react-msaview 4.5.0 → 4.8.0

package/dist/model.d.ts

@@ -1,8 +1,4 @@
-import A3mMSA from './parsers/A3mMSA';
-import ClustalMSA from './parsers/ClustalMSA';
-import EmfMSA from './parsers/EmfMSA';
-import FastaMSA from './parsers/FastaMSA';
-import StockholmMSA from './parsers/StockholmMSA';
+import { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA } from '@react-msaview/parsers';
 import type { InterProScanResults } from './launchInterProScan';
 import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
@@ -195,6 +191,57 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        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>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     collapsedLeaves: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
@@ -308,6 +355,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         nodeId: string;
         descendantNames: string[];
     } | undefined;
+    /**
+     * #volatile
+     * array of column indices to highlight
+     */
+    highlightedColumns: number[] | undefined;
     /**
      * #volatile
      * a dummy variable that is incremented when ref changes so autorun for
@@ -390,6 +442,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * set hovered tree node and its descendants
      */
     setHoveredTreeNode(nodeId?: string): void;
+    /**
+     * #action
+     * set highlighted columns
+     */
+    setHighlightedColumns(columns?: number[]): void;
     /**
      * #action
      */
@@ -451,6 +508,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setTreeFilehandle(treeFilehandle?: FileLocationType): void;
+    /**
+     * #action
+     */
+    setGFFFilehandle(gffFilehandle?: FileLocationType): void;
     /**
      * #action
      */
@@ -651,6 +712,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly allBranchesLength0: boolean;
+    /**
+     * #getter
+     * effective showBranchLen accounting for allBranchesLength0
+     */
+    readonly showBranchLenEffective: boolean;
 } & {
     /**
      * #getter
@@ -790,27 +856,62 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     readonly rowNamesSet: Map<string, number>;
     /**
      * #method
-     * return a row-specific letter, or undefined if gap
+     * Return a row-specific letter at a visible column, or undefined if gap.
+     *
+     * @param rowName - The name of the row
+     * @param visibleCol - The visible column index (what the user sees on screen)
+     * @returns The letter at that position, or undefined if it's a gap
+     */
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    /**
+     * #method
+     * Convert a visible column to a row-specific sequence position (0-based).
+     * Returns undefined if the position is a gap in the sequence.
+     *
+     * @param rowName - The name of the row
+     * @param visibleCol - The visible column index
+     * @returns The sequence position (0-based), or undefined if it's a gap
+     */
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    /**
+     * #method
+     * Convert a visible column to a row-specific sequence position (1-based).
+     * Returns undefined if the position is a gap in the sequence.
+     *
+     * @param rowName - The name of the row
+     * @param visibleCol - The visible column index
+     * @returns The sequence position (1-based), or undefined if it's a gap
      */
-    mouseOverCoordToRowLetter(rowName: string, pos: number): string | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
     /**
      * #method
-     * return a row-specific sequence coordinate, skipping gaps, given a
-     * global coordinate
+     * Convert a global column index to a visible column index.
+     * Returns undefined if the column is hidden (in blanks).
+     * This is the inverse of visibleColToGlobalCol.
+     *
+     * @param globalCol - The global column index in the full MSA
+     * @returns The visible column index, or undefined if the column is hidden
      */
-    mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
     /**
      * #method
-     * return a row-specific sequence coordinate, skipping gaps, given a
-     * global coordinate
+     * Convert a sequence position (ungapped) to a global column index.
+     *
+     * @param rowName - The name of the row
+     * @param seqPos - The sequence position (0-based, ungapped)
+     * @returns The global column index in the full MSA
      */
-    mouseOverCoordToGapRemovedRowCoordOneBased(rowName: string, position: number): number | undefined;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number;
     /**
      * #method
-     * return a global coordinate given a row-specific sequence coordinate
-     * which does not not include gaps
+     * Convert a sequence position (ungapped) directly to a visible column index.
+     * This combines seqPosToGlobalCol and globalColToVisibleCol.
