npm - jbrowse-plugin-msaview - Versions diffs - 2.2.11 → 2.3.3 - Mend

jbrowse-plugin-msaview 2.2.11 → 2.3.3

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.

Files changed (133) hide show

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import React, { useState } from 'react';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
-import { getContainingView, getEnv, getSession, } from '@jbrowse/core/util';
+import { getContainingView, getEnv, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
 import { observer } from 'mobx-react';
 import useSWR from 'swr';
@@ -18,7 +18,7 @@ const useStyles = makeStyles()({
         width: '80em',
     },
 });
-const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
+const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const session = getSession(model);
     const view = getContainingView(model);
     const { classes } = useStyles();
@@ -35,9 +35,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
             pluginManager,
         })
         : undefined, swrFlags);
-    const { options: transcripts, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, validSet, } = useTranscriptSelection({ feature, view, validIds: msaList });
+    const { options: transcripts, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view, validIds: msaList });
     const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDatasetId
-        ? `${selectedId}-${selectedId}-${msaList?.length}-msa`
+        ? `${selectedDatasetId}-${selectedId}-${msaList?.length}-msa`
         : 'none-msa', () => selectedId && selectedDataset && msaList
         ? fetchMSA({
             msaId: selectedId,
@@ -60,7 +60,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
                 msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
                 msaList ? (React.createElement("div", null,
                     React.createElement(SanitizedHTML, { html: selectedDataset.description }),
-                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence, validSet: validSet }))) : null)) : null),
+                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence, validIds: msaList }))) : null)) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript || !msaData?.length, onClick: () => {
                     try {
@@ -86,9 +86,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
                         setViewError(e);
                     }
                 } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: handleClose }, "Cancel"))));
 });
 export default PreLoadedMSA;
 //# sourceMappingURL=PreLoadedMSADataPanel.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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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,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE;gBAC1B,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,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
 import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export declare function fetchMSAList({ config, pluginManager, }: {
     config: AnyConfigurationModel;
     pluginManager: PluginManager;

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function preCalculatedLaunchView({ session, newViewTitle, view, feature, data, querySeqName, }: {
     data: {

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/TranscriptSelector.d.ts CHANGED Viewed

@@ -1,11 +1,11 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }: {
+import type { Feature } from '@jbrowse/core/util';
+export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validIds, }: {
     feature: Feature;
     options: Feature[];
     selectedId: string;
     selectedTranscript: Feature | undefined;
     onTranscriptChange: (transcriptId: string) => void;
     proteinSequence: string | undefined;
-    validSet?: Set<string>;
+    validIds?: string[];
 }): React.JSX.Element;

package/dist/LaunchMsaView/components/TranscriptSelector.js CHANGED Viewed

@@ -11,7 +11,7 @@ const useStyles = makeStyles()({
         minWidth: 300,
     },
 });
-export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }) {
+export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validIds, }) {
     const { classes } = useStyles();
     const [showSequence, setShowSequence] = useState(false);
     return (React.createElement(React.Fragment, null,
@@ -19,8 +19,8 @@ export default function TranscriptSelector({ feature, options, selectedId, selec
             React.createElement(TextField, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: selectedId, onChange: event => {
                     onTranscriptChange(event.target.value);
                 } }, options.map(val => {
-                const inSet = validSet
-                    ? [...validSet].some(id => featureMatchesId(val, id))
+                const inSet = validIds
+                    ? validIds.some(id => featureMatchesId(val, id))
                     : true;
                 const { len, mod } = getTranscriptLength(val);
                 return (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: !inSet },
@@ -30,7 +30,7 @@ export default function TranscriptSelector({ feature, options, selectedId, selec
                     " aa)",
                     ' ',
                     mod ? ` (possible fragment)` : '',
-                    validSet ? (inSet ? ' (has data)' : ' (no data)') : ''));
+                    validIds ? (inSet ? ' (has data)' : ' (no data)') : ''));
             })),
             React.createElement("div", { style: { alignContent: 'center', marginLeft: 20 } },
                 React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {

package/dist/LaunchMsaView/components/TranscriptSelector.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/useTranscriptSelection.d.ts CHANGED Viewed

