jbrowse-plugin-msaview 2.1.0 → 2.2.0

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

@@ -2,13 +2,13 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { useStyles } from './util';
-const GenomeMouseoverHighlight = observer(function GenomeMouseoverHighlight2({ model, }) {
+const GenomeMouseoverHighlight = observer(function ({ model, }) {
     const { hovered } = getSession(model);
     return hovered &&
         typeof hovered === 'object' &&
-        'hoverPosition' in hovered ? (React.createElement(HoverHighlight, { model: model })) : null;
+        'hoverPosition' in hovered ? (React.createElement(GenomeMouseoverHighlightPostNullCheck, { model: model })) : null;
 });
-const HoverHighlight = observer(function HoverHighlight2({ model, }) {
+const GenomeMouseoverHighlightPostNullCheck = observer(function ({ model, }) {
     const { classes } = useStyles();
     const session = getSession(model);
     if (session.views.some(s => s.type === 'MsaView')) {

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

@@ -1 +1 @@
-{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIlC,MAAM,wBAAwB,GAAG,QAAQ,CAAC,SAAS,yBAAyB,CAAC,EAC3E,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,OAAO,OAAO;QACZ,OAAO,OAAO,KAAK,QAAQ;QAC3B,eAAe,IAAI,OAAO,CAAC,CAAC,CAAC,CAC7B,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,SAAS,eAAe,CAAC,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,IAAI,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,EAAE,CAAC;QAClD,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QAC3B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QAC1B,mBAAmB;QACnB,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QAEhD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS,EAAE,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GAAI,CAAA;QACtE,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,eAAe,wBAAwB,CAAA"}
+{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIlC,MAAM,wBAAwB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,OAAO,OAAO;QACZ,OAAO,OAAO,KAAK,QAAQ;QAC3B,eAAe,IAAI,OAAO,CAAC,CAAC,CAAC,CAC7B,oBAAC,qCAAqC,IAAC,KAAK,EAAE,KAAK,GAAI,CACxD,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,MAAM,qCAAqC,GAAG,QAAQ,CAAC,UAAU,EAC/D,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,IAAI,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,EAAE,CAAC;QAClD,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QAC3B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QAC1B,mBAAmB;QACnB,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QAEhD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS,EAAE,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GAAI,CAAA;QACtE,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,eAAe,wBAAwB,CAAA"}

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -19,7 +19,9 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
             const left = Math.min(s.offsetPx, e.offsetPx) - model.offsetPx;
             return (React.createElement("div", { key: `${JSON.stringify(r)}-${idx}`, className: classes.highlight, style: { left, width } }));
         }
-        return null;
+        else {
+            return null;
+        }
     }))) : null;
 });
 export default MsaToGenomeHighlight;

package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map

@@ -1 +1 @@
-{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAGzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAOlC,SAAS,gBAAgB,CAAC,QAAkB,EAAE,CAAS;IACrD,OAAO,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;AAC7C,CAAC;AAED,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEjC,CAAA;IACb,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;IAC7D,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACrC,MAAM,OAAO,GAAG,gBAAgB,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAA;YAC9D,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}
+{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAGzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAOlC,SAAS,gBAAgB,CAAC,QAAkB,EAAE,CAAS;IACrD,OAAO,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;AAC7C,CAAC;AAED,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEjC,CAAA;IACb,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;IAC7D,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACrC,MAAM,OAAO,GAAG,gBAAgB,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAA;QACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAA;YAC9D,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;aAAM,CAAC;YACN,OAAO,IAAI,CAAA;QACb,CAAC;IACH,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/ExternalLink.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+import type { LinkProps } from '@mui/material';
+export default function ExternalLink(props: LinkProps): React.JSX.Element;

package/dist/ExternalLink.js

@@ -0,0 +1,11 @@
+import React from 'react';
+import OpenInNewIcon from '@mui/icons-material/OpenInNew';
+import { Link } from '@mui/material';
+export default function ExternalLink(props) {
+    const { children, ...rest } = props;
+    return (React.createElement(Link, { ...rest, target: "_blank", rel: "noreferrer" },
+        children,
+        " ",
+        React.createElement(OpenInNewIcon, { fontSize: "small" })));
+}
+//# sourceMappingURL=ExternalLink.js.map

package/dist/ExternalLink.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ExternalLink.js","sourceRoot":"","sources":["../src/ExternalLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,aAAa,MAAM,+BAA+B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAIpC,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,KAAgB;IACnD,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL,oBAAC,IAAI,OAAK,IAAI,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY;QAC7C,QAAQ;;QAAE,oBAAC,aAAa,IAAC,QAAQ,EAAC,OAAO,GAAG,CACxC,CACR,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js

