react-msaview 1.3.2 → 2.1.0

package/dist/model.d.ts

@@ -1,10 +1,20 @@
-/// <reference types="react" />
+import React from 'react';
 import { Instance, SnapshotIn } from 'mobx-state-tree';
 import { HierarchyNode } from 'd3-hierarchy';
 import { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
+export interface RowDetails {
+    [key: string]: unknown;
+    name: string;
+    range?: {
+        start: number;
+        end: number;
+    };
+}
+import { NodeWithIds, NodeWithIdsAndLength } from './util';
 import ClustalMSA from './parsers/ClustalMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
+import { StructureModel } from './StructureModel';
 interface BasicTrackModel {
     id: string;
     name: string;
@@ -12,9 +22,7 @@ interface BasicTrackModel {
     height: number;
 }
 export interface TextTrackModel extends BasicTrackModel {
-    customColorScheme?: {
-        [key: string]: string;
-    };
+    customColorScheme?: Record<string, string>;
     data: string;
 }
 export interface BoxTrackModel extends BasicTrackModel {
@@ -23,27 +31,19 @@ export interface BoxTrackModel extends BasicTrackModel {
         end: number;
     }[];
 }
-export interface TextTrack {
+export interface ITextTrack {
     ReactComponent: React.FC<any>;
     model: TextTrackModel;
 }
-export interface BoxTrack {
+export interface IBoxTrack {
     ReactComponent: React.FC<any>;
     model: BoxTrackModel;
 }
-declare type BasicTrack = BoxTrack | TextTrack;
-declare const StructureModel: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").ISimpleType<string>;
-    structure: import("mobx-state-tree").IModelType<{
-        pdb: import("mobx-state-tree").ISimpleType<string>;
-        startPos: import("mobx-state-tree").ISimpleType<number>;
-        endPos: import("mobx-state-tree").ISimpleType<number>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-    range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+type BasicTrack = IBoxTrack | ITextTrack;
 declare const model: import("mobx-state-tree").ISnapshotProcessor<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>;
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
@@ -83,13 +83,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }>> | 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;
@@ -99,13 +99,23 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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").ModelSnapshotType<{
+    }>, 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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    }, {}> | 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>>;
@@ -114,14 +124,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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").ModelInstanceTypeProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelInstanceTypeProps<{
-        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")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     msaFilehandle: 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>;
@@ -131,13 +134,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }>> | 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;
@@ -147,13 +150,23 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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").ModelSnapshotType<{
+    }>, 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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    }, {}> | 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>>;
@@ -162,14 +175,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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").ModelInstanceTypeProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelInstanceTypeProps<{
-        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")._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>>;
     showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -180,10 +186,10 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         associatedRowName: import("mobx-state-tree").ISimpleType<string>;
         height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
-        error: Error | undefined;
-        data: any;
+        error: unknown;
+        data: string | undefined;
     } & {
-        setError(error: Error): void;
+        setError(error: unknown): void;
         setData(data: string): void;
     } & {
         afterCreate(): void;
@@ -210,8 +216,8 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     }, {
-        setTree(tree?: string | undefined): void;
-        setMSA(msa?: string | undefined): void;
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     width: number;
@@ -220,13 +226,15 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
+    setMinimized(flag: boolean): void;
 } & {
-    error: Error | undefined;
+    rulerHeight: number;
+    error: unknown;
     margin: {
         left: number;
         top: number;
     };
-    DialogComponent: import("react").FC<any> | undefined;
+    DialogComponent: React.FC<any> | undefined;
     DialogProps: any;
     annotPos: {
         left: number;
@@ -246,8 +254,8 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         };
     }): void;
     clearSelectedStructures(): void;
-    setError(error?: Error | undefined): void;
-    setMousePos(col?: number | undefined, row?: number | undefined): void;
+    setError(error?: unknown): void;
+    setMousePos(col?: number, row?: number): void;
     setRowHeight(n: number): void;
     setColWidth(n: number): void;
