react-msaview 2.1.1 → 2.1.3

package/dist/model.d.ts

@@ -40,7 +40,8 @@ export interface IBoxTrack {
     model: BoxTrackModel;
 }
 type BasicTrack = IBoxTrack | ITextTrack;
-declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").IModelType<{
+type StructureSnap = SnapshotIn<typeof StructureModel>;
+declare const model: import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -104,14 +105,18 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         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>;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
     }>, 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>;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
@@ -155,14 +160,73 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         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>;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
     }>, 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>; /**
+         * #action
+         */
+    }, {}> | ({
+        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>>;
+    treeMetadataFilehandle: 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>; /**
+         * #action
+         */
+    }>, 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>; /**
+         * #action
+         */
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
@@ -215,9 +279,11 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     data: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     }, {
         setTree(tree?: string): void;
         setMSA(msa?: string): void;
+        setTreeMetadata(treeMetadata?: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     width: number;
@@ -241,10 +307,25 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         right: number;
     } | undefined;
 } & {
-    setDialogComponent(dlg: React.FC<any> | undefined, props: any): void;
+    /**
+     * #action
+     */
+    setDialogComponent(dlg?: React.FC<any>, props?: any): void;
+    /**
+     * #action
+     */
     setHeight(height: number): void;
-    addStructureToSelection(elt: SnapshotIn<typeof StructureModel>): void;
-    removeStructureFromSelection(elt: SnapshotIn<typeof StructureModel>): void;
+    /**
+     * #action
+     */
+    addStructureToSelection(elt: StructureSnap): void;
+    /**
+     * #action
+     */
+    removeStructureFromSelection(elt: StructureSnap): void;
+    /**
+     * #action
+     */
     toggleStructureSelection(elt: {
         id: string;
         structure: {
@@ -253,42 +334,139 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             pdb: string;
         };
     }): void;
+    /**
+     * #action
+     */
     clearSelectedStructures(): void;
+    /**
+     * #action
+     */
     setError(error?: unknown): void;
+    /**
+     * #action
+     */
     setMousePos(col?: number, row?: number): void;
+    /**
+     * #action
+     */
     setRowHeight(n: number): void;
+    /**
+     * #action
+     */
     setColWidth(n: number): void;
+    /**
+     * #action
+     */
     setColorSchemeName(name: string): void;
+    /**
+     * #action
+     */
     setScrollY(n: number): void;
+    /**
+     * #action
+     */
     setScrollX(n: number): void;
+    /**
+     * #action
+     */
     setTreeAreaWidth(n: number): void;
+    /**
+     * #action
+     */
     setTreeWidth(n: number): void;
+    /**
+     * #action
+     */
     setCurrentAlignment(n: number): void;
+    /**
+     * #action
+     */
     toggleLabelsAlignRight(): void;
+    /**
+     * #action
+     */
     toggleDrawTree(): void;
+    /**
+     * #action
+     */
     toggleCollapsed(node: string): void;
+    /**
+     * #action
+     */
     setShowOnly(node?: string): void;
+    /**
+     * #action
+     */
     toggleBranchLen(): void;
+    /**
+     * #action
+     */
     toggleBgColor(): void;
+    /**
+     * #action
+     */
     toggleNodeBubbles(): void;
+    /**
+     * #action
+     */
     setData(data: {
         msa?: string;
         tree?: string;
     }): void;
+    /**
+     * #action
+     */
     setMSAFilehandle(msaFilehandle?: FileLocationType): Promise<void>;
+    /**
+     * #action
+     */
     setTreeFilehandle(treeFilehandle?: FileLocationType): Promise<void>;
+    /**
+     * #action
+     */
     setMSA(result: string): void;
+    /**
+     * #action
+     */
     setTree(result: string): void;
+    /**
+     * #action
+     */
+    setTreeMetadata(result: string): void;
     afterCreate(): void;
 } & {
+    /**
+     * #getter
+     */
     readonly initialized: boolean | "" | undefined;
+    /**
+     * #getter
+     */
     readonly blocksX: number[];
+    /**
+     * #getter
+     */
     readonly blocksY: number[];
 } & {
+    /**
+     * #getter
+     */
     readonly blocks2d: number[][];
+    /**
+     * #getter
+     */
     readonly done: string | false | undefined;
+    /**
+     * #getter
+     */
     readonly colorScheme: Record<string, string>;
+    /**
+     * #getter
+     */
     readonly header: {};
+    /**
+     * #method
+     */
     getRowData(name: string): {
