jbrowse-plugin-protein3d 0.0.2 → 0.0.3

package/dist/LaunchProteinView/components/UserProvidedStructure.js.map

@@ -1 +1 @@
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package/dist/LaunchProteinView/components/calculateProteinSequence.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/useIsoformProteinSequences.d.ts

@@ -0,0 +1,14 @@
+import { Feature } from '@jbrowse/core/util';
+export default function useIsoformProteinSequences({ feature, view, }: {
+    feature: Feature;
+    view?: {
+        assemblyNames?: string[];
+    };
+}): {
+    isLoading: boolean;
+    isoformSequences: Record<string, {
+        feature: Feature;
+        seq: string;
+    }> | undefined;
+    error: unknown;
+};

package/dist/LaunchProteinView/{useProteinSequences.js → components/useIsoformProteinSequences.js}

@@ -2,29 +2,34 @@ import { useEffect, useState } from 'react';
 // locals
 import { getTranscriptFeatures } from './util';
 import { fetchProteinSeq } from './calculateProteinSequence';
-export default function useAllSequences({ feature, view, }) {
+export default function useIsoformProteinSequences({ feature, view, }) {
     const [error, setError] = useState();
-    const [seqs, setSeqs] = useState();
+    const [isoformSequences, setIsoformSequences] = useState();
+    const [isLoading, setLoading] = useState(false);
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
+                setLoading(true);
                 const ret = [];
                 for (const f of getTranscriptFeatures(feature)) {
                     const seq = await fetchProteinSeq({ view, feature: f });
                     if (seq) {
-                        ret.push([f.id(), seq]);
+                        ret.push([f.id(), { feature: f, seq }]);
                     }
                 }
-                setSeqs(Object.fromEntries(ret));
+                setIsoformSequences(Object.fromEntries(ret));
             }
             catch (e) {
                 console.error(e);
                 setError(e);
             }
+            finally {
+                setLoading(false);
+            }
         })();
     }, [feature, view]);
-    return { seqs, error };
+    return { isLoading, isoformSequences, error };
 }
-//# sourceMappingURL=useProteinSequences.js.map
+//# sourceMappingURL=useIsoformProteinSequences.js.map

package/dist/LaunchProteinView/components/useIsoformProteinSequences.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/useLocalStructureFileSequence.d.ts

@@ -0,0 +1,7 @@
+export default function useLocalStructureFileSequence({ file, }: {
+    file?: File;
+}): {
+    error: unknown;
+    isLoading: boolean;
+    seq: string | undefined;
+};

package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js

@@ -0,0 +1,44 @@
+import { useEffect, useState } from 'react';
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
+import { loadStructureFromData } from '../../ProteinView/loadStructureFromData';
+async function structureFileSequenceFetcher(file, format) {
+    const ret = document.createElement('div');
+    const p = await createPluginUI({
+        target: ret,
+        render: renderReact18,
+    });
+    const data = await file.text();
+    const { seq } = await loadStructureFromData({ data, plugin: p, format });
+    p.unmount();
+    ret.remove();
+    return seq;
+}
+export default function useLocalStructureFileSequence({ file, }) {
+    const [error, setError] = useState();
+    const [isLoading, setLoading] = useState(false);
+    const [seq, setSeq] = useState();
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                if (file) {
+                    setLoading(true);
+                    const ext = file.name.slice(file.name.lastIndexOf('.') + 1) || 'pdb';
+                    const seq = await structureFileSequenceFetcher(file, (ext === 'cif' ? 'mmcif' : ext));
+                    setSeq(seq);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [file]);
+    return { error, isLoading, seq };
+}
+//# sourceMappingURL=useLocalStructureFileSequence.js.map

package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/{useMyGeneInfo.d.ts → components/useMyGeneInfoUniprotIdLookup.d.ts}

@@ -1,7 +1,7 @@
 export default function useMyGeneInfo({ id }: {
     id: string;
 }): {
-    loading: boolean;
-    result: string | undefined;
+    isLoading: boolean;
+    uniprotId: string | undefined;
     error: unknown;
 };

package/dist/LaunchProteinView/{useMyGeneInfo.js → components/useMyGeneInfoUniprotIdLookup.js}

