IAAI,OAAO,EAAE,MAAM,MAAM;QAC7D,CAAC,CAAC,UAAU,EACd,GAAG,EAAE,CACH,UAAU,IAAI,eAAe,IAAI,OAAO;QACtC,CAAC,CAAC,QAAQ,CAAC;YACP,KAAK,EAAE,UAAU;YACjB,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,CAAC,GACL,iBAAiB,IAAI,iBAAiB,IAAI,oBAAoB,IAAI,SAAS,CAAA;IAC7E,IAAI,CAAC,EAAE,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAClB,CAAC;IACD,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;YAEtC,oBAAC,UAAU,IACT,MAAM,QACN,KAAK,EAAC,oBAAoB,EAC1B,KAAK,EAAE,iBAAiB,EACxB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,oBAAoB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC,IAEA,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClB,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,CAAC,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,SAAS,IAC3C,CAAC,CAAC,IAAI,CACE,CACZ,CAAC,CACS;YAEZ,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,SAAS,EAAE,OAAO,CAAC,iBAAiB;gBACtC,CAAC,cAAc,IAAI,cAAc,CAAC,CAAC,CAAC,CACnC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAE,oBAAoB,UAAU,GAAG,GAC1C,CACH,CAAC,CAAC,CAAC,IAAI;gBACP,cAAc,CAAC,CAAC,CAAC,CAChB,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAE,+BAA+B,eAAe,CAAC,IAAI,GAAG,GAC/D,CACH,CAAC,CAAC,CAAC,IAAI;gBAEP,OAAO,CAAC,CAAC,CAAC,CACT;oBACE,oBAAC,aAAa,IAAC,IAAI,EAAE,eAAe,CAAC,WAAW,GAAI;oBACpD,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,WAAW,EACpB,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,EAChC,QAAQ,EAAE,OAAO,GACjB,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACM;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,MAAM,EACjD,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,CAAC;4BACpC,OAAM;wBACR,CAAC;wBACD,MAAM,YAAY,GAAG,GAAG,UAAU,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAA;wBACxD,uBAAuB,CAAC;4BACtB,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,kBAAkB,CAAC;4BACpD,IAAI;4BACJ,YAAY;4BACZ,OAAO,EAAE,kBAAkB;4BAC3B,IAAI,EAAE;gCACJ,GAAG,EAAE,OAAO;qCACT,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;qCACjD,IAAI,CAAC,IAAI,CAAC;6BACd;yBACF,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,YAAY,CAAC,CAAC,CAAC,CAAA;oBACjB,CAAC;gBACH,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
2
|
// this is from MUI example
|
|
3
3
|
export default function TabPanel({ children, value, index, ...other }) {
|
|
4
|
-
return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index
|
|
4
|
+
return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index ? React.createElement("div", null, children) : null));
|
|
5
5
|
}
|
|
6
6
|
//# sourceMappingURL=TabPanel.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"TabPanel.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,2BAA2B;AAC3B,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAC/B,QAAQ,EACR,KAAK,EACL,KAAK,EACL,GAAG,KAAK,EAKT;IACC,OAAO,CACL,6BAAK,IAAI,EAAC,UAAU,EAAC,MAAM,EAAE,KAAK,KAAK,KAAK,KAAM,KAAK,IACpD,KAAK,KAAK,KAAK,
|
|
1
|
+
{"version":3,"file":"TabPanel.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,2BAA2B;AAC3B,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAC/B,QAAQ,EACR,KAAK,EACL,KAAK,EACL,GAAG,KAAK,EAKT;IACC,OAAO,CACL,6BAAK,IAAI,EAAC,UAAU,EAAC,MAAM,EAAE,KAAK,KAAK,KAAK,KAAM,KAAK,IACpD,KAAK,KAAK,KAAK,CAAC,CAAC,CAAC,iCAAM,QAAQ,CAAO,CAAC,CAAC,CAAC,IAAI,CAC3C,CACP,CAAA;AACH,CAAC"}
|
|
@@ -10,6 +10,10 @@ const useStyles = makeStyles()({
|
|
|
10
10
|
minWidth: {
|
|
11
11
|
minWidth: 300,
|
|
12
12
|
},
|
|
13
|
+
centered: {
|
|
14
|
+
alignContent: 'center',
|
|
15
|
+
marginLeft: 20,
|
|
16
|
+
},
|
|
13
17
|
});
|
|
14
18
|
export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validIds, }) {
|
|
15
19
|
const { classes } = useStyles();
|
|
@@ -32,12 +36,12 @@ export default function TranscriptSelector({ feature, options, selectedId, selec
|
|
|
32
36
|
mod ? ` (possible fragment)` : '',
|
|
33
37
|
validIds ? (inSet ? ' (has data)' : ' (no data)') : ''));
|
|
34
38
|
})),
|
|
35
|
-
React.createElement("div", {
|
|
39
|
+
React.createElement("div", { className: classes.centered },
|
|
36
40
|
React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
|
|
37
41
|
setShowSequence(!showSequence);
|
|
38
42
|
} }, showSequence ? 'Hide sequence' : 'Show sequence'))),
|
|
39
|
-
showSequence
|
|
43
|
+
showSequence ? (React.createElement(ReadOnlyTextField2, { value: proteinSequence
|
|
40
44
|
? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
|
|
41
|
-
: 'Loading...' }))));
|
|
45
|
+
: 'Loading...' })) : null));
|
|
42
46
|
}
|
|
43
47
|
//# sourceMappingURL=TranscriptSelector.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,qCAAqC,CAAA;AACpE,OAAO,EACL,gBAAgB,EAChB,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAIhB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,OAAO,EACP,OAAO,EACP,UAAU,EACV,kBAAkB,EAClB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAST;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACjB,MAAM,KAAK,GAAG,QAAQ;oBACpB,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,gBAAgB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;oBAChD,CAAC,CAAC,IAAI,CAAA;gBACR,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC7C,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAI,GAAG;;oBAAM,GAAG;oBAC7C,GAAG,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE;oBACjC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9C,CACZ,CAAA;YACH,CAAC,CAAC,CACQ;YACZ,6BAAK,
|
|
1
|
+
