react-msaview 4.4.6 → 4.6.0

package/dist/model.d.ts

@@ -1,3 +1,4 @@
+import A3mMSA from './parsers/A3mMSA';
 import ClustalMSA from './parsers/ClustalMSA';
 import EmfMSA from './parsers/EmfMSA';
 import FastaMSA from './parsers/FastaMSA';
@@ -307,6 +308,11 @@ 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
@@ -358,7 +364,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     setLoadingMSA(arg: boolean): void;
     /**
-     * #volatile
+     * #action
      */
     setShowZoomStar(arg: boolean): void;
     /**
@@ -389,6 +395,11 @@ 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
      */
@@ -429,7 +440,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    toggleCollapsed2(node: string): void;
+    toggleCollapsedLeaf(node: string): void;
     /**
      * #action
      */
@@ -463,6 +474,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     setTreeMetadata(result: string): void;
 } & {
+    /**
+     * #getter
+     * hideGaps takes effect when there are collapsed rows or allowedGappyness < 100
+     */
+    readonly hideGapsEffective: boolean;
     /**
      * #getter
      */
@@ -516,7 +532,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly MSA: StockholmMSA | FastaMSA | EmfMSA | ClustalMSA | null;
+    readonly MSA: StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA | null;
     /**
      * #getter
      */
@@ -533,6 +549,15 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly mouseOverRowName: string | undefined;
+    /**
+     * #getter
+     * Returns insertion info if mouse is hovering over an insertion indicator
+     */
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
     /**
      * #getter
      */
@@ -554,6 +579,14 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly blanksSet: Set<number>;
+    /**
+     * #getter
+     * Returns a map of row name to array of insertions with display position and letters
+     */
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
     /**
      * #getter
      */
@@ -588,6 +621,29 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly colStatsSums: number[];
+    /**
+     * #getter
+     * Pre-computed consensus letter and percent identity color per column.
+     * Used by percent_identity_dynamic color scheme.
+     */
+    readonly colConsensus: {
+        letter: string;
+        color: string | undefined;
+    }[];
+    /**
+     * #getter
+     * Pre-computed ClustalX colors per column.
+     * Returns a map of letter -> color for each column.
+     * ref http://www.jalview.org/help/html/colourSchemes/clustal.html
+     */
+    readonly colClustalX: Record<string, string>[];
+    /**
+     * #getter
+     * Conservation score per column using Shannon entropy (biojs-msa style).
+     * Conservation = (1 - H/Hmax) * (1 - gapFraction)
+     * Returns values 0-1 where 1 = fully conserved, 0 = no conservation.
+     */
+    readonly conservation: number[];
     /**
      * #getter
      * generates a new tree that is clustered with x,y positions
@@ -605,6 +661,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly allBranchesLength0: boolean;
+    /**
+     * #getter
+     * effective showBranchLen accounting for allBranchesLength0
+     */
+    readonly showBranchLenEffective: boolean;
 } & {
     /**
      * #getter
@@ -649,6 +710,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     * Calculate a neighbor joining tree from the current MSA using BLOSUM62 distances
+     */
+    calculateNeighborJoiningTreeFromMSA(): void;
     /**
      * #action
      */
@@ -717,10 +783,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly seqConsensus: string | undefined;
-    /**
-     * #getter
-     */
-    readonly conservation: string[];
     /**
      * #getter
      */
@@ -732,7 +794,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly turnedOnTracks: import("./types").ITextTrack[];
+    readonly turnedOnTracks: BasicTrack[];
     /**
      * #getter
      */
@@ -858,6 +920,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     exportSVG(opts: {
         theme: Theme;
         includeMinimap?: boolean;
+        includeTracks?: boolean;
         exportType: string;
     }): Promise<void>;
     /**
@@ -886,13 +949,206 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     fitHorizontally(): void;
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, {
-    data: {
-        treeMetadata?: string | undefined;
-        msa?: string | undefined;
-        tree?: string | undefined;
-    };
-}>;
+}, import("mobx-state-tree")._NotCustomized, Omit<import("mobx-state-tree").ModelSnapshotType<{
+    drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    bgColor: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
+} & {
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
+    contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    type: import("mobx-state-tree").ISimpleType<"MsaView">;
+    drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
+    scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
+    scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
+    colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
+    treeFilehandle: 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>>;
+    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>;
+        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>>;
+    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>;
+    }>, 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>>;
+    showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    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, {
+        tree: string | undefined;
+        msa: string | undefined;
+        treeMetadata: string | undefined;
+    }>, [undefined]>;
+    featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    relativeTo: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+}>, symbol>>;
 export default stateModelFactory;
 export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type MsaViewModel = Instance<MsaViewStateModel>;