     setColorSchemeName(name: string): void;
@@ -259,7 +267,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     toggleLabelsAlignRight(): void;
     toggleDrawTree(): void;
     toggleCollapsed(node: string): void;
-    setShowOnly(node: string | undefined): void;
+    setShowOnly(node?: string): void;
     toggleBranchLen(): void;
     toggleBgColor(): void;
     toggleNodeBubbles(): void;
@@ -267,8 +275,8 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         msa?: string;
         tree?: string;
     }): void;
-    setMSAFilehandle(msaFilehandle?: FileLocationType | undefined): Promise<void>;
-    setTreeFilehandle(treeFilehandle?: FileLocationType | undefined): Promise<void>;
+    setMSAFilehandle(msaFilehandle?: FileLocationType): Promise<void>;
+    setTreeFilehandle(treeFilehandle?: FileLocationType): Promise<void>;
     setMSA(result: string): void;
     setTree(result: string): void;
     afterCreate(): void;
@@ -279,39 +287,49 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
 } & {
     readonly blocks2d: number[][];
     readonly done: string | false | undefined;
-    readonly colorScheme: {
-        [key: string]: string;
+    readonly colorScheme: Record<string, string>;
+    readonly header: {};
+    getRowData(name: string): {
+        range?: {
+            start: number;
+            end: number;
+        } | undefined;
+        data: {
+            name: string;
+            accession: string;
+            dbxref: string;
+        } | Record<string, unknown>;
     };
-    readonly alignmentDetails: Record<string, any>;
-    getRowDetails(name: string): any;
     readonly currentAlignmentName: string;
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly menuItems: never[];
-    readonly MSA: ClustalMSA | StockholmMSA | FastaMSA | null;
+    readonly MSA: StockholmMSA | FastaMSA | ClustalMSA | null;
     readonly numColumns: number;
-    readonly tree: any;
+    readonly tree: NodeWithIds;
     readonly rowNames: string[];
     readonly mouseOverRowName: string | undefined;
     getMouseOverResidue(rowName: string): string;
-    readonly root: HierarchyNode<any>;
-    readonly structures: {
-        [key: string]: {
-            pdb: string;
-            startPos: number;
-            endPos: number;
-        }[];
+    readonly root: HierarchyNode<NodeWithIds>;
+    readonly structures: Record<string, {
+        pdb: string;
+        startPos: number;
+        endPos: number;
+    }[]>;
+    readonly inverseStructures: {
+        [k: string]: {
+            id: string;
+        };
     };
-    readonly inverseStructures: any;
     readonly msaAreaWidth: number;
     readonly blanks: number[];
-    readonly rows: string[][];
-    readonly columns: Record<string, string>;
+    readonly rows: [string, string[]][];
+    readonly columns: {
+        [k: string]: string;
+    };
     readonly columns2d: string[];
-    readonly colStats: {
-        [key: string]: number;
-    }[];
-    readonly hierarchy: HierarchyNode<any>;
+    readonly colStats: Record<string, number>[];
+    readonly hierarchy: HierarchyNode<NodeWithIdsAndLength>;
     readonly totalHeight: number;
 } & {
     addUniprotTrack(node: {
@@ -334,23 +352,31 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     relativePxToBp(rowName: string, position: number): number;
     getPos(pos: number): number;
 } & {
-    addAnnotation(start: number, end: number, attributes: {
-        [key: string]: string[];
-    }): void;
+    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, {
     id: string;
-    displayName: string | undefined;
     type: "MsaView";
     height: number;
-    treeAreaWidth: number;
-    treeWidth: number;
+    displayName: string | undefined;
+    minimized: boolean;
     rowHeight: number;
     scrollY: number;
     scrollX: number;
     resizeHandleWidth: number;
     blockSize: number;
+    labelsAlignRight: boolean;
+    colWidth: number;
+    showBranchLen: boolean;
+    bgColor: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    highResScaleFactor: number;
+    colorSchemeName: string;
+    currentAlignment: number;
+    treeAreaWidth: number;
+    treeWidth: number;
     mouseRow: number | undefined;
     mouseCol: number | undefined;
     selectedStructures: import("mobx-state-tree").ModelSnapshotType<{
@@ -362,14 +388,6 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
         range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     }>[];
-    labelsAlignRight: boolean;
-    colWidth: number;
-    showBranchLen: boolean;
-    bgColor: boolean;
-    drawTree: boolean;
-    drawNodeBubbles: boolean;
-    highResScaleFactor: number;
-    colorSchemeName: string;
     treeFilehandle: {
         locationType: "UriLocation";
         uri: string;
@@ -379,12 +397,12 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | 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";
@@ -395,14 +413,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | 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;
-    currentAlignment: number;
     collapsed: string[];
     showOnly: string | undefined;
     boxTracks: import("mobx-state-tree").ModelSnapshotType<{
@@ -424,5 +441,5 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     };
 }>;
 export default model;
-export declare type MsaViewStateModel = typeof model;
-export declare type MsaViewModel = Instance<MsaViewStateModel>;
+export type MsaViewStateModel = typeof model;
+export type MsaViewModel = Instance<MsaViewStateModel>;