{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,qCAAqC,CAAA;AACpE,OAAO,EACL,gBAAgB,EAChB,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAIhB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;IACD,QAAQ,EAAE;QACR,YAAY,EAAE,QAAQ;QACtB,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,OAAO,EACP,OAAO,EACP,UAAU,EACV,kBAAkB,EAClB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAST;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACjB,MAAM,KAAK,GAAG,QAAQ;oBACpB,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,gBAAgB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;oBAChD,CAAC,CAAC,IAAI,CAAA;gBACR,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC7C,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAI,GAAG;;oBAAM,GAAG;oBAC7C,GAAG,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE;oBACjC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9C,CACZ,CAAA;YACH,CAAC,CAAC,CACQ;YACZ,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ;gBAC9B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,eAAe,CAAC,CAAC,YAAY,CAAC,CAAA;oBAChC,CAAC,IAEA,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,eAAe,CAC1C,CACL,CACF;QAEL,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,kBAAkB,IACjB,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,GAElB,CACH,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}
|
|
@@ -2,12 +2,8 @@ import { getSession } from '@jbrowse/core/util';
|
|
|
2
2
|
import { doLaunchBlast } from './doLaunchBlast';
|
|
3
3
|
import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
|
|
4
4
|
import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
|
|
5
|
-
import { gappedToUngappedPosition } from './structureConnection';
|
|
5
|
+
import { gappedToUngappedPosition, isProteinView } from './structureConnection';
|
|
6
6
|
import { getUniprotIdFromAlphaFoldUrl } from './util';
|
|
7
|
-
function isProteinView(view) {
|
|
8
|
-
const v = view;
|
|
9
|
-
return v.type === 'ProteinView' && Array.isArray(v.structures);
|
|
10
|
-
}
|
|
11
7
|
export function loadStoredData(self) {
|
|
12
8
|
const { dataStoreId, rows } = self;
|
|
13
9
|
if (dataStoreId && rows.length === 0) {
|
|
@@ -154,7 +150,7 @@ export function highlightConnectedStructures(self) {
|
|
|
154
150
|
return;
|
|
155
151
|
}
|
|
156
152
|
for (const conn of connectedProteinViews) {
|
|
157
|
-
const structure = conn.proteinView
|
|
153
|
+
const structure = conn.proteinView.structures[conn.structureIdx];
|
|
158
154
|
if (!structure) {
|
|
159
155
|
continue;
|
|
160
156
|
}
|
|
@@ -181,7 +177,7 @@ export function highlightConnectedStructures(self) {
|
|
|
181
177
|
}
|
|
182
178
|
}
|
|
183
179
|
export function autoConnectStructures(self) {
|
|
184
|
-
const
|
|
180
|
+
const views = getSession(self).views;
|
|
185
181
|
const { connectedViewId, uniprotId, rows, connectedStructures } = self;
|
|
186
182
|
if (!uniprotId || rows.length === 0) {
|
|
187
183
|
return;
|
|
@@ -190,9 +186,8 @@ export function autoConnectStructures(self) {
|
|
|
190
186
|
if (!isProteinView(view)) {
|
|
191
187
|
continue;
|
|
192
188
|
}
|
|
193
|
-
|
|
194
|
-
|
|
195
|
-
const structure = v.structures[structureIdx];
|
|
189
|
+
for (let structureIdx = 0; structureIdx < view.structures.length; structureIdx++) {
|
|
190
|
+
const structure = view.structures[structureIdx];
|
|
196
191
|
if (!structure) {
|
|
197
192
|
continue;
|
|
198
193
|
}
|
|
@@ -202,7 +197,7 @@ export function autoConnectStructures(self) {
|
|
|
202
197
|
if (structure.uniprotId !== uniprotId) {
|
|
203
198
|
continue;
|
|
204
199
|
}
|
|
205
|
-
const alreadyConnected = connectedStructures.some(c => c.proteinViewId ===
|
|
200
|
+
const alreadyConnected = connectedStructures.some(c => c.proteinViewId === view.id && c.structureIdx === structureIdx);
|
|
206
201
|
if (alreadyConnected) {
|
|
207
202
|
continue;
|
|
208
203
|
}
|
|
@@ -210,7 +205,7 @@ export function autoConnectStructures(self) {
|
|
|
210
205
|
continue;
|
|
211
206
|
}
|
|
212
207
|
try {
|
|
213
|
-
self.connectToStructure(
|
|
208
|
+
self.connectToStructure(view.id, structureIdx);
|
|
214
209
|
}
|
|
215
210
|
catch (e) {
|
|
216
211
|
console.error('Failed to auto-connect to ProteinView:', e);
|
|
@@ -219,7 +214,7 @@ export function autoConnectStructures(self) {
|
|
|
219
214
|
}
|
|
220
215
|
}
|
|
221
216
|
export function observeProteinHighlights(self) {
|
|
222
|
-
const
|
|
217
|
+
const views = getSession(self).views;
|
|
223
218
|
const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
|
|
224
219
|
if (!connectedViewId || !transcriptToMsaMap) {
|
|
225
220
|
return;
|
|
@@ -229,8 +224,7 @@ export function observeProteinHighlights(self) {
|
|
|
229
224
|
if (!isProteinView(view)) {
|
|
230
225
|
continue;
|
|
231
226
|
}
|
|
232
|
-
const
|
|
233
|
-
for (const structure of v.structures) {
|
|
227
|
+
for (const structure of view.structures) {
|
|
234
228
|
if (structure.connectedViewId !== connectedViewId) {
|
|
235
229
|
continue;
|
|
236
230
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"afterCreateAutoruns.js","sourceRoot":"","sources":["../../src/MsaViewPanel/afterCreateAutoruns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,YAAY,GACb,MAAM,gBAAgB,CAAA;AACvB,OAAO,EAAE,wBAAwB,EAAE,MAAM,uBAAuB,CAAA;
|
|
1
|
+
{"version":3,"file":"afterCreateAutoruns.js","sourceRoot":"","sources":["../../src/MsaViewPanel/afterCreateAutoruns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,YAAY,GACb,MAAM,gBAAgB,CAAA;AACvB,OAAO,EAAE,wBAAwB,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAA;AAC/E,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAIrD,MAAM,UAAU,cAAc,CAAC,IAA+B;IAC5D,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAClC,IAAI,WAAW,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACrC,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,CAAA;gBAC/B,MAAM,UAAU,GAAG,MAAM,eAAe,CAAC,WAAW,CAAC,CAAA;gBACrD,IAAI,UAAU,EAAE,CAAC;oBACf,IAAI,UAAU,CAAC,GAAG,EAAE,CAAC;wBACnB,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;oBAC7B,CAAC;oBACD,IAAI,UAAU,CAAC,IAAI,EAAE,CAAC;wBACpB,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,yCAAyC,EAAE,CAAC,CAAC,CAAA;YAC7D,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,oBAAoB,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAA+B;IAClE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;IAClC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;QACpC,MAAM,aAAa,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,cAAc,CAAC,CAAA;QACnE,IAAI,aAAa,EAAE,CAAC;YAClB,OAAM;QACR,CAAC;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAA;QAE/B,IAAI,OAAO,IAAI,QAAQ,EAAE,CAAC;YACxB,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,MAAM,KAAK,GAAG,mBAAmB,EAAE,CAAA;oBACnC,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,KAAK,EAAE;wBACxC,GAAG,EAAE,OAAO;wBACZ,IAAI,EAAE,QAAQ;wBACd,YAAY,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY;qBACrC,CAAC,CAAA;oBACF,IAAI,OAAO,EAAE,CAAC;wBACZ,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,wCAAwC,EAAE,CAAC,CAAC,CAAA;gBAC5D,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,IAA+B;IACjE,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,WAAW,CAAC,kBAAkB,CAAC,CAAA;gBACpC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACxB,MAAM,IAAI,GAAG,MAAM,aAAa,CAAC,EAAE,IAAI,EAAE,CAAC,CAAA;gBAC1C,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBAClB,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;YAChC,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACtB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAA+B;IACzD,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,IAAI,IAAI,EAAE,CAAC;QACT,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACxB,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;gBAEjE,IAAI,MAAM,EAAE,CAAC;oBACX,MAAM,EAAE,GAAG,4BAA4B,CAAC,MAAM,CAAC,CAAA;oBAC/C,IAAI,EAAE,EAAE,CAAC;wBACP,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;wBACrB,IAAI,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;gBAED,IAAI,YAAY,EAAE,CAAC;oBACjB,IAAI,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;gBACpC,CAAC;gBAED,IAAI,OAAO,EAAE,CAAC;oBACZ,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;gBACtB,CAAC;qBAAM,IAAI,MAAM,EAAE,CAAC;oBAClB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;oBACpC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;wBACjB,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;oBAC5D,CAAC;oBACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBAClC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;gBACnB,CAAC;gBAED,IAAI,QAAQ,EAAE,CAAC;oBACb,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;gBACxB,CAAC;qBAAM,IAAI,OAAO,EAAE,CAAC;oBACnB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,CAAC,CAAA;oBACrC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;wBACjB,MAAM,IAAI,KAAK,CAAC,yBAAyB,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;oBAC7D,CAAC;oBACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBAClC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBACpB,CAAC;gBAED,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;YACzB,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,IAA+B;IACpE,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IACxC,MAAM,EAAE,GACN,QAAQ,KAAK,SAAS;QACpB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,CAAA;IAC7D,MAAM,EAAE,GACN,aAAa,KAAK,SAAS;QACzB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC,CAAA;IAElE,IAAI,CAAC,sBAAsB,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,4BAA4B,CAAC,IAA+B;IAC1E,MAAM,EAAE,QAAQ,EAAE,qBAAqB,EAAE,GAAG,IAAI,CAAA;IAChD,IAAI,qBAAqB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAM;IACR,CAAC;IAED,KAAK,MAAM,IAAI,IAAI,qBAAqB,EAAE,CAAC;QACzC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAChE,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,SAAQ;QACV,CAAC;QAED,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;YAC3B,SAAS,CAAC,0BAA0B,EAAE,EAAE,CAAA;YACxC,SAAQ;QACV,CAAC;QAED,MAAM,GAAG,GAAG,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,SAAQ;QACV,CAAC;QAED,MAAM,WAAW,GAAG,wBAAwB,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;QAC3D,IAAI,WAAW,KAAK,SAAS,EAAE,CAAC;YAC9B,SAAS,CAAC,0BAA0B,EAAE,EAAE,CAAA;YACxC,SAAQ;QACV,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,CAAC,cAAc,CAAC,WAAW,CAAC,CAAA;QACrD,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;YAC/B,SAAS,CAAC,0BAA0B,EAAE,EAAE,CAAA;QAC1C,CAAC;aAAM,CAAC;YACN,SAAS,CAAC,qBAAqB,EAAE,CAAC,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,IAA+B;IACnE,MAAM,KAAK,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC,KAAkB,CAAA;IACjD,MAAM,EAAE,eAAe,EAAE,SAAS,EAAE,IAAI,EAAE,mBAAmB,EAAE,GAAG,IAAI,CAAA;IAEtE,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpC,OAAM;IACR,CAAC;IAED,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,SAAQ;QACV,CAAC;QAED,KACE,IAAI,YAAY,GAAG,CAAC,EACpB,YAAY,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,EACrC,YAAY,EAAE,EACd,CAAC;YACD,MAAM,SAAS,GAAG,IAAI,CAAC,UAAU,CAAC,YAAY,CAAC,CAAA;YAC/C,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,SAAQ;YACV,CAAC;YAED,IAAI,SAAS,CAAC,eAAe,KAAK,eAAe,EAAE,CAAC;gBAClD,SAAQ;YACV,CAAC;YAED,IAAI,SAAS,CAAC,SAAS,KAAK,SAAS,EAAE,CAAC;gBACtC,SAAQ;YACV,CAAC;YAED,MAAM,gBAAgB,GAAG,mBAAmB,CAAC,IAAI,CAC/C,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,YAAY,KAAK,YAAY,CACpE,CAAA;YACD,IAAI,gBAAgB,EAAE,CAAC;gBACrB,SAAQ;YACV,CAAC;YAED,IAAI,CAAC,SAAS,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBACvC,SAAQ;YACV,CAAC;YAED,IAAI,CAAC;gBACH,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,EAAE,EAAE,YAAY,CAAC,CAAA;YAChD,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,wCAAwC,EAAE,CAAC,CAAC,CAAA;YAC5D,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,IAA+B;IACtE,MAAM,KAAK,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC,KAAkB,CAAA;IACjD,MAAM,EAAE,eAAe,EAAE,kBAAkB,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;IAElE,IAAI,CAAC,eAAe,IAAI,CAAC,kBAAkB,EAAE,CAAC;QAC5C,OAAM;IACR,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;IAEjC,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,SAAQ;QACV,CAAC;QAED,KAAK,MAAM,SAAS,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;YACxC,IAAI,SAAS,CAAC,eAAe,KAAK,eAAe,EAAE,CAAC;gBAClD,SAAQ;YACV,CAAC;YAED,MAAM,UAAU,GAAG,SAAS,CAAC,qBAAqB,CAAA;YAClD,IAAI,CAAC,UAAU,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC3C,SAAQ;YACV,CAAC;YAED,MAAM,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;YAClC,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;gBACnC,KAAK,IAAI,KAAK,GAAG,SAAS,CAAC,KAAK,EAAE,KAAK,GAAG,SAAS,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC;oBACjE,MAAM,UAAU,GAAG,GAAG,CAAC,KAAK,CAAC,CAAA;oBAC7B,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;wBAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,iBAAiB,CAAC,YAAY,EAAE,UAAU,CAAC,CAAA;wBAC5D,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM,cAAc,GAAG,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC;SACvC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAC;SAC3C,MAAM,CAAC,CAAC,GAAG,EAAiB,EAAE,CAAC,GAAG,KAAK,SAAS,CAAC,CAAA;IAEpD,IAAI,CAAC,qBAAqB,CACxB,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CACvD,CAAA;AACH,CAAC;AAED,MAAM,UAAU,UAAU;IACxB,cAAc,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;QACpC,OAAO,CAAC,KAAK,CAAC,iCAAiC,EAAE,CAAC,CAAC,CAAA;IACrD,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
