jbrowse-plugin-msaview 2.2.0 → 2.2.2

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

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

@@ -11,9 +11,11 @@ function extendStateModel(stateModel) {
             contextMenuItems() {
                 const feature = self.contextMenuFeature;
                 const track = getContainingTrack(self);
+                const featureType = feature?.get('type');
+                const showMsaMenuItem = feature && ['gene', 'mRNA', 'transcript'].includes(featureType);
                 return [
                     ...superContextMenuItems(),
-                    ...(feature
+                    ...(showMsaMenuItem
                         ? [
                             {
                                 label: 'Launch MSA view',

package/dist/LaunchMsaView/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchMsaView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAW,kBAAkB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC5E,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,OAAO,mBAAmB,MAAM,kCAAkC,CAAA;AAIlE,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CACrB,CAAC,IAGA,EAAE,EAAE;QACH,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,MAAM,WAAW,GAAG,OAAO,EAAE,GAAG,CAAC,MAAM,CAAC,CAAA;gBACxC,MAAM,eAAe,GACnB,OAAO,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,YAAY,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;gBACjE,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,eAAe;wBACjB,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,iBAAiB;gCACxB,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,mBAAmB;wCACnB;4CACE,KAAK,EAAE,KAAK;4CACZ,WAAW;4CACX,OAAO;yCACR;qCACF,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,aAA4B;IACjE,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/MsaViewPanel/components/RIDLink.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import { Typography } from '@mui/material';
-import ExternalLink from '../../ExternalLink';
+import ExternalLink from '../../components/ExternalLink';
 function RIDLink({ baseUrl, rid }) {
     return (React.createElement(Typography, null,
         "RID ",

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,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"}
+{"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,+BAA+B,CAAA;AAExD,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/genomeToMSA.js

@@ -2,7 +2,7 @@ import { getSession } from '@jbrowse/core/util';
 import { checkHovered } from './util';
 export function genomeToMSA({ model }) {
     const { hovered } = getSession(model);
-    const { transcriptToMsaMap, connectedView } = model;
+    const { querySeqName, transcriptToMsaMap, connectedView } = model;
     if (connectedView?.initialized &&
         transcriptToMsaMap &&
         checkHovered(hovered)) {
@@ -10,7 +10,7 @@ export function genomeToMSA({ model }) {
         const { g2p } = transcriptToMsaMap;
         const ret = g2p[hoverCoord];
         if (ret !== undefined) {
-            return model.seqCoordToRowSpecificGlobalCoord('QUERY', ret + 1);
+            return model.seqCoordToRowSpecificGlobalCoord(querySeqName, ret + 1);
         }
     }
     return undefined;

package/dist/MsaViewPanel/genomeToMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"genomeToMSA.js","sourceRoot":"","sources":["../../src/MsaViewPanel/genomeToMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAG/C,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAErC,MAAM,UAAU,WAAW,CAAC,EAAE,KAAK,EAAwC;IACzE,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,kBAAkB,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IACnD,IACE,aAAa,EAAE,WAAW;QAC1B,kBAAkB;QAClB,YAAY,CAAC,OAAO,CAAC,EACrB,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QACnD,MAAM,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;QAClC,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,OAAO,KAAK,CAAC,gCAAgC,CAAC,OAAO,EAAE,GAAG,GAAG,CAAC,CAAC,CAAA;QACjE,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC"}
+{"version":3,"file":"genomeToMSA.js","sourceRoot":"","sources":["../../src/MsaViewPanel/genomeToMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAG/C,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAErC,MAAM,UAAU,WAAW,CAAC,EAAE,KAAK,EAAwC;IACzE,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,YAAY,EAAE,kBAAkB,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IACjE,IACE,aAAa,EAAE,WAAW;QAC1B,kBAAkB;QAClB,YAAY,CAAC,OAAO,CAAC,EACrB,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QACnD,MAAM,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;QAClC,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,OAAO,KAAK,CAAC,gCAAgC,CAAC,YAAY,EAAE,GAAG,GAAG,CAAC,CAAC,CAAA;QACtE,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC"}