@@ -1,64 +1,59 @@
-import React, { useEffect, useState } from 'react';
+import React, { useState } from 'react';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { getContainingView, getSession, } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, Link } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView';
-import { geneTreeFetcher } from './ensemblGeneTreeUtils';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
+import { useGeneTree } from './useGeneTree';
+import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+import TranscriptSelector from '../TranscriptSelector';
+import { useFeatureSequence } from '../useFeatureSequence';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
+        display: 'flex',
+        flexDirection: 'column',
+        gap: 16,
     },
 });
 const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
     const session = getSession(model);
     const view = getContainingView(model);
     const { classes } = useStyles();
-    const [error, setError] = useState();
-    const [treeData, setTreeData] = useState();
-    const [isTreeLoading, setIsTreeLoading] = useState(false);
-    const [treeError, setTreeError] = useState();
+    const [launchViewError, setLaunchViewError] = useState();
     const options = getTranscriptFeatures(feature);
     const [userSelection, setUserSelection] = useState(getId(options[0]));
-    useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                setIsTreeLoading(true);
-                const result = await geneTreeFetcher(userSelection);
-                setTreeData(result);
-            }
-            catch (e) {
-                console.error(e);
-                setTreeError(e);
-            }
-            finally {
-                setIsTreeLoading(false);
-            }
-        })();
-    }, [userSelection]);
+    const { treeData, isTreeLoading, treeError } = useGeneTree(userSelection);
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { proteinSequence, error: featureSequenceError } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
     const loadingMessage = isTreeLoading
         ? 'Loading tree data from Ensembl GeneTree'
         : undefined;
-    const e = treeError ?? error;
+    const e = treeError ?? launchViewError ?? featureSequenceError;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             e ? React.createElement(ErrorMessage, { error: e }) : null,
             loadingMessage ? React.createElement(LoadingEllipses, { message: loadingMessage }) : null,
-            React.createElement(Typography, null, "Load data from Ensembl GeneTree"),
-            React.createElement(TextField, { select: true, label: "Choose isoform to view MSA for", value: userSelection, onChange: event => {
-                    setUserSelection(event.target.value);
-                } }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() }, getTranscriptDisplayName(val)))))),
+            treeData ? (React.createElement("div", null,
+                React.createElement("div", null,
+                    "Found Ensembl Compara GeneTree: ",
+                    treeData.geneTreeId),
+                React.createElement(Link, { target: "_blank", href: `https://useast.ensembl.org/Multi/GeneTree/Image?gt=${treeData.geneTreeId}` },
+                    "See ",
+                    treeData.geneTreeId,
+                    " at Ensembl"))) : null,
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     try {
                         if (!treeData) {
                             return;
                         }
-                        setError(undefined);
+                        setLaunchViewError(undefined);
                         ensemblGeneTreeLaunchView({
                             feature,
                             view,
@@ -70,7 +65,7 @@ const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
                     }
                     catch (e) {
                         console.error(e);
-                        setError(e);
+                        setLaunchViewError(e);
                     }
                 } }, "Submit"),
             React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js

@@ -2,14 +2,8 @@ export function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature
     session.addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
-        treeAreaWidth: 200,
-        treeWidth: 100,
-        drawNodeBubbles: false,
-        labelsAlignRight: true,
-        showBranchLen: false,
         colWidth: 10,
         rowHeight: 12,
-        colorSchemeName: 'percent_identity_dynamic',
         data,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ensemblGeneTreeLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,yBAAyB,CAAC,EACxC,OAAO,EACP,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,IAAI,GAWL;IACC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE;QACzB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,IAAI;QACJ,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;KACnC,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts

@@ -1,4 +1,5 @@
 export declare function geneTreeFetcher(id2: string): Promise<{
+    geneTreeId: string;
     tree: string;
     msa: string;
     treeMetadata: string;

