jbrowse-plugin-msaview 2.0.6 → 2.2.0

package/dist/LaunchMsaView/components/calculateProteinSequence.js

@@ -0,0 +1,39 @@
+import { dedupe, defaultCodonTable, generateCodonTable, revcom, } from '@jbrowse/core/util';
+export function stitch(subfeats, sequence) {
+    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
+}
+export function calculateProteinSequence({ cds, sequence, codonTable, }) {
+    const str = stitch(cds, sequence);
+    let protein = '';
+    for (let i = 0; i < str.length; i += 3) {
+        // use & symbol for undefined codon, or partial slice
+        protein += codonTable[str.slice(i, i + 3)] ?? '&';
+    }
+    return protein;
+}
+export function revlist(list, seqlen) {
+    return list
+        .map(sub => ({
+        ...sub,
+        start: seqlen - sub.end,
+        end: seqlen - sub.start,
+    }))
+        .toSorted((a, b) => a.start - b.start);
+}
+export function getProteinSequenceFromFeature({ selectedTranscript, seq, }) {
+    const { subfeatures, start, strand } = selectedTranscript.toJSON();
+    const cds = dedupe(subfeatures
+        ?.toSorted((a, b) => a.start - b.start)
+        .map(sub => ({
+        ...sub,
+        start: sub.start - start,
+        end: sub.end - start,
+    }))
+        .filter(subfeature => subfeature.type === 'CDS') ?? [], feat => `${feat.start}-${feat.end}`);
+    return calculateProteinSequence({
+        cds: strand === -1 ? revlist(cds, seq.length) : cds,
+        sequence: strand === -1 ? revcom(seq) : seq,
+        codonTable: generateCodonTable(defaultCodonTable),
+    });
+}
+//# sourceMappingURL=calculateProteinSequence.js.map

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

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

@@ -0,0 +1,8 @@
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+export declare function fetchSeq({ start, end, refName, session, assemblyName, }: {
+    start: number;
+    end: number;
+    refName: string;
+    assemblyName: string;
+    session: AbstractSessionModel;
+}): Promise<string>;

package/dist/LaunchMsaView/components/fetchSeq.js

@@ -0,0 +1,23 @@
+import { getConf } from '@jbrowse/core/configuration';
+export async function fetchSeq({ start, end, refName, session, assemblyName, }) {
+    const { assemblyManager, rpcManager } = session;
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        throw new Error('assembly not found');
+    }
+    const sessionId = 'getSequence';
+    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+        sessionId,
+        regions: [
+            {
+                start,
+                end,
+                refName: assembly.getCanonicalRefName(refName),
+                assemblyName,
+            },
+        ],
+    }));
+    return feats[0]?.get('seq') ?? '';
+}
+//# sourceMappingURL=fetchSeq.js.map

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

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

@@ -0,0 +1,10 @@
+export interface Feat {
+    start: number;
+    end: number;
+    type?: string;
+}
+export interface SeqState {
+    seq: string;
+    upstream?: string;
+    downstream?: string;
+}

package/dist/LaunchMsaView/components/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

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

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

package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.d.ts → useFeatureSequence.d.ts}

@@ -1,9 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-export interface SeqState {
-    seq: string;
-    upstream?: string;
-    downstream?: string;
-}
+import type { SeqState } from './types';
+import type { Feature } from '@jbrowse/core/util';
 export interface ErrorState {
     error: string;
 }
@@ -15,6 +11,7 @@ export declare function useFeatureSequence({ view, feature, upDownBp, forceLoad,
     upDownBp?: number;
     forceLoad?: boolean;
 }): {
+    proteinSequence: string;
     sequence: SeqState | ErrorState | undefined;
     error: unknown;
 };

package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.js → useFeatureSequence.js}