package/dist/MsaViewPanel/model.d.ts

@@ -233,6 +233,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         end: import("mobx-state-tree").ISimpleType<number>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     blastParams: import("mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
+    querySeqName: import("mobx-state-tree").IType<string | undefined, string, string>;
     zoomToBaseLevel: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     width: number;
@@ -279,6 +280,10 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     mouseCol: number | undefined;
     mouseClickRow: number | undefined;
     mouseClickCol: number | undefined;
+    hoveredTreeNode: {
+        nodeId: string;
+        descendantNames: string[];
+    } | undefined;
     nref: number;
     minimapHeight: number;
     marginLeft: number;
@@ -289,7 +294,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     } | undefined;
     interProAnnotations: undefined | Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>;
 } & {
-    drawRelativeTo(id: string): void;
+    drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
     setAllowedGappyness(arg: number): void;
     setContrastLettering(arg: boolean): void;
@@ -300,6 +305,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setHeight(height: number): void;
     setError(error?: unknown): void;
     setMousePos(col?: number, row?: number): void;
+    setHoveredTreeNode(nodeId?: string): void;
     setShowDomains(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
@@ -353,9 +359,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly columns2d: string[];
     readonly fontSize: number;
     readonly colStats: Record<string, number>[];
-    readonly colStatsSums: {
-        [k: string]: number;
-    };
+    readonly colStatsSums: number[];
     readonly hierarchy: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>;
     readonly totalHeight: number;
     readonly leaves: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>[];
@@ -400,8 +404,9 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly turnedOnTracks: import("react-msaview/dist/types").ITextTrack[];
     readonly showHorizontalScrollbar: boolean;
     readonly rowNamesSet: Map<string, number>;
-    mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
+    mouseOverCoordToRowLetter(rowName: string, pos: number): string | undefined;
     mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
+    mouseOverCoordToGapRemovedRowCoordOneBased(rowName: string, position: number): number | undefined;
     seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
 } & {
     readonly msaAreaHeight: number;
@@ -458,7 +463,9 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     incrementRef(): void;
     initFilter(arg: string): void;
     setFilter(arg: string, flag: boolean): void;
-    showEntire(): void;
+    fit(): void;
+    fitVertically(): void;
+    fitHorizontally(): void;
     afterCreate(): void;
 } & {
     /**
@@ -561,84 +568,6 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, {
-    drawLabels: boolean;
-    labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
-    treeWidthMatchesArea: boolean;
-    showBranchLen: boolean;
-    drawTree: boolean;
-    drawNodeBubbles: boolean;
-    bgColor: boolean;
-    colorSchemeName: string;
-    id: string;
-    showDomains: boolean;
-    hideGaps: boolean;
-    allowedGappyness: number;
-    contrastLettering: boolean;
-    subFeatureRows: boolean;
-    drawMsaLetters: boolean;
-    rowHeight: number;
-    scrollY: number;
-    scrollX: number;
-    colWidth: number;
-    currentAlignment: number;
-    type: "MsaView";
-    height: number;
-    treeFilehandle: {
-        locationType: "UriLocation";
-        uri: string;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
-    } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | undefined;
-    msaFilehandle: {
-        locationType: "UriLocation";
-        uri: string;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
-    } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | undefined;
-    treeMetadataFilehandle: {
-        locationType: "UriLocation";
-        uri: string;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
-    } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | undefined;
-    collapsed: string[];
-    collapsedLeaves: string[];
-    showOnly: string | undefined;
-    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
-    relativeTo: string | undefined;
     data: {
         treeMetadata?: string | undefined;
         msa?: string | undefined;

package/dist/MsaViewPanel/model.js

@@ -35,6 +35,10 @@ export default function stateModelFactory() {
          * #property
          */
         blastParams: types.frozen(),
+        /**
+         * #property
+         */
+        querySeqName: 'QUERY',
         /**
          * #property
          */
@@ -200,12 +204,12 @@ export default function stateModelFactory() {
                 if (self.blastParams) {
                     try {
                         self.setProgress('Submitting query');
+                        self.setError(undefined);
                         const data = await doLaunchBlast({
-                            self: self,
+                            self,
                         });
                         self.setData(data);
                         self.setBlastParams(undefined);
-                        self.setProgress('');
                     }
                     catch (e) {
                         self.setError(e);