@@ -1,29 +1,34 @@
 import { useEffect, useState } from 'react';
-import { jsonfetch } from '../fetchUtils';
+import { jsonfetch } from '../../fetchUtils';
 import { stripTrailingVersion } from './util';
 export default function useMyGeneInfo({ id }) {
     const [result, setResult] = useState();
     const [error, setError] = useState();
-    const [loading, setLoading] = useState(false);
+    const [isLoading, setLoading] = useState(false);
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
-                if (!id) {
-                    return;
+                if (id) {
+                    setLoading(true);
+                    const res = await jsonfetch(`https://mygene.info/v3/query?q=${stripTrailingVersion(id)}&fields=uniprot,symbol`);
+                    setResult(res);
                 }
-                setLoading(true);
-                const res = await jsonfetch(`https://mygene.info/v3/query?q=${stripTrailingVersion(id)}&fields=uniprot,symbol`);
-                setLoading(false);
-                setResult(res);
             }
             catch (e) {
                 console.error(e);
                 setError(e);
             }
+            finally {
+                setLoading(false);
+            }
         })();
     }, [id]);
-    return { loading, result: result?.hits[0]?.uniprot['Swiss-Prot'], error };
+    return {
+        isLoading,
+        uniprotId: result?.hits[0]?.uniprot?.['Swiss-Prot'],
+        error,
+    };
 }
-//# sourceMappingURL=useMyGeneInfo.js.map
+//# sourceMappingURL=useMyGeneInfoUniprotIdLookup.js.map

package/dist/LaunchProteinView/components/useMyGeneInfoUniprotIdLookup.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.d.ts

@@ -0,0 +1,7 @@
+export default function useRemoteStructureFileSequence({ url, }: {
+    url?: string;
+}): {
+    error: unknown;
+    isLoading: boolean;
+    seq: string | undefined;
+};

package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js

@@ -0,0 +1,42 @@
+import { useEffect, useState } from 'react';
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
+import { loadStructureFromURL } from '../../ProteinView/loadStructureFromURL';
+async function structureFileSequenceFetcher(url) {
+    const ret = document.createElement('div');
+    const p = await createPluginUI({
+        target: ret,
+        render: renderReact18,
+    });
+    const { seq } = await loadStructureFromURL({ url, plugin: p });
+    p.unmount();
+    ret.remove();
+    return seq;
+}
+export default function useRemoteStructureFileSequence({ url, }) {
+    const [error, setError] = useState();
+    const [isLoading, setLoading] = useState(false);
+    const [seq, setSeq] = useState();
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                if (url) {
+                    setLoading(true);
+                    const seq = await structureFileSequenceFetcher(url);
+                    setSeq(seq);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [url]);
+    return { error, isLoading, seq };
+}
+//# sourceMappingURL=useRemoteStructureFileSequence.js.map

package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/{util.d.ts → components/util.d.ts}

@@ -1,17 +1,7 @@
 import { Feature } from '@jbrowse/core/util';
-export interface Row {
-    gene_id: string;
-    gene_id_version: string;
-    transcript_id_version: string;
-    transcript_id: string;
-    pdb_id: string;
-    refseq_mrna_predicted_id: string;
-    refseq_mrna_id: string;
-}
 export declare function getTranscriptFeatures(feature: Feature): Feature[];
 export declare function stripTrailingVersion(s?: string): string | undefined;
 export declare function z(n: number): string;
-export declare function createMapFromData(data?: Row[]): Map<string, string>;
 export declare function getDisplayName(f: Feature): string;
 export declare function getId(val?: Feature): string;
 export declare function getTranscriptDisplayName(val?: Feature): string;

package/dist/LaunchProteinView/{util.js → components/util.js}

@@ -12,29 +12,8 @@ export function stripTrailingVersion(s) {
 export function z(n) {
     return n.toLocaleString('en-US');
 }
-export function createMapFromData(data) {
-    const map = new Map();
-    if (data) {
-        for (const d of data) {
-            const { pdb_id, transcript_id, refseq_mrna_id, transcript_id_version } = d;
-            if (!pdb_id) {
-                continue;
-            }
-            if (transcript_id) {
-                map.set(transcript_id, pdb_id);
-            }
-            if (refseq_mrna_id) {
-                map.set(refseq_mrna_id, pdb_id);
-            }
-            if (transcript_id_version) {
-                map.set(transcript_id_version, pdb_id);
-            }
-        }
-    }
-    return map;
-}
 export function getDisplayName(f) {
-    return f.get('id');
+    return f.get('name') || f.get('id');
 }
 export function getId(val) {
     return val === undefined ? '' : val.id();
@@ -42,12 +21,12 @@ export function getId(val) {
 export function getTranscriptDisplayName(val) {
     return val === undefined
         ? ''
-        : [val.get('name'), val.get('id')].filter(f => !!f).join(' ');
+        : [val.get('name') || val.get('id')].filter(f => !!f).join(' ');
 }
 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')]
             .filter(f => !!f)
             .join(' ');
 }