@@ -12,5 +12,5 @@ export declare function useTranscriptSelection({ feature, view, validIds, }: {
     selectedTranscript: Feature | undefined;
     proteinSequence: string;
     error: any;
-    validSet: Set<string> | undefined;
+    validIds: string[] | undefined;
 };

package/dist/LaunchMsaView/components/useTranscriptSelection.js CHANGED Viewed

@@ -12,7 +12,6 @@ export function useTranscriptSelection({ feature, view, validIds, }) {
         view,
         feature: selectedTranscript,
     });
-    const validSet = useMemo(() => (validIds ? new Set(validIds) : undefined), [validIds]);
     useEffect(() => {
         if (validIds && validIds.length > 0) {
             const currentFeature = options.find(opt => getId(opt) === selectedId);
@@ -31,7 +30,7 @@ export function useTranscriptSelection({ feature, view, validIds, }) {
         selectedTranscript,
         proteinSequence,
         error,
-        validSet,
+        validIds,
     };
 }
 //# sourceMappingURL=useTranscriptSelection.js.map

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package/dist/LaunchMsaView/components/util.js CHANGED Viewed

@@ -12,6 +12,6 @@ export function makeId(h, taxonomyInfo) {
     return `${h.accession}-${speciesName}`;
 }
 export function strip(s) {
-    return s.replace('-', '');
+    return s.replaceAll('-', '');
 }
 //# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/components/util.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,MAAM,CACpB,CAAyD,EACzD,YAAwC;IAExC,IAAI,WAAW,GAAG,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IAChD,IAAI,CAAC,CAAC,KAAK,IAAI,YAAY,EAAE,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;QAC1C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAE,CAAA;QACvC,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;YACpB,WAAW,GAAG,IAAI,CAAC,UAAU;iBAC1B,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC;iBACvE,IAAI,CAAC,GAAG,CAAC,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAC,CAAC,SAAS,IAAI,WAAW,EAAE,CAAA;AACxC,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,CAAS;IAC7B,OAAO,CAAC,CAAC,~~OAAO~~,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;~~AAC3B~~,CAAC"}
1	+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,MAAM,CACpB,CAAyD,EACzD,YAAwC;IAExC,IAAI,WAAW,GAAG,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IAChD,IAAI,CAAC,CAAC,KAAK,IAAI,YAAY,EAAE,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;QAC1C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAE,CAAA;QACvC,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;YACpB,WAAW,GAAG,IAAI,CAAC,UAAU;iBAC1B,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC;iBACvE,IAAI,CAAC,GAAG,CAAC,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAC,CAAC,SAAS,IAAI,WAAW,EAAE,CAAA;AACxC,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,CAAS;IAC7B,OAAO,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;AAC9B,CAAC"}

package/dist/LaunchMsaView/index.d.ts CHANGED Viewed

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LaunchMsaViewF(pluginManager: PluginManager): void;

package/dist/LaunchMsaView/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/util.d.ts CHANGED Viewed

@@ -11,3 +11,4 @@ export declare function getTranscriptDisplayName(val?: Feature): string;
 export declare function getGeneDisplayName(val?: Feature): string;
 export declare function getSortedTranscriptFeatures(feature: Feature): Feature[];
 export declare function cleanProteinSequence(seq: string): string;
+export declare function getGeneIdentifiers(feature: Feature): string[];

package/dist/LaunchMsaView/util.js CHANGED Viewed

@@ -64,4 +64,14 @@ export function getSortedTranscriptFeatures(feature) {
 export function cleanProteinSequence(seq) {
     return seq.replaceAll('*', '').replaceAll('&', '');
 }
+export function getGeneIdentifiers(feature) {
+    const ids = [
+        feature.id(),
+        feature.get('id'),
+        feature.get('name'),
+        feature.get('gene_id'),
+        feature.get('gene_name'),
+    ].filter((id) => !!id);
+    return [...new Set(ids)];
+}
 //# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/afterCreateAutoruns.d.ts ADDED Viewed