package/dist/MsaViewPanel/model.js.map

@@ -1 +1 @@
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package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,20 +1,45 @@
+/**
+ * Convert gapped MSA column coordinate to ungapped sequence coordinate
+ * This is the inverse of ungappedCoordMap
+ */
+function gappedToUngappedCoord(seq, gappedPos) {
+    let ungappedPos = 0;
+    for (let i = 0; i < gappedPos && i < seq.length; i++) {
+        if (seq[i] !== '-') {
+            ungappedPos++;
+        }
+    }
+    return ungappedPos;
+}
 export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
-    const { transcriptToMsaMap } = model;
+    const { querySeqName, transcriptToMsaMap } = model;
     if (transcriptToMsaMap === undefined) {
-        return;
+        return undefined;
     }
-    const c = mouseCol;
-    const k1 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c) || 0;
-    const k2 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c + 1) || 0;
-    const { refName, p2g } = transcriptToMsaMap;
-    const s = p2g[k1];
-    const e = p2g[k2];
-    return s !== undefined && e !== undefined
-        ? {
-            refName,
-            start: Math.min(s, e),
-            end: Math.max(s, e),
+    else {
+        // Get the query sequence
+        const queryRow = model.rows.find(f => f[0] === querySeqName);
+        const querySeq = queryRow?.[1];
+        if (!querySeq) {
+            return undefined;
         }
-        : undefined;
+        // Check if the position in the query sequence is a gap
+        if (querySeq[mouseCol] === '-') {
+            return undefined;
+        }
+        // Convert gapped MSA column to ungapped sequence coordinate
+        const ungappedPos = gappedToUngappedCoord(querySeq, mouseCol);
+        // Use the ungapped position to look up in the p2g map
+        const { refName, p2g } = transcriptToMsaMap;
+        const s = p2g[ungappedPos];
+        const e = p2g[ungappedPos + 1];
+        return s !== undefined && e !== undefined
+            ? {
+                refName,
+                start: Math.min(s, e),
+                end: Math.max(s, e),
+            }
+            : undefined;
+    }
 }
 //# sourceMappingURL=msaCoordToGenomeCoord.js.map

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map

@@ -1 +1 @@
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+{"version":3,"file":"msaCoordToGenomeCoord.js","sourceRoot":"","sources":["../../src/MsaViewPanel/msaCoordToGenomeCoord.ts"],"names":[],"mappings":"AAEA;;;GAGG;AACH,SAAS,qBAAqB,CAAC,GAAW,EAAE,SAAiB;IAC3D,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,WAAW,EAAE,CAAA;QACf,CAAC;IACH,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,EACpC,KAAK,EACL,KAAK,EAAE,QAAQ,GAIhB;IACC,MAAM,EAAE,YAAY,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAClD,IAAI,kBAAkB,KAAK,SAAS,EAAE,CAAC;QACrC,OAAO,SAAS,CAAA;IAClB,CAAC;SAAM,CAAC;QACN,yBAAyB;QACzB,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,YAAY,CAAC,CAAA;QAC5D,MAAM,QAAQ,GAAG,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAA;QAC9B,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,uDAAuD;QACvD,IAAI,QAAQ,CAAC,QAAQ,CAAC,KAAK,GAAG,EAAE,CAAC;YAC/B,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,4DAA4D;QAC5D,MAAM,WAAW,GAAG,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAE7D,sDAAsD;QACtD,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;QAC3C,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,CAAC,CAAA;QAC1B,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,GAAG,CAAC,CAAC,CAAA;QAC9B,OAAO,CAAC,KAAK,SAAS,IAAI,CAAC,KAAK,SAAS;YACvC,CAAC,CAAC;gBACE,OAAO;gBACP,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACrB,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;aACpB;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;AACH,CAAC"}

package/dist/MsaViewPanel/util.js

@@ -1,6 +1,6 @@
 export function checkHovered(hovered) {
-    return (!!hovered &&
-        typeof hovered == 'object' &&
+    return (typeof hovered === 'object' &&
+        hovered !== null &&
         'hoverFeature' in hovered &&
         'hoverPosition' in hovered);
 }