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js

@@ -1,35 +1,25 @@
+import { gatherSequencesFromTree } from './gatherSequencesFromTree';
 import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util';
-function gatherSequencesFromTree(tree, arr = []) {
-    if (tree.children) {
-        for (const child of tree.children) {
-            if (child.sequence) {
-                const id = child.sequence.id[0]?.accession;
-                if (id) {
-                    arr.push({
-                        id,
-                        seq: child.sequence.mol_seq.seq,
-                        species: child.taxonomy.common_name || child.taxonomy.scientific_name,
-                        genomicLocString: child.sequence.mol_seq.location,
-                    });
-                }
-            }
-            gatherSequencesFromTree(child, arr);
-        }
-    }
-    return arr;
-}
 const base = 'https://rest.ensembl.org';
 export async function geneTreeFetcher(id2) {
     const id = id2.replace(/\..*/, '');
     const { species } = await fetchWithLocalStorageCache(`${id}-ensembl`, () => jsonfetch(`${base}/lookup/id/${id}?content-type=application/json`));
     const treeBase = `${base}/genetree/member/id/${species}/${id}`;
-    const msa = await fetchWithLocalStorageCache(`${id}-msa`, () => jsonfetch(`${treeBase}?content-type=application/json;aligned=1;sequence=pep`));
+    const geneTreeResult = await fetchWithLocalStorageCache(`${id}-msa`, () => jsonfetch(`${treeBase}?content-type=application/json;aligned=1;sequence=pep`));
+    // we query again to get newick format tree. could probably extract from json
+    // as alternative
     const tree = await fetchWithLocalStorageCache(`${id}-tree`, () => textfetch(`${treeBase}?nh_format=simple;content-type=text/x-nh`));
-    const res = gatherSequencesFromTree(msa.tree);
+    const res = gatherSequencesFromTree(geneTreeResult.tree);
     return {
+        geneTreeId: geneTreeResult.id,
         tree,
         msa: res.map(r => `>${r.id}\n${r.seq}`).join('\n'),
-        treeMetadata: JSON.stringify(Object.fromEntries(res.map(r => [r.id, { genome: r.species }]))),
+        treeMetadata: JSON.stringify(Object.fromEntries(res.map(r => [
+            r.id,
+            {
+                genome: r.species,
+            },
+        ]))),
     };
 }
 //# sourceMappingURL=ensemblGeneTreeUtils.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map

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package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts

@@ -0,0 +1,2 @@
+import type { TreeNode, TreeRow } from './types';
+export declare function gatherSequencesFromTree(tree: TreeNode, arr?: TreeRow[]): TreeRow[];

package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js

@@ -0,0 +1,20 @@
+export function gatherSequencesFromTree(tree, arr = []) {
+    if (tree.children) {
+        for (const child of tree.children) {
+            if (child.sequence) {
+                const id = child.sequence.id[0]?.accession;
+                if (id) {
+                    arr.push({
+                        id,
+                        seq: child.sequence.mol_seq.seq,
+                        species: child.taxonomy.common_name || child.taxonomy.scientific_name,
+                        genomicLocString: child.sequence.mol_seq.location,
+                    });
+                }
+            }
+            gatherSequencesFromTree(child, arr);
+        }
+    }
+    return arr;
+}
+//# sourceMappingURL=gatherSequencesFromTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts

@@ -0,0 +1,24 @@
+export interface TreeNodeSequence {
+    mol_seq: {
+        seq: string;
+        location?: string;
+    };
+    id: {
+        accession: string;
+    }[];
+}
+export interface TreeNodeTaxonomy {
+    common_name: string;
+    scientific_name: string;
+}
+export interface TreeNode {
+    children?: TreeNode[];
+    sequence?: TreeNodeSequence;
+    taxonomy: TreeNodeTaxonomy;
+}
+export interface TreeRow {
+    id: string;
+    seq: string;
+    species: string;
+    genomicLocString?: string;
+}

package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/types.ts"],"names":[],"mappings":""}

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts

@@ -0,0 +1,10 @@
+export declare function useGeneTree(geneId: string): {
+    treeData: {
+        geneTreeId: string;
+        tree: string;
+        msa: string;
+        treeMetadata: string;
+    } | undefined;
+    isTreeLoading: boolean;
+    treeError: unknown;
+};

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js

@@ -0,0 +1,27 @@
+import { useEffect, useState } from 'react';
+import { geneTreeFetcher } from './ensemblGeneTreeUtils';
+export function useGeneTree(geneId) {
+    const [treeData, setTreeData] = useState();
+    const [isTreeLoading, setIsTreeLoading] = useState(false);
+    const [treeError, setTreeError] = useState();
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                setIsTreeLoading(true);
+                const result = await geneTreeFetcher(geneId);
+                setTreeData(result);
+            }
+            catch (e) {
+                console.error(e);
+                setTreeError(e);
+            }
+            finally {
+                setIsTreeLoading(false);
+            }
+        })();
+    }, [geneId]);
+    return { treeData, isTreeLoading, treeError };
+}
+//# sourceMappingURL=useGeneTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js