|
@@ -1,20 +1,25 @@
|
|
|
1
1
|
import React, { useState } from 'react';
|
|
2
|
-
import { Dialog } from '@jbrowse/core/ui';
|
|
2
|
+
import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
|
|
3
3
|
import { getSession } from '@jbrowse/core/util';
|
|
4
4
|
import { Button, DialogActions, DialogContent, FormControl, InputLabel, MenuItem, Select, Typography, } from '@mui/material';
|
|
5
5
|
import { observer } from 'mobx-react';
|
|
6
|
+
import { makeStyles } from 'tss-react/mui';
|
|
7
|
+
import { isProteinView } from '../structureConnection';
|
|
8
|
+
const useStyles = makeStyles()(theme => ({
|
|
9
|
+
formControl: {
|
|
10
|
+
marginBottom: theme.spacing(2),
|
|
11
|
+
},
|
|
12
|
+
}));
|
|
6
13
|
const ConnectStructureDialog = observer(function ConnectStructureDialog({ model, handleClose, }) {
|
|
14
|
+
const { classes } = useStyles();
|
|
7
15
|
const session = getSession(model);
|
|
8
16
|
const [selectedViewId, setSelectedViewId] = useState('');
|
|
9
17
|
const [selectedStructureIdx, setSelectedStructureIdx] = useState(0);
|
|
10
18
|
const [selectedMsaRow, setSelectedMsaRow] = useState(model.querySeqName);
|
|
11
19
|
const [error, setError] = useState();
|
|
12
|
-
|
|
13
|
-
const proteinViews = session.views.filter((v) => v.type === 'ProteinView');
|
|
14
|
-
// Get structures for the selected view
|
|
20
|
+
const proteinViews = session.views.filter(isProteinView);
|
|
15
21
|
const selectedView = proteinViews.find(v => v.id === selectedViewId);
|
|
16
22
|
const structures = selectedView?.structures ?? [];
|
|
17
|
-
// Get MSA row names
|
|
18
23
|
const msaRowNames = model.rows.map(r => r[0]);
|
|
19
24
|
const handleConnect = () => {
|
|
20
25
|
if (!selectedViewId) {
|
|
@@ -31,23 +36,23 @@ const ConnectStructureDialog = observer(function ConnectStructureDialog({ model,
|
|
|
31
36
|
};
|
|
32
37
|
return (React.createElement(Dialog, { maxWidth: "sm", title: "Connect to Protein Structure", open: true, onClose: handleClose },
|
|
33
38
|
React.createElement(DialogContent, null, proteinViews.length === 0 ? (React.createElement(Typography, { color: "textSecondary" }, "No protein views are currently open. Please open a protein structure view first.")) : (React.createElement(React.Fragment, null,
|
|
34
|
-
React.createElement(FormControl, { fullWidth: true,
|
|
39
|
+
React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
|
|
35
40
|
React.createElement(InputLabel, null, "Protein View"),
|
|
36
41
|
React.createElement(Select, { value: selectedViewId, label: "Protein View", onChange: e => {
|
|
37
42
|
setSelectedViewId(e.target.value);
|
|
38
43
|
setSelectedStructureIdx(0);
|
|
39
44
|
} }, proteinViews.map(view => (React.createElement(MenuItem, { key: view.id, value: view.id }, view.displayName ?? `ProteinView ${view.id}`))))),
|
|
40
|
-
structures.length > 1
|
|
45
|
+
structures.length > 1 ? (React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
|
|
41
46
|
React.createElement(InputLabel, null, "Structure"),
|
|
42
47
|
React.createElement(Select, { value: selectedStructureIdx, label: "Structure", onChange: e => {
|
|
43
48
|
setSelectedStructureIdx(e.target.value);
|
|
44
|
-
} }, structures.map((structure, idx) => (React.createElement(MenuItem, { key: idx, value: idx }, structure.url ?? `Structure ${idx + 1}`)))))),
|
|
45
|
-
React.createElement(FormControl, { fullWidth: true,
|
|
49
|
+
} }, structures.map((structure, idx) => (React.createElement(MenuItem, { key: idx, value: idx }, structure.url ?? `Structure ${idx + 1}`)))))) : null,
|
|
50
|
+
React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
|
|
46
51
|
React.createElement(InputLabel, null, "MSA Row"),
|
|
47
52
|
React.createElement(Select, { value: selectedMsaRow, label: "MSA Row", onChange: e => {
|
|
48
53
|
setSelectedMsaRow(e.target.value);
|
|
49
54
|
} }, msaRowNames.map(name => (React.createElement(MenuItem, { key: name, value: name }, name))))),
|
|
50
|
-
error
|
|
55
|
+
error ? React.createElement(ErrorMessage, { error: error }) : null))),
|
|
51
56
|
React.createElement(DialogActions, null,
|
|
52
57
|
React.createElement(Button, { onClick: handleClose }, "Cancel"),
|
|
53
58
|
React.createElement(Button, { onClick: handleConnect, variant: "contained", disabled: proteinViews.length === 0 || !selectedViewId }, "Connect"))));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ConnectStructureDialog.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/ConnectStructureDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;
|
|
1
|
+