@@ -1,28 +1,8 @@
 import { useEffect, useState } from 'react';
-import { getConf } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
+import { getProteinSequenceFromFeature } from './calculateProteinSequence';
+import { fetchSeq } from './fetchSeq';
 const BPLIMIT = 500_000;
-async function fetchSeq({ start, end, refName, session, assemblyName, }) {
-    const { assemblyManager, rpcManager } = session;
-    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-    if (!assembly) {
-        throw new Error('assembly not found');
-    }
-    const sessionId = 'getSequence';
-    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-        sessionId,
-        regions: [
-            {
-                start,
-                end,
-                refName: assembly.getCanonicalRefName(refName),
-                assemblyName,
-            },
-        ],
-    }));
-    return feats[0]?.get('seq') ?? '';
-}
 export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
     const [sequence, setSequence] = useState();
     const [error, setError] = useState();
@@ -80,6 +60,16 @@ export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = tr
             })();
         }
     }, [feature, view, upDownBp, assemblyName, forceLoad]);
-    return { sequence, error };
+    const proteinSequence = sequence && !('error' in sequence)
+        ? getProteinSequenceFromFeature({
+            seq: sequence.seq,
+            selectedTranscript: feature,
+        })
+        : '';
+    return {
+        proteinSequence,
+        sequence,
+        error,
+    };
 }
 //# sourceMappingURL=useFeatureSequence.js.map

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

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

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,MAAM,CAAC,CAAyC;IAC9D,OAAO,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,CAAS;IAC7B,OAAO,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;AAC3B,CAAC"}

package/dist/LaunchMsaView/util.d.ts

@@ -1,5 +1,9 @@
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 export declare function getTranscriptFeatures(feature: Feature): Feature[];
+export declare function getTranscriptLength(feature: Feature): {
+    len: number;
+    mod: number;
+};
 export declare function getId(val?: Feature): string;
 export declare function getTranscriptDisplayName(val?: Feature): string;
 export declare function getGeneDisplayName(val?: Feature): string;

package/dist/LaunchMsaView/util.js

@@ -1,3 +1,4 @@
+import { sum } from '@jbrowse/core/util';
 export function getTranscriptFeatures(feature) {
     // check if we are looking at a 'two-level' or 'three-level' feature by
     // finding exon/CDS subfeatures. we want to select from transcript names
@@ -7,6 +8,16 @@ export function getTranscriptFeatures(feature) {
         : // filter out non-coding by finding subfeatures with CDS subfeatures
             subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
 }
+export function getTranscriptLength(feature) {
+    const cdsLen = sum(feature
+        .get('subfeatures')
+        ?.filter(f => f.get('type')?.toLowerCase() === 'cds')
+        .map(s => s.get('end') - s.get('start')) ?? []);
+    return {
+        len: Math.floor(cdsLen / 3),
+        mod: cdsLen % 3,
+    };
+}
 export function getId(val) {
     return val?.get('name') ?? val?.get('id') ?? '';
 }
@@ -18,7 +29,10 @@ export function getTranscriptDisplayName(val) {
 export function getGeneDisplayName(val) {
     return val === undefined
         ? ''
-        : [val.get('gene_name') ?? val.get('name'), val.get('id')]
+        : [
+            val.get('gene_name') ?? val.get('name'),
+            val.get('id') ? `(${val.get('id')})` : '',
+        ]
             .filter(f => !!f)
             .join(' ');
 }

package/dist/LaunchMsaView/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LaunchMsaView/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,oBAAoB,CAAA;AAIxC,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAA;IACpD,OAAO,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC;QACnD,CAAC,CAAC,CAAC,OAAO,CAAC;QACX,CAAC,CAAC,oEAAoE;YACpE,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CACrB,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,CAAC,CACzD,CAAA;AACP,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,OAAgB;IAClD,MAAM,MAAM,GAAG,GAAG,CAChB,OAAO;SACJ,GAAG,CAAC,aAAa,CAAC;QACnB,EAAE,MAAM,CACN,CAAC,CAAC,EAAE,CAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAwB,EAAE,WAAW,EAAE,KAAK,KAAK,CACpE;SACA,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CACjD,CAAA;IACD,OAAO;QACL,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC;QAC3B,GAAG,EAAE,MAAM,GAAG,CAAC;KAChB,CAAA;AACH,CAAC;AACD,MAAM,UAAU,KAAK,CAAC,GAAa;IACjC,OAAO,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,IAAI,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,GAAa;IACpD,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACjE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAa;IAC9C,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC;YACE,GAAG,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC;YACvC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;SAC1C;aACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,IAAI,CAAC,GAAG,CAAC,CAAA;AAClB,CAAC"}