@@ -2,8 +2,8 @@ import React, { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { Tab, Tabs } from '@mui/material';
 import EnsemblGeneTree from './EnsemblGeneTree/EnsemblGeneTree';
-import MSALoader from './MSALoader/MSALoader';
-import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
+import ManualMSALoader from './ManualMSALoader/ManualMSALoader';
+import NCBIBlastPanel from './NCBIBlastQuery/NCBIBlastPanel';
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
 import TabPanel from './TabPanel';
 export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
@@ -17,14 +17,14 @@ export default function LaunchProteinViewDialog({ handleClose, feature, model, }
             React.createElement(Tab, { label: "NCBI BLAST query", value: 0 }),
             React.createElement(Tab, { label: "UCSC 100-way dataset", value: 1 }),
             React.createElement(Tab, { label: "Ensembl GeneTree", value: 2 }),
-            React.createElement(Tab, { label: "Manually open MSA", value: 3 })),
+            React.createElement(Tab, { label: "Manually open MSA/tree", value: 3 })),
         React.createElement(TabPanel, { value: value, index: 0 },
-            React.createElement(NewNcbiBlastQueryPanel, { handleClose: handleClose, feature: feature, model: model })),
+            React.createElement(NCBIBlastPanel, { handleClose: handleClose, feature: feature, model: model })),
         React.createElement(TabPanel, { value: value, index: 1 },
             React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose })),
         React.createElement(TabPanel, { value: value, index: 2 },
             React.createElement(EnsemblGeneTree, { model: model, feature: feature, handleClose: handleClose })),
         React.createElement(TabPanel, { value: value, index: 3 },
-            React.createElement(MSALoader, { model: model, feature: feature, handleClose: handleClose }))));
+            React.createElement(ManualMSALoader, { model: model, feature: feature, handleClose: handleClose }))));
 }
 //# sourceMappingURL=LaunchMsaViewDialog.js.map

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/NcbiBlastPanel.d.ts → ManualMSALoader/ManualMSALoader.d.ts}

@@ -1,8 +1,8 @@
 import React from 'react';
 import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const NcbiBlastPanel: ({ handleClose, feature, model, }: {
+declare const ManualMSALoader: ({ model, feature, handleClose, }: {
     model: AbstractTrackModel;
     feature: Feature;
     handleClose: () => void;
 }) => React.JSX.Element;
-export default NcbiBlastPanel;
+export default ManualMSALoader;