{"version":3,"file":"ConnectStructureDialog.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/ConnectStructureDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,QAAQ,EACR,MAAM,EACN,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAA;AAItD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,sBAAsB,GAAG,QAAQ,CAAC,SAAS,sBAAsB,CAAC,EACtE,KAAK,EACL,WAAW,GAIZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxD,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACnE,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;IACxE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAU,CAAA;IAE5C,MAAM,YAAY,GAAI,OAAO,CAAC,KAAmB,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IAEvE,MAAM,YAAY,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,cAAc,CAAC,CAAA;IACpE,MAAM,UAAU,GAAG,YAAY,EAAE,UAAU,IAAI,EAAE,CAAA;IAEjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAE7C,MAAM,aAAa,GAAG,GAAG,EAAE;QACzB,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,QAAQ,CAAC,8BAA8B,CAAC,CAAA;YACxC,OAAM;QACR,CAAC;QAED,IAAI,CAAC;YACH,KAAK,CAAC,kBAAkB,CACtB,cAAc,EACd,oBAAoB,EACpB,cAAc,CACf,CAAA;YACD,WAAW,EAAE,CAAA;QACf,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,QAAQ,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;QACtD,CAAC;IACH,CAAC,CAAA;IAED,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,8BAA8B,EACpC,IAAI,QACJ,OAAO,EAAE,WAAW;QAEpB,oBAAC,aAAa,QACX,YAAY,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAC3B,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,uFAGpB,CACd,CAAC,CAAC,CAAC,CACF;YACE,oBAAC,WAAW,IAAC,SAAS,QAAC,SAAS,EAAE,OAAO,CAAC,WAAW;gBACnD,oBAAC,UAAU,uBAA0B;gBACrC,oBAAC,MAAM,IACL,KAAK,EAAE,cAAc,EACrB,KAAK,EAAC,cAAc,EACpB,QAAQ,EAAE,CAAC,CAAC,EAAE;wBACZ,iBAAiB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBACjC,uBAAuB,CAAC,CAAC,CAAC,CAAA;oBAC5B,CAAC,IAEA,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,IACnC,IAAI,CAAC,WAAW,IAAI,eAAe,IAAI,CAAC,EAAE,EAAE,CACpC,CACZ,CAAC,CACK,CACG;YAEb,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACvB,oBAAC,WAAW,IAAC,SAAS,QAAC,SAAS,EAAE,OAAO,CAAC,WAAW;gBACnD,oBAAC,UAAU,oBAAuB;gBAClC,oBAAC,MAAM,IACL,KAAK,EAAE,oBAAoB,EAC3B,KAAK,EAAC,WAAW,EACjB,QAAQ,EAAE,CAAC,CAAC,EAAE;wBACZ,uBAAuB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACzC,CAAC,IAEA,UAAU,CAAC,GAAG,CAAC,CAAC,SAAS,EAAE,GAAG,EAAE,EAAE,CAAC,CAClC,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAC3B,SAAS,CAAC,GAAG,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAC/B,CACZ,CAAC,CACK,CACG,CACf,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,WAAW,IAAC,SAAS,QAAC,SAAS,EAAE,OAAO,CAAC,WAAW;gBACnD,oBAAC,UAAU,kBAAqB;gBAChC,oBAAC,MAAM,IACL,KAAK,EAAE,cAAc,EACrB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,CAAC,EAAE;wBACZ,iBAAiB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACnC,CAAC,IAEA,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CACvB,oBAAC,QAAQ,IAAC,GAAG,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,IAC7B,IAAI,CACI,CACZ,CAAC,CACK,CACG;YAEb,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CAC7C,CACJ,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,WAAW,aAAiB;YAC7C,oBAAC,MAAM,IACL,OAAO,EAAE,aAAa,EACtB,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,YAAY,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,cAAc,cAG/C,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,sBAAsB,CAAA"}
|
|
@@ -2,12 +2,19 @@ import React from 'react';
|
|
|
2
2
|
import { LoadingEllipses } from '@jbrowse/core/ui';
|
|
3
3
|
import { observer } from 'mobx-react';
|
|
4
4
|
import { MSAView } from 'react-msaview';
|
|
5
|
+
import { makeStyles } from 'tss-react/mui';
|
|
5
6
|
import { ErrorBoundary } from './ErrorBoundary';
|
|
6
7
|
import LoadingBLAST from './LoadingBLAST';
|
|
8
|
+
const useStyles = makeStyles()({
|
|
9
|
+
loadingContainer: {
|
|
10
|
+
padding: 20,
|
|
11
|
+
},
|
|
12
|
+
});
|
|
7
13
|
const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
|
|
14
|
+
const { classes } = useStyles();
|
|
8
15
|
const { blastParams, loadingStoredData } = model;
|
|
9
16
|
return (React.createElement(ErrorBoundary, null,
|
|
10
|
-
React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", {
|
|
17
|
+
React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", { className: classes.loadingContainer },
|
|
11
18
|
React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model })))));
|
|
12
19
|
});
|
|
13
20
|
export default MsaViewPanel;
|
|
@@ -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,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;
|
|
1
|
+
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AACvC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAIzC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,gBAAgB,EAAE;QAChB,OAAO,EAAE,EAAE;KACZ;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,WAAW,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAChD,OAAO,CACL,oBAAC,aAAa;QACZ,iCACG,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,GAAI,CAC7D,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,CACtB,6BAAK,SAAS,EAAE,OAAO,CAAC,gBAAgB;YACtC,oBAAC,eAAe,IAAC,OAAO,EAAC,kBAAkB,EAAC,OAAO,EAAC,IAAI,GAAG,CACvD,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACG,CACQ,CACjB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import type { StructureConnection } from './structureConnection';
|
|
1
|
+
import type { ProteinView, StructureConnection } from './structureConnection';
|
|
2
2
|
import type { MafRegion, MsaViewInitState } from './types';
|
|
3
3
|
import type { Feature } from '@jbrowse/core/util';
|
|
4
4
|
import type { Instance } from '@jbrowse/mobx-state-tree';
|
|
@@ -644,7 +644,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
|
|
|
644
644
|
* #getter
|
|
645
645
|
*/
|
|
646
646
|
readonly connectedProteinViews: (StructureConnection & {
|
|
647
|
-
proteinView:
|
|
647
|
+
proteinView: ProteinView;
|
|
648
648
|
})[];
|
|
649
649
|
} & {
|
|
650
650
|
/**
|
|
@@ -9,7 +9,7 @@ import { autoConnectStructures, highlightConnectedStructures, launchBlastIfNeede
|
|
|
9
9
|
import { genomeToMSA } from './genomeToMSA';
|
|
10
10
|
import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
|
|
11
11
|
import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
|
|
12
|
-
import { mapToRecord, ungappedToGappedPosition } from './structureConnection';
|
|
12
|
+
import { isProteinView, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
|
|
13
13
|
