jbrowse-plugin-msaview 2.7.0 → 2.7.1

package/dist/MsaViewPanel/model.d.ts

@@ -42,7 +42,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
 }, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "currentAlignment" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -456,42 +456,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
-}, "init" | "connectedViewId" | "connectedFeature" | "blastParams" | "querySeqName" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
-    /**
-     * #property
-     */
+}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
-    /**
-     * #property
-     */
-    querySeqName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
+    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    /**
-     * #property
-     */
+    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
-    /**
-     * #property
-     */
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
 }, {
     width: number;
@@ -522,7 +495,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
 } & {
     headerHeight: number;
     status: {
@@ -609,7 +582,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noDomains: boolean;
     menuItems(): never[];
     readonly treeMetadata: any;
-    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
@@ -631,12 +604,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
+    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
     readonly fontSize: number;
-    readonly colStats: Record<string, number>[];
-    readonly colStatsSums: number[];
+    readonly colStats: import("react-msaview").ColumnCounts;
+    readonly colStatsSums: Uint32Array<ArrayBufferLike>;
     readonly sequenceType: "dna" | "rna" | "amino";
     readonly colConsensus: {
         letter: string;
@@ -788,15 +762,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         end: number;
         strand: number | undefined;
     }[];
-    readonly mouseOverDomains: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
+    readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
+    readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
+    readonly mouseOverDomains: import("react-msaview").TidyDomainAnnotation[];
+    readonly referenceRowIndex: number | undefined;
+    readonly hoveredRowIndices: number[];
+    readonly highlightedColumnRuns: {
         start: number;
         end: number;
-        strand: number | undefined;
     }[];
     readonly mouseOverColumnStats: {
         col: number;
@@ -978,7 +951,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     id: string;
     showDomains: boolean;
     hideGaps: boolean;

package/dist/MsaViewPanel/model.js

@@ -29,7 +29,12 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        querySeqName: types.stripDefault(types.string, 'QUERY'),
+        // Plain defaults, not types.stripDefault: that postdates the
+        // mobx-state-tree every released core exposes (present only on main), and
+        // the missing function throws while this model is being built, which
+        // error-pages the whole app rather than just this view. Restore
+        // stripDefault once a release ships it.
+        querySeqName: 'QUERY',
         /**
          * #property
          */
@@ -37,7 +42,8 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        zoomToBaseLevel: types.stripDefault(types.boolean, false),
+        // see querySeqName above re: types.stripDefault
+        zoomToBaseLevel: false,
         /**
          * #property
          */