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js

@@ -0,0 +1,103 @@
+import React, { useState } from 'react';
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import { getContainingView, getSession, } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { launchView } from './launchView';
+import TextField2 from '../../../TextField2';
+import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+import TranscriptSelector from '../TranscriptSelector';
+import { useFeatureSequence } from '../useFeatureSequence';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
+    const session = getSession(model);
+    const view = getContainingView(model);
+    const { classes } = useStyles();
+    const [launchViewError, setLaunchViewError] = useState();
+    const [inputMethod, setInputMethod] = useState('file');
+    const [msaText, setMsaText] = useState('');
+    const [treeText, setTreeText] = useState('');
+    const [msaFileLocation, setMsaFileLocation] = useState();
+    const [treeFileLocation, setTreeFileLocation] = useState();
+    const options = getTranscriptFeatures(feature);
+    const [userSelection, setUserSelection] = useState(getId(options[0]));
+    const ret = options.find(val => userSelection === getId(val));
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { proteinSequence, error: error2 } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
+    const e = launchViewError ?? error2;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
+            React.createElement(FormControl, { component: "fieldset" },
+                React.createElement(RadioGroup, { row: true, value: inputMethod, onChange: event => {
+                        setInputMethod(event.target.value);
+                    } },
+                    React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "Open files" }),
+                    React.createElement(FormControlLabel, { value: "text", control: React.createElement(Radio, null), label: "Paste text" }))),
+            React.createElement("div", { style: { marginBottom: 30 } }, inputMethod === 'file' ? (React.createElement("div", { style: { maxWidth: 500 } },
+                React.createElement(FileSelector, { name: "MSA File .aln (Clustal), .fa/.mfa (aligned FASTA), .stock (Stockholm), etc)", inline: true, location: msaFileLocation, setLocation: setMsaFileLocation }),
+                React.createElement(FileSelector, { name: "Tree file .nh (Newick) or .asn (NCBI COBALT ASN.1)", inline: true, location: treeFileLocation, setLocation: setTreeFileLocation }))) : (React.createElement(React.Fragment, null,
+                React.createElement(TextField2, { variant: "outlined", name: "MSA", multiline: true, minRows: 5, style: { marginBottom: '20px' }, maxRows: 10, fullWidth: true, placeholder: "Paste MSA here", value: msaText, onChange: event => {
+                        setMsaText(event.target.value);
+                    } }),
+                React.createElement(TextField2, { variant: "outlined", name: "Tree", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, placeholder: "Paste newick tree (optional)", value: treeText, onChange: event => {
+                        setTreeText(event.target.value);
+                    } })))),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "contained", disabled: !ret ||
+                    (inputMethod === 'file' && !msaFileLocation) ||
+                    (inputMethod === 'text' && !msaText.trim()), onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            if (!ret) {
+                                return;
+                            }
+                            setLaunchViewError(undefined);
+                            launchView({
+                                session,
+                                newViewTitle: getGeneDisplayName(ret),
+                                view,
+                                feature: ret,
+                                data: inputMethod === 'file'
+                                    ? {
+                                        msa: msaFileLocation
+                                            ? await openLocation(msaFileLocation).readFile('utf8')
+                                            : '',
+                                        tree: treeFileLocation
+                                            ? await openLocation(treeFileLocation).readFile('utf8')
+                                            : undefined,
+                                    }
+                                    : {
+                                        msa: msaText,
+                                        tree: treeText,
+                                    },
+                            });
+                            handleClose();
+                        }
+                        catch (e) {
+                            console.error(e);
+                            setLaunchViewError(e);
+                        }
+                    })();
+                } }, "Submit"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
+});
+export default ManualMSALoader;
+//# sourceMappingURL=ManualMSALoader.js.map

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.js.map

@@ -1 +1 @@
-{"version":3,"file":"fetchGeneList.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/fetchGeneList.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,GAAG,GAAG,MAAM,KAAK,CACrB,2DAA2D,CAC5D,CAAA;IACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,kBAAkB,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;IAC/B,OAAO,MAAM;SACV,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrB,CAAC"}
+{"version":3,"file":"fetchGeneList.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/ManualMSALoader/fetchGeneList.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,GAAG,GAAG,MAAM,KAAK,CACrB,2DAA2D,CAC5D,CAAA;IACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,kBAAkB,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;IAC/B,OAAO,MAAM;SACV,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrB,CAAC"}

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts

@@ -0,0 +1,14 @@
+import { AbstractSessionModel, Feature, FileLocation } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export declare function launchView({ session, newViewTitle, view, feature, msaFileLocation, treeFileLocation, data, }: {
+    session: AbstractSessionModel;
+    newViewTitle: string;
+    view: LinearGenomeViewModel;
+    feature: Feature;
+    msaFileLocation?: FileLocation;
+    treeFileLocation?: FileLocation;
+    data?: {
+        msa: string;
+        tree?: string;
+    };
+}): void;

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js

@@ -0,0 +1,12 @@
+export function launchView({ session, newViewTitle, view, feature, msaFileLocation, treeFileLocation, data, }) {
+    session.addView('MsaView', {
+        type: 'MsaView',
+        displayName: newViewTitle,
+        connectedViewId: view.id,
+        connectedFeature: feature.toJSON(),
+        msaFileLocation,
+        treeFileLocation,
+        data,
+    });
+}
+//# sourceMappingURL=launchView.js.map

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/{MSALoader/MSALoader.d.ts → NCBIBlastQuery/NCBIBlastAutomaticPanel.d.ts}

@@ -1,8 +1,10 @@
 import React from 'react';
 import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const PreLoadedMSA: ({ model, feature, handleClose, }: {
+declare const NCBIBlastAutomaticPanel: ({ handleClose, feature, model, children, baseUrl, }: {
     model: AbstractTrackModel;
     feature: Feature;
+    baseUrl: string;
     handleClose: () => void;
+    children: React.ReactNode;
 }) => React.JSX.Element;
-export default PreLoadedMSA;
+export default NCBIBlastAutomaticPanel;