const ConnectStructureDialog = lazy(() => import('./components/ConnectStructureDialog'));
|
|
14
14
|
/**
|
|
15
15
|
* #stateModel MsaViewPlugin
|
|
@@ -127,12 +127,15 @@ export default function stateModelFactory() {
|
|
|
127
127
|
*/
|
|
128
128
|
get connectedProteinViews() {
|
|
129
129
|
const { views } = getSession(self);
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
130
|
+
const unknownViews = views;
|
|
131
|
+
const result = [];
|
|
132
|
+
for (const conn of self.connectedStructures) {
|
|
133
|
+
const proteinView = unknownViews.find((v) => isProteinView(v) && v.id === conn.proteinViewId);
|
|
134
|
+
if (proteinView) {
|
|
135
|
+
result.push({ ...conn, proteinView });
|
|
136
|
+
}
|
|
137
|
+
}
|
|
138
|
+
return result;
|
|
136
139
|
},
|
|
137
140
|
}))
|
|
138
141
|
.views(self => ({
|
|
@@ -141,7 +144,7 @@ export default function stateModelFactory() {
|
|
|
141
144
|
*/
|
|
142
145
|
get structureHoverCol() {
|
|
143
146
|
for (const conn of self.connectedProteinViews) {
|
|
144
|
-
const structure = conn.proteinView
|
|
147
|
+
const structure = conn.proteinView.structures[conn.structureIdx];
|
|
145
148
|
const structurePos = structure?.hoverPosition?.structureSeqPos;
|
|
146
149
|
if (structurePos !== undefined) {
|
|
147
150
|
const msaUngapped = conn.structureToMsa[structurePos];
|
|
@@ -293,11 +296,11 @@ export default function stateModelFactory() {
|
|
|
293
296
|
}
|
|
294
297
|
const ungappedMsaSequence = msaSequence.replaceAll('-', '');
|
|
295
298
|
const { views } = getSession(self);
|
|
296
|
-
const proteinView = views.find((v) => v.id === proteinViewId);
|
|
299
|
+
const proteinView = views.find((v) => isProteinView(v) && v.id === proteinViewId);
|
|
297
300
|
if (!proteinView) {
|
|
298
301
|
throw new Error(`ProteinView "${proteinViewId}" not found`);
|
|
299
302
|
}
|
|
300
|
-
const structure = proteinView.structures
|
|
303
|
+
const structure = proteinView.structures[structureIdx];
|
|
301
304
|
if (!structure) {
|
|
302
305
|
throw new Error(`Structure at index ${structureIdx} not found`);
|
|
303
306
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/MsaViewPanel/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AACnE,OAAO,EAAE,4BAA4B,EAAE,MAAM,YAAY,CAAA;AACzD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,EACL,qBAAqB,EACrB,4BAA4B,EAC5B,mBAAmB,EACnB,cAAc,EACd,wBAAwB,EACxB,WAAW,EACX,UAAU,EACV,oBAAoB,EACpB,sBAAsB,GACvB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAA;AAC9E,OAAO,
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/MsaViewPanel/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AACnE,OAAO,EAAE,4BAA4B,EAAE,MAAM,YAAY,CAAA;AACzD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,EACL,qBAAqB,EACrB,4BAA4B,EAC5B,mBAAmB,EACnB,cAAc,EACd,wBAAwB,EACxB,WAAW,EACX,UAAU,EACV,oBAAoB,EACpB,sBAAsB,GACvB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAA;AAC9E,OAAO,EACL,aAAa,EACb,WAAW,EACX,wBAAwB,GACzB,MAAM,uBAAuB,CAAA;AAQ9B,MAAM,sBAAsB,GAAG,IAAI,CACjC,GAAG,EAAE,CAAC,MAAM,CAAC,qCAAqC,CAAC,CACpD,CAAA;AAsBD;;;;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;QACpD;;WAEG;QACH,YAAY,EAAE,OAAO;QAErB;;WAEG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEpC;;WAEG;QACH,eAAe,EAAE,KAAK;QAEtB;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,MAAM,EAAgC;QAElD;;WAEG;QACH,mBAAmB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAuB,CAAC;QAErE;;WAEG;QACH,WAAW,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEtC;;WAEG;QACH,SAAS,EAAE,KAAK,CAAC,MAAM,EAAyB;KACjD,CAAC,CACH;SAEA,QAAQ,CACP,GAKE,EAAE,CAAC,CAAC;QACJ;;WAEG;QACH,GAAG,EAAE,SAAS;QACd;;WAEG;QACH,QAAQ,EAAE,EAAE;QACZ;;WAEG;QACH,KAAK,EAAE,SAAS;QAChB;;WAEG;QACH,iBAAiB,EAAE,KAAK;KACzB,CAAC,CACH;SAEA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,YAAY,CAAC,OAAe;YAC1B,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC9C,CAAC;QAED;;WAEG;QACH,oBAAoB,CAAC,OAAe;YAClC,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACnD,CAAC;KACF,CAAC,CAAC;SAEF,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;QAED;;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;QAED;;WAEG;QACH,IAAI,qBAAqB;YACvB,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,YAAY,GAAG,KAAkB,CAAA;YACvC,MAAM,MAAM,GACV,EAAE,CAAA;YACJ,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,mBAAmB,EAAE,CAAC;gBAC5C,MAAM,WAAW,GAAG,YAAY,CAAC,IAAI,CACnC,CAAC,CAAC,EAAoB,EAAE,CACtB,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC,aAAa,CAClD,CAAA;gBACD,IAAI,WAAW,EAAE,CAAC;oBAChB,MAAM,CAAC,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,WAAW,EAAE,CAAC,CAAA;gBACvC,CAAC;YACH,CAAC;YACD,OAAO,MAAM,CAAA;QACf,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,iBAAiB;YACnB,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,qBAAqB,EAAE,CAAC;gBAC9C,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;gBAChE,MAAM,YAAY,GAAG,SAAS,EAAE,aAAa,EAAE,eAAe,CAAA;gBAC9D,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;oBAC/B,MAAM,WAAW,GAAG,IAAI,CAAC,cAAc,CAAC,YAAY,CAAC,CAAA;oBACrD,IAAI,WAAW,KAAK,SAAS,EAAE,CAAC;wBAC9B,MAAM,GAAG,GAAG,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;wBACtD,IAAI,GAAG,EAAE,CAAC;4BACR,MAAM,SAAS,GAAG,wBAAwB,CAAC,GAAG,EAAE,WAAW,CAAC,CAAA;4BAC5D,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gCAC5B,OAAO,IAAI,CAAC,qBAAqB,CAAC,SAAS,CAAC,CAAA;4BAC9C,CAAC;wBACH,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,SAAS;YACX,MAAM,YAAY,GAAG,IAAI,CAAC,iBAAiB,CAAA;YAC3C,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;gBAC/B,OAAO,YAAY,CAAA;YACrB,CAAC;YACD,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,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;QACD;;WAEG;QACH,OAAO,CAAC,GAAsB;YAC5B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACjB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,GAAW;YACzB,IAAI,CAAC,YAAY,GAAG,GAAG,CAAA;QACzB,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,GAAY;YACvB,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;QACD;;WAEG;QACH,cAAc,CAAC,GAAY;YACzB,IAAI,CAAC,WAAW,GAAG,GAAG,CAAA;QACxB,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,GAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;QACD;;WAEG;QACH,oBAAoB,CAAC,GAAY;YAC/B,IAAI,CAAC,iBAAiB,GAAG,GAAG,CAAA;QAC9B,CAAC;QACD;;WAEG;QACH,cAAc,CAAC,KAAa;YAC1B,MAAM,EAAE,aAAa,EAAE,eAAe,EAAE,GAAG,IAAI,CAAA;YAC/C,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAC5C,MAAM,EAAE,GAAG,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,CAAA;YAExD,IAAI,CAAC,EAAE,IAAI,CAAC,aAAa,EAAE,CAAC;gBAC1B,OAAM;YACR,CAAC;YAED,IAAI,eAAe,EAAE,CAAC;gBACpB,aAAa,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;YACzB,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,GACL,eAAe;qBACZ,GAAG,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC;oBACrC,EAAE,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,OAAO,CAAA;gBACnD,aAAa,CAAC,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;YACrC,CAAC;QACH,CAAC;QAED;;WAEG;QACH,kBAAkB,CAChB,aAAqB,EACrB,YAAoB,EACpB,UAAmB;YAEnB,MAAM,OAAO,GAAG,UAAU,IAAI,IAAI,CAAC,YAAY,CAAA;YAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,oBAAoB,CAAC,OAAO,CAAC,CAAA;YACtD,IAAI,CAAC,WAAW,EAAE,CAAC;gBACjB,MAAM,IAAI,KAAK,CAAC,YAAY,OAAO,aAAa,CAAC,CAAA;YACnD,CAAC;YAED,MAAM,mBAAmB,GAAG,WAAW,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;YAE3D,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAElC,MAAM,WAAW,GAAI,KAAmB,CAAC,IAAI,CAC3C,CAAC,CAAC,EAAoB,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,KAAK,aAAa,CACpE,CAAA;YACD,IAAI,CAAC,WAAW,EAAE,CAAC;gBACjB,MAAM,IAAI,KAAK,CAAC,gBAAgB,aAAa,aAAa,CAAC,CAAA;YAC7D,CAAC;YAED,MAAM,SAAS,GAAG,WAAW,CAAC,UAAU,CAAC,YAAY,CAAC,CAAA;YACtD,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CAAC,sBAAsB,YAAY,YAAY,CAAC,CAAA;YACjE,CAAC;YAED,MAAM,iBAAiB,GAAG,SAAS,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAA;YAC3D,IAAI,CAAC,iBAAiB,EAAE,CAAC;gBACvB,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAA;YACrD,CAAC;YAED,MAAM,SAAS,GAAG,oBAAoB,CACpC,mBAAmB,EACnB,iBAAiB,CAClB,CAAA;YACD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,GAAG,kBAAkB,CAAC,SAAS,CAAC,CAAA;YAEhE,MAAM,UAAU,GAAwB;gBACtC,aAAa;gBACb,YAAY;gBACZ,UAAU,EAAE,OAAO;gBACnB,cAAc,EAAE,WAAW,CAAC,UAAU,CAAC;gBACvC,cAAc,EAAE,WAAW,CAAC,UAAU,CAAC;aACxC,CAAA;YAED,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QAC3C,CAAC;QAED;;WAEG;QACH,uBAAuB,CAAC,aAAqB,EAAE,YAAoB;YACjE,MAAM,GAAG,GAAG,IAAI,CAAC,mBAAmB,CAAC,SAAS,CAC5C,CAAC,CAAC,EAAE,CACF,CAAC,CAAC,aAAa,KAAK,aAAa;gBACjC,CAAC,CAAC,YAAY,KAAK,YAAY,CAClC,CAAA;YACD,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;gBACf,IAAI,CAAC,mBAAmB,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,CAAC;QACH,CAAC;QAED;;WAEG;QACH,uBAAuB;YACrB,IAAI,CAAC,mBAAmB,CAAC,KAAK,EAAE,CAAA;QAClC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL;;eAEG;YACH,gBAAgB,CAAC,GAAY,EAAE,GAAY;gBACzC,qBAAqB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;gBAC/B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;oBACtB,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;gBAC1B,CAAC;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SAED,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;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;gBACD;oBACE,KAAK,EAAE,iCAAiC;oBACxC,OAAO,EAAE,GAAG,EAAE;wBACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;4BAC1C,sBAAsB;4BACtB;gCACE,KAAK,EAAE,IAAI;gCACX,WAAW;6BACZ;yBACF,CAAC,CAAA;oBACJ,CAAC;iBACF;gBACD,GAAG,CAAC,IAAI,CAAC,mBAAmB,CAAC,MAAM,GAAG,CAAC;oBACrC,CAAC,CAAC;wBACE;4BACE,KAAK,EAAE,oCAAoC;4BAC3C,OAAO,EAAE,GAAG,EAAE;gCACZ,IAAI,CAAC,uBAAuB,EAAE,CAAA;4BAChC,CAAC;yBACF;qBACF;oBACH,CAAC,CAAC,EAAE,CAAC;aACR,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SAEF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,UAAU,EAAE,CAAA;YACZ,KAAK,MAAM,EAAE,IAAI;gBACf,cAAc;gBACd,oBAAoB;gBACpB,mBAAmB;gBACnB,WAAW;gBACX,sBAAsB;gBACtB,4BAA4B;gBAC5B,qBAAqB;gBACrB,wBAAwB;aACzB,EAAE,CAAC;gBACF,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;oBACX,EAAE,CAAC,IAAI,CAAC,CAAA;gBACV,CAAC,CAAC,CACH,CAAA;YACH,CAAC;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
|
|
@@ -1,8 +1,6 @@
|
|
|
1
1
|
import BLOSUM62 from './blosum62';
|
|
2
2
|
function getScore(a, b) {
|
|
3
|
-
|
|
4
|
-
const upper_b = b.toUpperCase();
|
|
5
|
-
return BLOSUM62[upper_a]?.[upper_b] ?? -4;
|
|
3
|
+
return BLOSUM62[a.toUpperCase()]?.[b.toUpperCase()] ?? -4;
|
|
6
4
|
}
|
|
7
5
|
const GAP_OPEN = -10;
|
|
8
6
|
const GAP_EXTEND = -0.5;
|
|
@@ -43,9 +41,11 @@ export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_
|
|
|
43
41
|
let alignedSeq2 = '';
|
|
44
42
|
let i = m;
|
|
45
43
|
let j = n;
|
|
46
|
-
const
|
|
47
|
-
const
|
|
48
|
-
|
|
44
|
+
const mScore = M[m][n];
|
|
45
|
+
const ixScore = Ix[m][n];
|
|
46
|
+
const iyScore = Iy[m][n];
|
|
47
|
+
const score = Math.max(mScore, ixScore, iyScore);
|
|
48
|
+
let currentMatrix = score === mScore ? 'M' : score === ixScore ? 'Ix' : 'Iy';
|
|
49
49
|
while (i > 0 || j > 0) {
|
|
50
50
|
if (currentMatrix === 'M' && i > 0 && j > 0) {
|
|
51
51
|
alignedSeq1 = seq1[i - 1] + alignedSeq1;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"pairwiseAlignment.js","sourceRoot":"","sources":["../../src/MsaViewPanel/pairwiseAlignment.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,SAAS,QAAQ,CAAC,CAAS,EAAE,CAAS;IACpC,
|
|
1
|
+