+     *
+     * @param rowName - The name of the row
+     * @param seqPos - The sequence position (0-based, ungapped)
+     * @returns The visible column index, or undefined if the column is hidden
      */
-    seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
     /**
      * #getter
@@ -1113,6 +1214,57 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        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>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     collapsedLeaves: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;

package/dist/model.js

@@ -1,14 +1,13 @@
 import { clamp, fetchAndMaybeUnzipText, groupBy, localStorageGetBoolean, localStorageSetBoolean, notEmpty, sum, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
+import { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, generateNodeIds, gffToInterProResults, parseEmfTree, parseGFF, parseNewick, stockholmSniff, } from '@react-msaview/parsers';
 import { colord } from 'colord';
 import { ascending } from 'd3-array';
 import { cluster, hierarchy } from 'd3-hierarchy';
-import { parseEmfTree } from 'emf-js';
 import { saveAs } from 'file-saver';
 import { autorun, transaction } from 'mobx';
 import { addDisposer, cast, types } from 'mobx-state-tree';
-import Stockholm from 'stockholm-js';
 import { blocksX, blocksY } from './calculateBlocks';
 import colorSchemes from './colorSchemes';
 import ConservationTrack from './components/ConservationTrack';
@@ -23,16 +22,10 @@ import { MSAModelF } from './model/msaModel';
 import { TreeModelF } from './model/treeModel';
 import { calculateNeighborJoiningTree } from './neighborJoining';
 import { parseAsn1 } from './parseAsn1';
-import parseNewick from './parseNewick';
-import A3mMSA from './parsers/A3mMSA';
-import ClustalMSA from './parsers/ClustalMSA';
-import EmfMSA from './parsers/EmfMSA';
-import FastaMSA from './parsers/FastaMSA';
-import StockholmMSA from './parsers/StockholmMSA';
 import { reparseTree } from './reparseTree';
-import { mouseOverCoordToGapRemovedRowCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
-import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord';
-import { collapse, generateNodeIds, len, maxLength, setBrLength, skipBlanks, } from './util';
+import { globalColToVisibleCol, visibleColToGlobalCol, visibleColToSeqPosForRow, } from './rowCoordinateCalculations';
+import { seqPosToGlobalCol } from './seqPosToGlobalCol';
+import { collapse, len, maxLength, setBrLength, skipBlanks } from './util';
 const showZoomStarKey = 'msa-showZoomStar';
 /**
  * #stateModel MsaView
@@ -119,6 +112,11 @@ function stateModelFactory() {
          * filehandle object for tree metadata
          */
         treeMetadataFilehandle: types.maybe(FileLocation),
+        /**
+         * #property
+         * filehandle object for InterProScan GFF file
+         */
+        gffFilehandle: types.maybe(FileLocation),
         /**
          * #property
          *
@@ -232,6 +230,11 @@ function stateModelFactory() {
          * the currently hovered tree node ID and its descendant leaf names
          */
         hoveredTreeNode: undefined,
+        /**
+         * #volatile
+         * array of column indices to highlight
+         */
+        highlightedColumns: undefined,
         /**
          * #volatile
          * a dummy variable that is incremented when ref changes so autorun for
@@ -349,6 +352,13 @@ function stateModelFactory() {
             const descendantNames = node.leaves().map((leaf) => leaf.data.name);
             self.hoveredTreeNode = { nodeId, descendantNames };
         },
+        /**
+         * #action
+         * set highlighted columns
+         */
+        setHighlightedColumns(columns) {
+            self.highlightedColumns = columns;
+        },
         /**
          * #action
          */
@@ -443,6 +453,12 @@ function stateModelFactory() {
         setTreeFilehandle(treeFilehandle) {
             self.treeFilehandle = treeFilehandle;
         },
+        /**
+         * #action
+         */
+        setGFFFilehandle(gffFilehandle) {
+            self.gffFilehandle = gffFilehandle;
+        },
         /**
          * #action
          */
@@ -557,7 +573,7 @@ function stateModelFactory() {
         get MSA() {
             const text = self.data.msa;
             if (text) {
-                if (Stockholm.sniff(text)) {
+                if (stockholmSniff(text)) {
                     return new StockholmMSA(text, self.currentAlignment);
                 }
                 else if (A3mMSA.sniff(text)) {
@@ -1046,6 +1062,13 @@ function stateModelFactory() {
         get allBranchesLength0() {
             return this.hierarchy.links().every(s => !s.source.data.length);
         },
+        /**
+         * #getter
+         * effective showBranchLen accounting for allBranchesLength0
+         */
+        get showBranchLenEffective() {
+            return this.allBranchesLength0 ? false : self.showBranchLen;
+        },
     }))
         .views(self => ({
         /**
@@ -1314,49 +1337,93 @@ function stateModelFactory() {
         },
         /**
          * #method
-         * return a row-specific letter, or undefined if gap
+         * Return a row-specific letter at a visible column, or undefined if gap.
+         *
+         * @param rowName - The name of the row
+         * @param visibleCol - The visible column index (what the user sees on screen)
+         * @returns The letter at that position, or undefined if it's a gap
          */
-        mouseOverCoordToRowLetter(rowName, pos) {
+        visibleColToRowLetter(rowName, visibleCol) {
             const { rowMap, blanks } = self;
-            return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, pos)];
+            return rowMap.get(rowName)?.[visibleColToGlobalCol(blanks, visibleCol)];
         },
         /**
          * #method
-         * return a row-specific sequence coordinate, skipping gaps, given a
-         * global coordinate
+         * Convert a visible column to a row-specific sequence position (0-based).