package/dist/LaunchProteinView/components/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/util.ts"],"names":[],"mappings":"AAEA,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,CACrB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CACzD;QACC,CAAC,CAAC,CAAC,OAAO,CAAC;QACX,CAAC,CAAC,WAAW,CAAA;AACjB,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,CAAU;IAC7C,OAAO,CAAC,EAAE,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,CAAC,CAAC,CAAS;IACzB,OAAO,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,CAAU;IACvC,OAAO,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAa;IACjC,OAAO,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAA;AAC1C,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,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACnE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAa;IAC9C,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;aACvD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,IAAI,CAAC,GAAG,CAAC,CAAA;AAClB,CAAC"}

package/dist/LaunchProteinView/index.js

@@ -18,7 +18,7 @@ function extendStateModel(stateModel) {
                     ...(feature
                         ? [
                             {
-                                label: 'Launch protein view',
+                                label: 'Launch 3-D protein view',
                                 icon: AddIcon,
                                 onClick: () => {
                                     getSession(track).queueDialog(handleClose => [

package/dist/LaunchProteinView/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchProteinView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAA;AAEnE,QAAQ;AACR,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,SAAS;AACT,OAAO,uBAAuB,MAAM,sCAAsC,CAAA;AAE1E,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE;QAC7B,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,qBAAqB;gCAC5B,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,uBAAuB;wCACvB,EAAE,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,OAAO,EAAE;qCACvC,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B,EAC7B,CAAC,GAAyB,EAAE,EAAE;QAC5B,IAAI,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,GAAG,CAAC,UAAU,GAAG,gBAAgB,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QACnD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchProteinView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAA;AAEnE,QAAQ;AACR,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,SAAS;AACT,OAAO,uBAAuB,MAAM,sCAAsC,CAAA;AAE1E,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE;QAC7B,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,yBAAyB;gCAChC,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,uBAAuB;wCACvB,EAAE,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,OAAO,EAAE;qCACvC,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B,EAC7B,CAAC,GAAyB,EAAE,EAAE;QAC5B,IAAI,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,GAAG,CAAC,UAAU,GAAG,gBAAgB,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QACnD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/ProteinView/components/Header.js

@@ -10,7 +10,7 @@ const ProteinViewHeader = observer(function ({ model, }) {
     const { alignment, showAlignment } = model;
     return (React.createElement("div", null,
         React.createElement(InformativeHeaderArea, { model: model }),
-        showAlignment && alignment ? (React.createElement(ProteinAlignment, { model: model })) : (React.createElement(LoadingEllipses, { message: "Loading pairwise alignment" }))));
+        showAlignment ? (alignment ? (React.createElement(ProteinAlignment, { model: model })) : (React.createElement(LoadingEllipses, { message: "Loading pairwise alignment" }))) : null));
 });
 const InformativeHeaderArea = observer(function ({ model, }) {
     const { showAlignment, clickString, hoverString, showHighlight, zoomToBaseLevel, } = model;