@@ -0,0 +1,10 @@
+import type { JBrowsePluginMsaViewModel } from './model';
+export declare function loadStoredData(self: JBrowsePluginMsaViewModel): void;
+export declare function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel): void;
+export declare function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel): void;
+export declare function processInit(self: JBrowsePluginMsaViewModel): void;
+export declare function updateGenomeHighlights(self: JBrowsePluginMsaViewModel): void;
+export declare function highlightConnectedStructures(self: JBrowsePluginMsaViewModel): void;
+export declare function autoConnectStructures(self: JBrowsePluginMsaViewModel): void;
+export declare function observeProteinHighlights(self: JBrowsePluginMsaViewModel): void;
+export declare function runCleanup(): void;

package/dist/MsaViewPanel/afterCreateAutoruns.js ADDED Viewed

@@ -0,0 +1,258 @@
+import { getSession } from '@jbrowse/core/util';
+import { doLaunchBlast } from './doLaunchBlast';
+import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
+import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
+import { gappedToUngappedPosition } from './structureConnection';
+import { getUniprotIdFromAlphaFoldUrl } from './util';
+export function loadStoredData(self) {
+    const { dataStoreId, rows } = self;
+    if (dataStoreId && rows.length === 0) {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                self.setLoadingStoredData(true);
+                const storedData = await retrieveMsaData(dataStoreId);
+                if (storedData) {
+                    if (storedData.msa) {
+                        self.setMSA(storedData.msa);
+                    }
+                    if (storedData.tree) {
+                        self.setTree(storedData.tree);
+                    }
+                }
+            }
+            catch (e) {
+                console.error('Failed to load MSA data from IndexedDB:', e);
+            }
+            finally {
+                self.setLoadingStoredData(false);
+            }
+        })();
+    }
+}
+export function storeDataToIndexedDB(self) {
+    const { rows, dataStoreId } = self;
+    if (rows.length > 0 && !dataStoreId) {
+        const hasFilehandle = !!(self.msaFilehandle ?? self.treeFilehandle);
+        if (hasFilehandle) {
+            return;
+        }
+        const msaData = self.data.msa;
+        const treeData = self.data.tree;
+        if (msaData || treeData) {
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;
+            (async () => {
+                try {
+                    const newId = generateDataStoreId();
+                    const success = await storeMsaData(newId, {
+                        msa: msaData,
+                        tree: treeData,
+                        treeMetadata: self.data.treeMetadata,
+                    });
+                    if (success) {
+                        self.setDataStoreId(newId);
+                    }
+                }
+                catch (e) {
+                    console.error('Failed to store MSA data to IndexedDB:', e);
+                }
+            })();
+        }
+    }
+}
+export function launchBlastIfNeeded(self) {
+    if (self.blastParams) {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                self.setProgress('Submitting query');
+                self.setError(undefined);
+                const data = await doLaunchBlast({ self });
+                self.setData(data);
+                self.setBlastParams(undefined);
+            }
+            catch (e) {
+                self.setError(e);
+                console.error(e);
+            }
+            finally {
+                self.setProgress('');
+            }
+        })();
+    }
+}
+export function processInit(self) {
+    const { init } = self;
+    if (init) {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                self.setError(undefined);
+                const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init;
+                if (msaUrl) {
+                    const id = getUniprotIdFromAlphaFoldUrl(msaUrl);
+                    if (id) {
+                        self.setUniprotId(id);
+                        self.setQuerySeqName('query');
+                    }
+                }
+                if (querySeqName) {
+                    self.setQuerySeqName(querySeqName);
+                }
+                if (msaData) {
+                    self.setMSA(msaData);
+                }
+                else if (msaUrl) {
+                    const response = await fetch(msaUrl);
+                    if (!response.ok) {
+                        throw new Error(`Failed to fetch MSA: ${response.status}`);
+                    }
+                    const data = await response.text();
+                    self.setMSA(data);
+                }
+                if (treeData) {
+                    self.setTree(treeData);
+                }
+                else if (treeUrl) {
+                    const response = await fetch(treeUrl);
+                    if (!response.ok) {
+                        throw new Error(`Failed to fetch tree: ${response.status}`);
+                    }
+                    const data = await response.text();