+         * Returns undefined if the position is a gap in the sequence.
+         *
+         * @param rowName - The name of the row
+         * @param visibleCol - The visible column index
+         * @returns The sequence position (0-based), or undefined if it's a gap
          */
-        mouseOverCoordToGapRemovedRowCoord(rowName, position) {
-            return mouseOverCoordToGapRemovedRowCoord({
+        visibleColToSeqPos(rowName, visibleCol) {
+            return visibleColToSeqPosForRow({
                 rowName,
-                position,
+                visibleCol,
                 rowMap: self.rowMap,
                 blanks: self.blanks,
             });
         },
         /**
          * #method
-         * return a row-specific sequence coordinate, skipping gaps, given a
-         * global coordinate
+         * Convert a visible column to a row-specific sequence position (1-based).
+         * Returns undefined if the position is a gap in the sequence.
+         *
+         * @param rowName - The name of the row
+         * @param visibleCol - The visible column index
+         * @returns The sequence position (1-based), or undefined if it's a gap
          */
-        mouseOverCoordToGapRemovedRowCoordOneBased(rowName, position) {
-            const val = this.mouseOverCoordToGapRemovedRowCoord(rowName, position);
+        visibleColToSeqPosOneBased(rowName, visibleCol) {
+            const val = this.visibleColToSeqPos(rowName, visibleCol);
             return val !== undefined ? val + 1 : undefined;
         },
         /**
          * #method
-         * return a global coordinate given a row-specific sequence coordinate
-         * which does not not include gaps
+         * Convert a global column index to a visible column index.
+         * Returns undefined if the column is hidden (in blanks).
+         * This is the inverse of visibleColToGlobalCol.
+         *
+         * @param globalCol - The global column index in the full MSA
+         * @returns The visible column index, or undefined if the column is hidden
+         */
+        globalColToVisibleCol(globalCol) {
+            const { blanks, hideGapsEffective } = self;
+            if (!hideGapsEffective) {
+                return globalCol;
+            }
+            return globalColToVisibleCol(blanks, globalCol);
+        },
+        /**
+         * #method
+         * Convert a sequence position (ungapped) to a global column index.
+         *
+         * @param rowName - The name of the row
+         * @param seqPos - The sequence position (0-based, ungapped)
+         * @returns The global column index in the full MSA
          */
-        seqCoordToRowSpecificGlobalCoord(rowName, position) {
+        seqPosToGlobalCol(rowName, seqPos) {
             const { rowNames, rows } = self;
             const index = rowNames.indexOf(rowName);
             return index !== -1 && rows[index]
-                ? seqCoordToRowSpecificGlobalCoord({
+                ? seqPosToGlobalCol({
                     row: rows[index][1],
-                    position,
+                    seqPos,
                 })
                 : 0;
         },
+        /**
+         * #method
+         * Convert a sequence position (ungapped) directly to a visible column index.
+         * This combines seqPosToGlobalCol and globalColToVisibleCol.
+         *
+         * @param rowName - The name of the row
+         * @param seqPos - The sequence position (0-based, ungapped)
+         * @returns The visible column index, or undefined if the column is hidden
+         */
+        seqPosToVisibleCol(rowName, seqPos) {
+            const globalCol = this.seqPosToGlobalCol(rowName, seqPos);
+            return this.globalColToVisibleCol(globalCol);
+        },
     }))
         .views(self => ({
         /**
@@ -1595,6 +1662,26 @@ function stateModelFactory() {
                     }
                 }
             }));
+            // autorun opens gffFilehandle for InterProScan domains
+            addDisposer(self, autorun(async () => {
+                const { gffFilehandle } = self;
+                if (gffFilehandle) {
+                    try {
+                        const gffText = await fetchAndMaybeUnzipText(openLocation(gffFilehandle));
+                        const gffRecords = parseGFF(gffText);
+                        const interProResults = gffToInterProResults(gffRecords);
+                        self.setInterProAnnotations(interProResults);
+                        self.setShowDomains(true);
+                        if (gffFilehandle.locationType === 'BlobLocation') {
+                            self.setGFFFilehandle(undefined);
+                        }
+                    }
+                    catch (e) {
+                        console.error(e);
+                        self.setError(e);
+                    }
+                }
+            }));
             // autorun opens msaFilehandle
             addDisposer(self, autorun(async () => {
                 const { msaFilehandle } = self;