         range?: {
             start: number;
@@ -300,62 +478,184 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             dbxref: string;
         } | Record<string, unknown>;
     };
+    /**
+     * #getter
+     */
     readonly currentAlignmentName: string;
+    /**
+     * #getter
+     */
     readonly alignmentNames: string[];
+    /**
+     * #getter
+     */
     readonly noTree: boolean;
+    /**
+     * #getter
+     */
     readonly menuItems: never[];
+    /**
+     * #getter
+     */
+    readonly treeMetadata: any;
+    /**
+     * #getter
+     */
     readonly MSA: StockholmMSA | FastaMSA | ClustalMSA | null;
+    /**
+     * #getter
+     */
     readonly numColumns: number;
+    /**
+     * #getter
+     */
     readonly tree: NodeWithIds;
+    /**
+     * #getter
+     */
     readonly rowNames: string[];
-    readonly mouseOverRowName: string | undefined;
+    /**
+     * #getter
+     */ readonly mouseOverRowName: string | undefined;
+    /**
+     * #method
+     */
     getMouseOverResidue(rowName: string): string;
+    /**
+     * #getter
+     */
     readonly root: HierarchyNode<NodeWithIds>;
+    /**
+     * #getter
+     */
     readonly structures: Record<string, {
         pdb: string;
         startPos: number;
         endPos: number;
     }[]>;
+    /**
+     * #getter
+     */
     readonly inverseStructures: {
         [k: string]: {
             id: string;
         };
     };
+    /**
+     * #getter
+     */
     readonly msaAreaWidth: number;
+    /**
+     * #getter
+     */
     readonly blanks: number[];
+    /**
+     * #getter
+     */
     readonly rows: [string, string[]][];
+    /**
+     * #getter
+     */
     readonly columns: {
         [k: string]: string;
     };
+    /**
+     * #getter
+     */
     readonly columns2d: string[];
+    /**
+     * #getter
+     */
     readonly colStats: Record<string, number>[];
+    /**
+     * #getter
+     * generates a new tree that is clustered with x,y positions
+     */
     readonly hierarchy: HierarchyNode<NodeWithIdsAndLength>;
+    /**
+     * #getter
+     */
     readonly totalHeight: number;
 } & {
+    /**
+     * #action
+     */
     addUniprotTrack(node: {
         name: string;
         accession: string;
     }): void;
+    /**
+     * #action
+     */
     doScrollY(deltaY: number): void;
+    /**
+     * #action
+     */
     doScrollX(deltaX: number): void;
+    /**
+     * #action
+     */
     setMouseoveredColumn(n: number, chain: string, file: string): void;
+    /**
+     * #action
+     */
     toggleTrack(id: string): void;
 } & {
+    /**
+     * #getter
+     */
     readonly secondaryStructureConsensus: string | undefined;
+    /**
+     * #getter
+     */
     readonly seqConsensus: string | undefined;
+    /**
+     * #getter
+     */
     readonly conservation: string[];
+    /**
+     * #getter
+     */
     readonly tracks: BasicTrack[];
+    /**
+     * #getter
+     */
     readonly turnedOnTracks: BasicTrack[];
+    /**
+     * #method
+     * returns coordinate in the current relative coordinate scheme
+     */
     pxToBp(coord: number): number;
+    /**
+     * #method
+     */
     rowSpecificBpToPx(rowName: string, position: number): number;
+    /**
+     * #method
+     */
     globalBpToPx(position: number): number;
+    /**
+     * #method
+     */
     relativePxToBp(rowName: string, position: number): number;
+    /**
+     * #method
+     */
     getPos(pos: number): number;
 } & {
+    /**
+     * #action
+     */
     addAnnotation(start: number, end: number, attributes: Record<string, string[]>): void;
-    setOffsets(left: number, right: number): void;
-    clearAnnotPos(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, import("mobx-state-tree")._NotCustomized, {
+    /**
+     * #action
+     */
+    setAnnotationClickBoundaries(left: number, right: number): void;
+    /**
+     * #action
+     */
+    clearAnnotationClickBoundaries(): void;
+}, import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "MsaView";
     height: number;
@@ -402,7 +702,9 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         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>;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
     }> | undefined;
     msaFilehandle: {
         locationType: "UriLocation";
@@ -418,7 +720,27 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         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>;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
+    }> | 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>; /**
+         * #action
+         */
     }> | undefined;
     collapsed: string[];
     showOnly: string | undefined;
@@ -436,6 +758,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         attributes: import("mobx-state-tree").IType<Record<string, string[]>, Record<string, string[]>, Record<string, string[]>>;
     }>[];
     data: {
+        treeMetadata?: string | undefined;
         msa?: string | undefined;
         tree?: string | undefined;
     };