package/dist/MsaViewPanel/components/LoadingBLAST.d.ts

@@ -1,6 +1,7 @@
 import React from 'react';
 import { JBrowsePluginMsaViewModel } from '../model';
-declare const LoadingBLAST: ({ model, }: {
+declare const LoadingBLAST: ({ model, baseUrl, }: {
     model: JBrowsePluginMsaViewModel;
+    baseUrl: string;
 }) => React.JSX.Element;
 export default LoadingBLAST;

package/dist/MsaViewPanel/components/LoadingBLAST.js

@@ -12,23 +12,23 @@ const useStyles = makeStyles()(theme => ({
         background: theme.palette.background.paper,
     },
 }));
-function RIDError({ rid, error }) {
+function RIDError({ baseUrl, rid, error, }) {
     return (React.createElement("div", null,
-        rid ? React.createElement(RIDLink, { rid: rid }) : null,
+        rid ? React.createElement(RIDLink, { rid: rid, baseUrl: baseUrl }) : null,
         React.createElement(ErrorMessage, { error: error })));
 }
-function RIDProgress({ rid, progress }) {
+function RIDProgress({ baseUrl, rid, progress, }) {
     const { classes } = useStyles();
     return (React.createElement("div", { className: classes.loading },
-        rid ? React.createElement(RIDLink, { rid: rid }) : null,
+        rid ? React.createElement(RIDLink, { baseUrl: baseUrl, rid: rid }) : null,
         React.createElement(Typography, null, progress)));
 }
-const LoadingBLAST = observer(function LoadingBLAST2({ model, }) {
+const LoadingBLAST = observer(function LoadingBLAST2({ model, baseUrl, }) {
     const { progress, rid, error, processing } = model;
     const { classes } = useStyles();
     return (React.createElement("div", { className: classes.margin },
         React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
-        error ? (React.createElement(RIDError, { rid: rid, error: error })) : (rid ? (React.createElement(RIDProgress, { rid: rid, progress: progress })) : null),
+        error ? (React.createElement(RIDError, { baseUrl: baseUrl, rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { baseUrl: baseUrl, rid: rid, progress: progress })) : null,
         React.createElement(Typography, null, processing || 'Initializing BLAST query')));
 });
 export default LoadingBLAST;

package/dist/MsaViewPanel/components/LoadingBLAST.js.map

@@ -1 +1 @@
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+{"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAG1C,OAAO,OAAO,MAAM,WAAW,CAAA;AAE/B,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,EAAE;KACZ;IACD,OAAO,EAAE;QACP,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;KAC3C;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,QAAQ,CAAC,EAChB,OAAO,EACP,GAAG,EACH,KAAK,GAKN;IACC,OAAO,CACL;QACG,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,GAAG,EAAE,GAAG,EAAE,OAAO,EAAE,OAAO,GAAI,CAAC,CAAC,CAAC,IAAI;QACrD,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EACnB,OAAO,EACP,GAAG,EACH,QAAQ,GAKT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,OAAO;QAC5B,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,GAAI,CAAC,CAAC,CAAC,IAAI;QACrD,oBAAC,UAAU,QAAE,QAAQ,CAAc,CAC/B,CACP,CAAA;AACH,CAAC;AAED,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAClD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM;QAC5B,oBAAC,eAAe,IAAC,OAAO,EAAC,oBAAoB,EAAC,OAAO,EAAC,IAAI,GAAG;QAC5D,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,QAAQ,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,GAAI,CACvD,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAChE,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,UAAU,QAAE,UAAU,IAAI,0BAA0B,CAAc,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/MsaViewPanel/components/MsaViewPanel.js

@@ -4,7 +4,7 @@ import { MSAView } from 'react-msaview';
 import LoadingBLAST from './LoadingBLAST';
 const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
     const { blastParams } = model;
-    return (React.createElement("div", null, blastParams ? React.createElement(LoadingBLAST, { model: model }) : React.createElement(MSAView, { model: model })));
+    return (React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : (React.createElement(MSAView, { model: model }))));
 });
 export default MsaViewPanel;
 //# sourceMappingURL=MsaViewPanel.js.map

package/dist/MsaViewPanel/components/MsaViewPanel.js.map

@@ -1 +1 @@
-{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAGvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CACL,iCACG,WAAW,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
+{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAGvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CACL,iCACG,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,GAAI,CAC7D,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/MsaViewPanel/components/RIDLink.d.ts