package/dist/ProteinView/components/Header.js.map

@@ -1 +1 @@
-{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/ProteinView/components/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AAEtE,QAAQ;AACR,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAC/C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAElD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,KAAK,GAGN;IACC,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC1C,OAAO,CACL;QACE,oBAAC,qBAAqB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,aAAa,IAAI,SAAS,CAAC,CAAC,CAAC,CAC5B,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI,CACnC,CAAC,CAAC,CAAC,CACF,oBAAC,eAAe,IAAC,OAAO,EAAC,4BAA4B,GAAG,CACzD,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAC/C,KAAK,GAGN;IACC,MAAM,EACJ,aAAa,EACb,WAAW,EACX,WAAW,EACX,aAAa,EACb,eAAe,GAChB,GAAG,KAAK,CAAA;IACT,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,kCACG;YACC,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;YAC1C,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;SAC3C,CAAC,IAAI,CAAC,GAAG,CAAC,CACN;QACP,8BAAM,KAAK,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,GAAI;QAChC,oBAAC,mBAAmB,IAClB,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,8BAA8B;oBACrC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC;iBACtD;gBACD;oBACE,KAAK,EAAE,sCAAsC;oBAC7C,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC;iBACtD;gBACD;oBACE,KAAK,EAAE,6BAA6B;oBACpC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,eAAe;oBACxB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC;iBAC1D;aACF;YAED,oBAAC,QAAQ,OAAG,CACQ,CAClB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}
+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/ProteinView/components/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AAEtE,QAAQ;AACR,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAC/C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAElD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,KAAK,GAGN;IACC,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC1C,OAAO,CACL;QACE,oBAAC,qBAAqB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,aAAa,CAAC,CAAC,CAAC,CACf,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI,CACnC,CAAC,CAAC,CAAC,CACF,oBAAC,eAAe,IAAC,OAAO,EAAC,4BAA4B,GAAG,CACzD,CACF,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAC/C,KAAK,GAGN;IACC,MAAM,EACJ,aAAa,EACb,WAAW,EACX,WAAW,EACX,aAAa,EACb,eAAe,GAChB,GAAG,KAAK,CAAA;IACT,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,kCACG;YACC,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;YAC1C,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;SAC3C,CAAC,IAAI,CAAC,GAAG,CAAC,CACN;QACP,8BAAM,KAAK,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,GAAI;QAChC,oBAAC,mBAAmB,IAClB,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,8BAA8B;oBACrC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC;iBACtD;gBACD;oBACE,KAAK,EAAE,sCAAsC;oBAC7C,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC;iBACtD;gBACD;oBACE,KAAK,EAAE,6BAA6B;oBACpC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,eAAe;oBACxB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC;iBAC1D;aACF;YAED,oBAAC,QAAQ,OAAG,CACQ,CAClB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/ProteinView/components/SplitString.js

@@ -2,7 +2,7 @@ import React from 'react';
 export default function SplitString({ str, col, set, onMouseOver, onClick, showHighlight, }) {
     return str.split('').map((d, i) => (React.createElement("span", { key: `${d}-${i}`, onMouseOver: () => onMouseOver?.(i), onClick: () => onClick?.(i), style: {
             background: col !== undefined && i === col
-                ? '#f69'
+                ? '#f698'
                 : set?.has(i) && showHighlight
                     ? '#33ff19'
                     : undefined,

package/dist/ProteinView/components/SplitString.js.map

@@ -1 +1 @@
-{"version":3,"file":"SplitString.js","sourceRoot":"","sources":["../../../src/ProteinView/components/SplitString.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAClC,GAAG,EACH,GAAG,EACH,GAAG,EACH,WAAW,EACX,OAAO,EACP,aAAa,GAQd;IACC,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CACjC,8BACE,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,EAAE,EAChB,WAAW,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EACnC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAC3B,KAAK,EAAE;YACL,UAAU,EACR,GAAG,KAAK,SAAS,IAAI,CAAC,KAAK,GAAG;gBAC5B,CAAC,CAAC,MAAM;gBACR,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,aAAa;oBAC5B,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,SAAS;SAClB,IAEA,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,mDAAW,CAAC,CAAC,CAAC,CAAC,CACvB,CACR,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"SplitString.js","sourceRoot":"","sources":["../../../src/ProteinView/components/SplitString.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAClC,GAAG,EACH,GAAG,EACH,GAAG,EACH,WAAW,EACX,OAAO,EACP,aAAa,GAQd;IACC,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CACjC,8BACE,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,EAAE,EAChB,WAAW,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EACnC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAC3B,KAAK,EAAE;YACL,UAAU,EACR,GAAG,KAAK,SAAS,IAAI,CAAC,KAAK,GAAG;gBAC5B,CAAC,CAAC,OAAO;gBACT,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,aAAa;oBAC5B,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,SAAS;SAClB,IAEA,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,mDAAW,CAAC,CAAC,CAAC,CAAC,CACvB,CACR,CAAC,CAAA;AACJ,CAAC"}

package/dist/ProteinView/model.d.ts

@@ -20,12 +20,15 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     url: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     data: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     clickGenomeHighlights: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        refName: import("mobx-state-tree").ISimpleType<string>;
+        refName: import(
+        /**
+         * #property
+         * url to structure file
+         */
+        "mobx-state-tree").ISimpleType<string>;
         start: import("mobx-state-tree").ISimpleType<number>;
         end: import("mobx-state-tree").ISimpleType<number>;
-        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
-         * #property
-         */).ISimpleType<boolean>, [undefined]>;
+        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     } & {
         assemblyName: import("mobx-state-tree").ISimpleType<string>;
     }, {
@@ -218,6 +221,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly structureSeqHoverPos: number | undefined;
+    readonly exactMatch: boolean;
 } & {
     afterAttach(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/ProteinView/model.js