+                    self.setTree(data);
+                }
+                self.setInit(undefined);
+            }
+            catch (e) {
+                self.setError(e);
+                console.error(e);
+            }
+        })();
+    }
+}
+export function updateGenomeHighlights(self) {
+    const { mouseCol, mouseClickCol } = self;
+    const r1 = mouseCol === undefined
+        ? undefined
+        : msaCoordToGenomeCoord({ model: self, coord: mouseCol });
+    const r2 = mouseClickCol === undefined
+        ? undefined
+        : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
+    self.setConnectedHighlights([r1, r2].filter(f => !!f));
+}
+export function highlightConnectedStructures(self) {
+    const { mouseCol, connectedProteinViews } = self;
+    if (connectedProteinViews.length === 0) {
+        return;
+    }
+    for (const conn of connectedProteinViews) {
+        const structure = conn.proteinView?.structures?.[conn.structureIdx];
+        if (!structure) {
+            continue;
+        }
+        if (mouseCol === undefined) {
+            structure.clearHighlightFromExternal?.();
+            continue;
+        }
+        const seq = self.getSequenceByRowName(conn.msaRowName);
+        if (!seq) {
+            continue;
+        }
+        const msaUngapped = gappedToUngappedPosition(seq, mouseCol);
+        if (msaUngapped === undefined) {
+            structure.clearHighlightFromExternal?.();
+            continue;
+        }
+        const structurePos = conn.msaToStructure[msaUngapped];
+        if (structurePos === undefined) {
+            structure.clearHighlightFromExternal?.();
+        }
+        else {
+            structure.highlightFromExternal?.(structurePos);
+        }
+    }
+}
+export function autoConnectStructures(self) {
+    const { views } = getSession(self);
+    const { connectedViewId, uniprotId, rows, connectedStructures } = self;
+    if (!uniprotId || rows.length === 0) {
+        return;
+    }
+    for (const view of views) {
+        const v = view;
+        if (v.type !== 'ProteinView' || !v.structures) {
+            continue;
+        }
+        for (let structureIdx = 0; structureIdx < v.structures.length; structureIdx++) {
+            const structure = v.structures[structureIdx];
+            if (structure.connectedViewId !== connectedViewId) {
+                continue;
+            }
+            if (structure.uniprotId !== uniprotId) {
+                continue;
+            }
+            const alreadyConnected = connectedStructures.some(c => c.proteinViewId === v.id && c.structureIdx === structureIdx);
+            if (alreadyConnected) {
+                continue;
+            }
+            if (!structure.structureSequences?.[0]) {
+                continue;
+            }
+            try {
+                self.connectToStructure(v.id, structureIdx);
+            }
+            catch (e) {
+                console.error('Failed to auto-connect to ProteinView:', e);
+            }
+        }
+    }
+}
+export function observeProteinHighlights(self) {
+    const { views } = getSession(self);
+    const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
+    if (!connectedViewId || !transcriptToMsaMap) {
+        return;
+    }
+    const columns = [];
+    for (const view of views) {
+        const v = view;
+        if (v.type !== 'ProteinView' || !v.structures) {
+            continue;
+        }
+        for (const structure of v.structures) {
+            if (structure.connectedViewId !== connectedViewId) {
+                continue;
+            }
+            const highlights = structure.hoverGenomeHighlights;
+            if (!highlights || highlights.length === 0) {
+                continue;
+            }
+            const { g2p } = transcriptToMsaMap;
+            for (const highlight of highlights) {
+                for (let coord = highlight.start; coord < highlight.end; coord++) {
+                    const proteinPos = g2p[coord];
+                    if (proteinPos !== undefined) {
+                        const col = self.seqPosToGlobalCol(querySeqName, proteinPos);
+                        if (!columns.includes(col)) {
+                            columns.push(col);
+                        }
+                    }
+                }
+            }
+        }
+    }
+    const visibleColumns = columns
+        .map(col => self.globalColToVisibleCol(col))
+        .filter((col) => col !== undefined);
+    self.setHighlightedColumns(visibleColumns.length > 0 ? visibleColumns : undefined);
+}
+export function runCleanup() {
+    cleanupOldData().catch((e) => {
+        console.error('Failed to cleanup old MSA data:', e);
+    });
+}
+//# sourceMappingURL=afterCreateAutoruns.js.map

package/dist/MsaViewPanel/afterCreateAutoruns.js.map ADDED Viewed

@@ -0,0 +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;AAChE,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,EAAE,UAAU,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;Q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package/dist/MsaViewPanel/blosum62.d.ts ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ declare const BLOSUM62: Record<string, Record<string, number>>;
2	+ export default BLOSUM62;