@@ -1,5 +1,6 @@
 import React from 'react';
-declare function RIDLink({ rid }: {
+declare function RIDLink({ baseUrl, rid }: {
     rid: string;
+    baseUrl: string;
 }): React.JSX.Element;
 export default RIDLink;

package/dist/MsaViewPanel/components/RIDLink.js

@@ -1,16 +1,13 @@
 import React from 'react';
-import { Link, Typography } from '@mui/material';
-import OpenInNewIcon from '../../OpenInNewIcon';
-import { BLAST_URL } from '../../utils/ncbiBlast';
-function RIDLink({ rid }) {
+import { Typography } from '@mui/material';
+import ExternalLink from '../../ExternalLink';
+function RIDLink({ baseUrl, rid }) {
     return (React.createElement(Typography, null,
         "RID ",
         rid,
-        ' ',
-        React.createElement(Link, { target: "_black", href: `${BLAST_URL}?CMD=Get&RID=${rid}` },
-            "(see status at NCBI ",
-            React.createElement(OpenInNewIcon, null),
-            ")")));
+        " (",
+        React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${rid}` }, "see status"),
+        ")"));
 }
 export default RIDLink;
 //# sourceMappingURL=RIDLink.js.map

package/dist/MsaViewPanel/components/RIDLink.js.map

@@ -1 +1 @@
-{"version":3,"file":"RIDLink.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/RIDLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAEhD,OAAO,aAAa,MAAM,qBAAqB,CAAA;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAA;AAEjD,SAAS,OAAO,CAAC,EAAE,GAAG,EAAmB;IACvC,OAAO,CACL,oBAAC,UAAU;;QACJ,GAAG;QAAE,GAAG;QACb,oBAAC,IAAI,IAAC,MAAM,EAAC,QAAQ,EAAC,IAAI,EAAE,GAAG,SAAS,gBAAgB,GAAG,EAAE;;YACvC,oBAAC,aAAa,OAAG;gBAChC,CACI,CACd,CAAA;AACH,CAAC;AAED,eAAe,OAAO,CAAA"}
+{"version":3,"file":"RIDLink.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/RIDLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,YAAY,MAAM,oBAAoB,CAAA;AAE7C,SAAS,OAAO,CAAC,EAAE,OAAO,EAAE,GAAG,EAAoC;IACjE,OAAO,CACL,oBAAC,UAAU;;QACJ,GAAG;;QACR,oBAAC,YAAY,IAAC,IAAI,EAAE,GAAG,OAAO,gBAAgB,GAAG,EAAE,iBAEpC;YAEJ,CACd,CAAA;AACH,CAAC;AAED,eAAe,OAAO,CAAA"}

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -1,13 +1,13 @@
-import { makeId, strip, } from '../LaunchMsaView/components/NewNCBIBlastQuery/util';
+import { makeId, strip } from '../LaunchMsaView/components/util';
 import { launchMSA } from '../utils/msa';
 import { queryBlast } from '../utils/ncbiBlast';
 export async function doLaunchBlast({ self, }) {
-    const { blastDatabase, blastProgram, msaAlgorithm, proteinSequence } = self.blastParams;
-    const query = proteinSequence.replaceAll('*', '').replaceAll('&', '');
+    const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, } = self.blastParams;
     const { hits } = await queryBlast({
-        query,
+        query: proteinSequence.replaceAll('*', '').replaceAll('&', ''),
         blastDatabase,
         blastProgram,
+        baseUrl,
         onProgress: arg => {
             self.setProgress(arg);
         },
@@ -15,26 +15,24 @@ export async function doLaunchBlast({ self, }) {
             self.setRid(rid);
         },
     });
-    const sequence = [
-        `>QUERY\n${query}`,
-        ...hits
-            .map(h => [
-            makeId(h.description[0] ?? {
-                accession: 'unknown',
-                id: 'unknown',
-                sciname: 'unknown',
-            }),
-            strip(h.hsps[0]?.hseq ?? ''),
-        ])
-            .map(([id, seq]) => `>${id}\n${seq}`),
-    ].join('\n');
-    const data = await launchMSA({
+    return launchMSA({
         algorithm: msaAlgorithm,
-        sequence,
+        sequence: [
+            `>QUERY\n${proteinSequence.replaceAll('*', '').replaceAll('&', '')}`,
+            ...hits
+                .map(h => [
+                makeId(h.description[0] ?? {
+                    accession: 'unknown',
+                    id: 'unknown',
+                    sciname: 'unknown',
+                }),
+                strip(h.hsps[0]?.hseq ?? ''),
+            ])
+                .map(([id, seq]) => `>${id}\n${seq}`),
+        ].join('\n'),
         onProgress: arg => {
             self.setProgress(arg);
         },
     });
-    return data;
 }
 //# sourceMappingURL=doLaunchBlast.js.map