@@ -14,7 +14,7 @@ import { structureSeqVsTranscriptSeqMap, genomeToTranscriptSeqMapping, structure
  */
 function stateModelFactory() {
     return types
-        .compose(BaseViewModel, types.model({
+        .compose('ProteinView', BaseViewModel, types.model({
         /**
          * #property
          */
@@ -72,15 +72,15 @@ function stateModelFactory() {
         /**
          * #property
          */
-        showHighlight: true,
+        showHighlight: false,
         /**
          * #property
          */
-        zoomToBaseLevel: false,
+        zoomToBaseLevel: true,
         /**
          * #property
          */
-        showAlignment: true,
+        showAlignment: false,
     }))
         .volatile(() => ({
         /**
@@ -275,23 +275,49 @@ function stateModelFactory() {
         get structureSeqHoverPos() {
             return self.hoverPosition?.structureSeqPos;
         },
+        get exactMatch() {
+            const r1 = self.seq1?.replaceAll('*', '');
+            const r2 = self.seq2?.replaceAll('*', '');
+            return r1 === r2;
+        },
     }))
         .actions(self => ({
         afterAttach() {
-            // pairwise align transcript sequence to structure sequence
+            // pairwise align transcript sequence to structure residues
             addDisposer(self, autorun(async () => {
                 try {
-                    const { seq1, seq2 } = self;
+                    const { seq1, seq2, exactMatch } = self;
                     if (!!self.alignment || !seq1 || !seq2) {
                         return;
                     }
-                    const alignment = await launchPairwiseAlignment({
-                        seq1,
-                        seq2,
-                        algorithm: 'emboss_needle',
-                        onProgress: arg => self.setProgress(arg),
-                    });
-                    self.setAlignment(alignment.alignment);
+                    const r1 = seq1.replaceAll('*', '');
+                    const r2 = seq2.replaceAll('*', '');
+                    if (!exactMatch) {
+                        const alignment = await launchPairwiseAlignment({
+                            seq1: r1,
+                            seq2: r2,
+                            algorithm: 'emboss_needle',
+                            onProgress: arg => self.setProgress(arg),
+                        });
+                        self.setAlignment(alignment.alignment);
+                        // showHighlight when we are
+                        self.setShowHighlight(true);
+                        self.setShowAlignment(true);
+                    }
+                    else {
+                        let consensus = '';
+                        // eslint-disable-next-line @typescript-eslint/prefer-for-of
+                        for (let i = 0; i < r1.length; i++) {
+                            consensus += '|';
+                        }
+                        self.setAlignment({
+                            consensus,
+                            alns: [
+                                { id: 'seq1', seq: r1 },
+                                { id: 'seq2', seq: r2 },
+                            ],
+                        });
+                    }
                 }
                 catch (e) {
                     console.error(e);

package/dist/ProteinView/model.js.map

@@ -1 +1 @@
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package/dist/index.js

@@ -1,11 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { types } from 'mobx-state-tree';
 // locals
 import { version } from '../package.json';
 import ProteinViewF from './ProteinView';
 import LaunchProteinViewF from './LaunchProteinView';
 import AddHighlightModelF from './AddHighlightModel';
-import ProteinModelSessionExtension from './ProteinModelSessionExtension';
 export default class ProteinViewer extends Plugin {
     name = 'ProteinViewer';
     version = version;
@@ -13,13 +11,6 @@ export default class ProteinViewer extends Plugin {
         ProteinViewF(pluginManager);
         LaunchProteinViewF(pluginManager);
         AddHighlightModelF(pluginManager);
-        pluginManager.addToExtensionPoint('Core-extendSession', session => {
-            return types.compose(types.model({
-                proteinModel: types.optional(ProteinModelSessionExtension, {}),
-            }), 
-            // @ts-expect-error
-            session);
-        });
     }
     configure(_pluginManager) { }
 }

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,SAAS;AACT,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,YAAY,MAAM,eAAe,CAAA;AACxC,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AAEpD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,MAAM;IAC/C,IAAI,GAAG,eAAe,CAAA;IACtB,OAAO,GAAG,OAAO,CAAA;IAEjB,OAAO,CAAC,aAA4B;QAClC,YAAY,CAAC,aAAa,CAAC,CAAA;QAC3B,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C"}