package/dist/MsaViewPanel/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/MsaViewPanel/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,YAAY,CAAC,OAAgB;IAI3C,OAAO,CACL,CAAC,CAAC,OAAO;QACT,OAAO,OAAO,IAAI,QAAQ;QAC1B,cAAc,IAAI,OAAO;QACzB,eAAe,IAAI,OAAO,CAC3B,CAAA;AACH,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/MsaViewPanel/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,YAAY,CAAC,OAAgB;IAI3C,OAAO,CACL,OAAO,OAAO,KAAK,QAAQ;QAC3B,OAAO,KAAK,IAAI;QAChB,cAAc,IAAI,OAAO;QACzB,eAAe,IAAI,OAAO,CAC3B,CAAA;AACH,CAAC"}

package/dist/components/ExternalLink.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ExternalLink.js","sourceRoot":"","sources":["../../src/components/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/components/ReadOnlyTextField2.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ReadOnlyTextField2.js","sourceRoot":"","sources":["../../src/components/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/components/TextField2.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TextField2.js","sourceRoot":"","sources":["../../src/components/TextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAIzC,SAAS,UAAU,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAkB;IACvD,OAAO,CACL;QACE,oBAAC,SAAS,OAAK,IAAI,IAAG,QAAQ,CAAa,CACvC,CACP,CAAA;AACH,CAAC;AAED,eAAe,UAAU,CAAA"}

package/dist/index.d.ts

@@ -5,18 +5,22 @@ export default class MsaViewPlugin extends Plugin {
     version: any;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
-    rootConfigurationSchema: {
+    rootConfigurationSchema(pluginManager: PluginManager): {
         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: {
+                datasetId: {
+                    type: string;
+                    defaultValue: string;
+                };
+                description: {
                     type: string;
                     defaultValue: string;
                 };
-                adapter: {
+                name: {
                     type: string;
-                    description: string;
-                    defaultValue: {};
+                    defaultValue: string;
                 };
+                adapter: import("mobx-state-tree").IAnyModelType;
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     };

package/dist/index.js

@@ -5,6 +5,7 @@ import GridOn from '@mui/icons-material/GridOn';
 import { types } from 'mobx-state-tree';
 import { version } from '../package.json';
 import AddHighlightModelF from './AddHighlightModel';
+import BgzipFastaMsaAdapterF from './BgzipFastaMsaAdapter';
 import LaunchMsaViewF from './LaunchMsaView';
 import MsaViewF from './MsaViewPanel';
 export default class MsaViewPlugin extends Plugin {
@@ -12,26 +13,12 @@ export default class MsaViewPlugin extends Plugin {
         super(...arguments);
         this.name = 'MsaViewPlugin';
         this.version = version;
-        this.rootConfigurationSchema = {
-            msa: ConfigurationSchema('MSA', {
-                datasets: types.maybe(types.array(ConfigurationSchema('MSAEntry', {
-                    name: {
-                        type: 'string',
-                        defaultValue: '',
-                    },
-                    adapter: {
-                        type: 'frozen',
-                        description: 'This can be a data adapter config for a IndexedFasta for example, which has a special way of being interpreted',
-                        defaultValue: {},
-                    },
-                }))),
-            }),
-        };
     }
     install(pluginManager) {
         MsaViewF(pluginManager);
         LaunchMsaViewF(pluginManager);
         AddHighlightModelF(pluginManager);
+        BgzipFastaMsaAdapterF(pluginManager);
     }
     configure(pluginManager) {
         if (isAbstractMenuManager(pluginManager.rootModel)) {
@@ -44,5 +31,27 @@ export default class MsaViewPlugin extends Plugin {
             });
         }
     }
+    // @ts-expect-error
+    rootConfigurationSchema(pluginManager) {
+        return {
+            msa: ConfigurationSchema('MSA', {
+                datasets: types.maybe(types.array(ConfigurationSchema('MSAEntry', {
+                    datasetId: {
+                        type: 'string',
+                        defaultValue: '',
+                    },
+                    description: {
+                        type: 'string',
+                        defaultValue: '',
+                    },
+                    name: {
+                        type: 'string',
+                        defaultValue: '',
+                    },
+                    adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+                }))),
+            }),
+        };
+    }
 }
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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