package/dist/MsaViewPanel/doLaunchBlast.js.map

@@ -1 +1 @@
-{"version":3,"file":"doLaunchBlast.js","sourceRoot":"","sources":["../../src/MsaViewPanel/doLaunchBlast.ts"],"names":[],"mappings":"AACA,OAAO,EACL,MAAM,EACN,KAAK,GACN,MAAM,oDAAoD,CAAA;AAC3D,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,EAClC,IAAI,GAGL;IACC,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,GAClE,IAAI,CAAC,WAAY,CAAA;IACnB,MAAM,KAAK,GAAG,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;IACrE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,UAAU,CAAC;QAChC,KAAK;QACL,aAAa;QACb,YAAY;QACZ,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;QACD,KAAK,EAAE,GAAG,CAAC,EAAE;YACX,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;KACF,CAAC,CAAA;IAEF,MAAM,QAAQ,GAAG;QACf,WAAW,KAAK,EAAE;QAClB,GAAG,IAAI;aACJ,GAAG,CACF,CAAC,CAAC,EAAE,CACF;YACE,MAAM,CACJ,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI;gBAClB,SAAS,EAAE,SAAS;gBACpB,EAAE,EAAE,SAAS;gBACb,OAAO,EAAE,SAAS;aACnB,CACF;YACD,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,IAAI,EAAE,CAAC;SACpB,CACb;aACA,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;KACxC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAEZ,MAAM,IAAI,GAAG,MAAM,SAAS,CAAC;QAC3B,SAAS,EAAE,YAAY;QACvB,QAAQ;QACR,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"doLaunchBlast.js","sourceRoot":"","sources":["../../src/MsaViewPanel/doLaunchBlast.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,kCAAkC,CAAA;AAChE,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,EAClC,IAAI,GAGL;IACC,MAAM,EACJ,OAAO,EACP,aAAa,EACb,YAAY,EACZ,YAAY,EACZ,eAAe,GAChB,GAAG,IAAI,CAAC,WAAY,CAAA;IACrB,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,UAAU,CAAC;QAChC,KAAK,EAAE,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;QAC9D,aAAa;QACb,YAAY;QACZ,OAAO;QACP,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;QACD,KAAK,EAAE,GAAG,CAAC,EAAE;YACX,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;KACF,CAAC,CAAA;IAEF,OAAO,SAAS,CAAC;QACf,SAAS,EAAE,YAAY;QACvB,QAAQ,EAAE;YACR,WAAW,eAAe,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE;YACpE,GAAG,IAAI;iBACJ,GAAG,CACF,CAAC,CAAC,EAAE,CACF;gBACE,MAAM,CACJ,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI;oBAClB,SAAS,EAAE,SAAS;oBACpB,EAAE,EAAE,SAAS;oBACb,OAAO,EAAE,SAAS;iBACnB,CACF;gBACD,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,IAAI,EAAE,CAAC;aACpB,CACb;iBACA,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;SACxC,CAAC,IAAI,CAAC,IAAI,CAAC;QACZ,UAAU,EAAE,GAAG,CAAC,EAAE;YAChB,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAA;AACJ,CAAC"}