{"version":3,"file":"pairwiseAlignment.js","sourceRoot":"","sources":["../../src/MsaViewPanel/pairwiseAlignment.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,SAAS,QAAQ,CAAC,CAAS,EAAE,CAAS;IACpC,OAAO,QAAQ,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,IAAI,CAAC,CAAC,CAAA;AAC3D,CAAC;AAED,MAAM,QAAQ,GAAG,CAAC,EAAE,CAAA;AACpB,MAAM,UAAU,GAAG,CAAC,GAAG,CAAA;AAkBvB,MAAM,UAAU,eAAe,CAC7B,IAAY,EACZ,IAAY,EACZ,OAAO,GAAG,QAAQ,EAClB,SAAS,GAAG,UAAU;IAEtB,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IAErB,MAAM,CAAC,GAAe,EAAE,CAAA;IACxB,MAAM,EAAE,GAAe,EAAE,CAAA;IACzB,MAAM,EAAE,GAAe,EAAE,CAAA;IAEzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;QACT,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;QACV,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;QACV,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAA;YACpB,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAA;YACrB,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAA;QACvB,CAAC;IACH,CAAC;IAED,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAA;IAC3C,CAAC;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAA;IAC3C,CAAC;IAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,EAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;YAEvD,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC;gBACN,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC;oBACnE,UAAU,CAAA;YAEZ,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,CAAE,GAAG,OAAO,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,CAAE,GAAG,SAAS,CAAC,CAAA;YACzE,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,OAAO,EAAE,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,SAAS,CAAC,CAAA;QAC3E,CAAC;IACH,CAAC;IAED,IAAI,WAAW,GAAG,EAAE,CAAA;IACpB,IAAI,WAAW,GAAG,EAAE,CAAA;IACpB,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IAET,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;IACxB,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,CAAA;IAChD,IAAI,aAAa,GACf,KAAK,KAAK,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAA;IAE1D,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACtB,IAAI,aAAa,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YAC5C,WAAW,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAA;YACvC,WAAW,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAA;YAEvC,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,EAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAA;YACvD,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YAC/B,MAAM,MAAM,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YACjC,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;YAE9B,IAAI,YAAY,KAAK,KAAK,GAAG,UAAU,EAAE,CAAC;gBACxC,aAAa,GAAG,GAAG,CAAA;YACrB,CAAC;iBAAM,IAAI,YAAY,KAAK,MAAM,GAAG,UAAU,EAAE,CAAC;gBAChD,aAAa,GAAG,IAAI,CAAA;YACtB,CAAC;iBAAM,CAAC;gBACN,aAAa,GAAG,IAAI,CAAA;YACtB,CAAC;YACD,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,aAAa,KAAK,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YAC3C,WAAW,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAA;YACvC,WAAW,GAAG,GAAG,GAAG,WAAW,CAAA;YAE/B,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;YAC1B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,CAAC,CAAE,GAAG,OAAO,CAAA;YACtC,aAAa,GAAG,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;YAC/C,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACjB,WAAW,GAAG,GAAG,GAAG,WAAW,CAAA;YAC/B,WAAW,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAA;YAEvC,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;YAC1B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,OAAO,CAAA;YACtC,aAAa,GAAG,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;YAC/C,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,MAAK;QACP,CAAC;IACH,CAAC;IAED,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;AAC5C,CAAC;AAED,SAAS,cAAc,CAAC,WAAmB,EAAE,WAAmB;IAC9D,IAAI,SAAS,GAAG,EAAE,CAAA;IAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5C,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAE,CAAA;QACzB,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAE,CAAA;QACzB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;YAC3B,SAAS,IAAI,GAAG,CAAA;QAClB,CAAC;aAAM,IAAI,CAAC,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC;YAC/C,SAAS,IAAI,GAAG,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,SAAS,IAAI,GAAG,CAAA;QAClB,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,IAAY,EACZ,IAAY;IAEZ,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,eAAe,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAEhE,OAAO;QACL,SAAS,EAAE,cAAc,CAAC,WAAW,EAAE,WAAW,CAAC;QACnD,IAAI,EAAE;YACJ,EAAE,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,WAAW,EAAE;YAC/B,EAAE,EAAE,EAAE,WAAW,EAAE,GAAG,EAAE,WAAW,EAAE;SACtC;KACF,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,iBAAoC;IACrE,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC1C,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAE1C,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,EAAE,CAAC;QAChC,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;IAC5D,CAAC;IAED,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,MAAM,UAAU,GAAG,IAAI,GAAG,EAAkB,CAAA;IAC5C,MAAM,UAAU,GAAG,IAAI,GAAG,EAAkB,CAAA;IAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAClB,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAElB,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YAC7B,UAAU,CAAC,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC1B,UAAU,CAAC,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC1B,IAAI,EAAE,CAAA;YACN,IAAI,EAAE,CAAA;QACR,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,IAAI,EAAE,CAAA;QACR,CAAC;aAAM,CAAC;YACN,IAAI,EAAE,CAAA;QACR,CAAC;IACH,CAAC;IAED,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AACnC,CAAC"}
|
|
@@ -1,3 +1,25 @@
|
|
|
1
|
+
export interface ProteinViewStructure {
|
|
2
|
+
url?: string;
|
|
3
|
+
connectedViewId?: string;
|
|
4
|
+
uniprotId?: string;
|
|
5
|
+
structureSequences?: string[];
|
|
6
|
+
hoverGenomeHighlights?: {
|
|
7
|
+
start: number;
|
|
8
|
+
end: number;
|
|
9
|
+
}[];
|
|
10
|
+
hoverPosition?: {
|
|
11
|
+
structureSeqPos?: number;
|
|
12
|
+
};
|
|
13
|
+
clearHighlightFromExternal?: () => void;
|
|
14
|
+
highlightFromExternal?: (pos: number) => void;
|
|
15
|
+
}
|
|
16
|
+
export interface ProteinView {
|
|
17
|
+
type: 'ProteinView';
|
|
18
|
+
id: string;
|
|
19
|
+
displayName?: string;
|
|
20
|
+
structures: ProteinViewStructure[];
|
|
21
|
+
}
|
|
22
|
+
export declare function isProteinView(view: unknown): view is ProteinView;
|
|
1
23
|
/**
|
|
2
24
|
* Represents a connection between the MSA view and a protein structure
|
|
3
25
|
*/
|