package/dist/MsaViewPanel/model.d.ts

@@ -9,6 +9,7 @@ export interface IRegion {
     end: number;
 }
 export interface BlastParams {
+    baseUrl: string;
     blastDatabase: string;
     msaAlgorithm: string;
     blastProgram: string;
@@ -39,13 +40,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
     contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
     drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawTreeText: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
@@ -269,6 +269,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         url?: string;
     } | undefined;
     highResScaleFactor: number;
+    showZoomStar: boolean;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -293,6 +294,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setAllowedGappyness(arg: number): void;
     setContrastLettering(arg: boolean): void;
     setLoadingMSA(arg: boolean): void;
+    setShowZoomStar(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
     setHeight(height: number): void;
@@ -334,10 +336,10 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly treeMetadata: any;
     readonly MSA: import("react-msaview/dist/parsers/StockholmMSA").default | import("react-msaview/dist/parsers/FastaMSA").default | import("react-msaview/dist/parsers/EmfMSA").default | import("react-msaview/dist/parsers/ClustalMSA").default | null;
     readonly numColumns: number;
-    readonly tree: import("react-msaview/dist/util").NodeWithIds;
+    readonly tree: import("react-msaview/dist/types").NodeWithIds;
     readonly rowNames: string[];
     readonly mouseOverRowName: string | undefined;
-    readonly root: HierarchyNode<import("react-msaview/dist/util").NodeWithIds>;
+    readonly root: HierarchyNode<import("react-msaview/dist/types").NodeWithIds>;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
@@ -354,9 +356,10 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly colStatsSums: {
         [k: string]: number;
     };
-    readonly hierarchy: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>;
+    readonly hierarchy: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>;
     readonly totalHeight: number;
-    readonly leaves: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>[];
+    readonly leaves: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>[];
+    readonly allBranchesLength0: boolean;
 } & {
     readonly totalWidth: number;
 } & {
@@ -371,6 +374,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly showTreeText: boolean;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -391,9 +395,9 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
     readonly conservation: string[];
-    readonly adapterTrackModels: import("react-msaview/dist/model").BasicTrack[];
-    readonly tracks: import("react-msaview/dist/model").BasicTrack[];
-    readonly turnedOnTracks: import("react-msaview/dist/model").ITextTrack[];
+    readonly adapterTrackModels: import("react-msaview/dist/types").BasicTrack[];
+    readonly tracks: import("react-msaview/dist/types").BasicTrack[];
+    readonly turnedOnTracks: import("react-msaview/dist/types").ITextTrack[];
     readonly showHorizontalScrollbar: boolean;
     readonly rowNamesSet: Map<string, number>;
     mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
@@ -402,7 +406,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview/dist/model").Accession>;
+    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview/dist/types").Accession>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
@@ -569,12 +573,11 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     colorSchemeName: string;
     id: string;
     showDomains: boolean;
+    hideGaps: boolean;
     allowedGappyness: number;
     contrastLettering: boolean;
     subFeatureRows: boolean;
     drawMsaLetters: boolean;
-    hideGaps: boolean;
-    drawTreeText: boolean;
     rowHeight: number;
     scrollY: number;
     scrollX: number;

package/dist/MsaViewPanel/model.js.map

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package/dist/ReadOnlyTextField2.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+export default function ReadOnlyTextField2({ value }: {
+    value: string;
+}): React.JSX.Element;

package/dist/ReadOnlyTextField2.js

@@ -0,0 +1,20 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+import TextField2 from './TextField2';
+const useStyles = makeStyles()({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+export default function ReadOnlyTextField2({ value }) {
+    const { classes } = useStyles();
+    return (React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: value, slotProps: {
+            input: {
+                readOnly: true,
+                classes: {
+                    input: classes.textAreaFont,
+                },
+            },
+        } }));
+}
+//# sourceMappingURL=ReadOnlyTextField2.js.map

package/dist/ReadOnlyTextField2.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ReadOnlyTextField2.js","sourceRoot":"","sources":["../src/ReadOnlyTextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAAqB;IACrE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE;YACT,KAAK,EAAE;gBACL,QAAQ,EAAE,IAAI;gBACd,OAAO,EAAE;oBACP,KAAK,EAAE,OAAO,CAAC,YAAY;iBAC5B;aACF;SACF,GACD,CACH,CAAA;AACH,CAAC"}

package/dist/index.d.ts

@@ -5,4 +5,19 @@ export default class MsaViewPlugin extends Plugin {
     version: any;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
+    rootConfigurationSchema: {
+        msa: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            datasets: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                name: {
+                    type: string;
+                    defaultValue: string;
+                };
+                adapter: {
+                    type: string;
+                    description: string;
+                    defaultValue: {};
+                };
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    };
 }