react-msaview 1.2.10 → 1.3.2

package/bundle/layout.d.ts

@@ -0,0 +1,23 @@
+export default class Layout {
+    rectangles: Map<string, {
+        minY: number;
+        maxY: number;
+        minX: number;
+        maxX: number;
+        id: string;
+        data: unknown;
+    }>;
+    maxHeightReached: boolean;
+    private maxHeight;
+    private rbush;
+    private pTotalHeight;
+    constructor({ maxHeight, }?: {
+        maxHeight?: number;
+    });
+    /**
+     * @returns top position for the rect, or Null if laying
+     *  out the rect would exceed maxHeighe
+     */
+    addRect(id: string, left: number, right: number, height: number, data: unknown): number | null;
+    get totalHeight(): number;
+}

package/bundle/layout.js

@@ -0,0 +1,53 @@
+import RBush from 'rbush';
+var Layout = /** @class */ (function () {
+    function Layout(_a) {
+        var _b = _a === void 0 ? {} : _a, _c = _b.maxHeight, maxHeight = _c === void 0 ? 10000 : _c;
+        this.maxHeightReached = false;
+        this.rbush = new RBush();
+        this.rectangles = new Map();
+        this.maxHeight = Math.ceil(maxHeight);
+        this.pTotalHeight = 0; // total height, in units of bitmap squares (px/pitchY)
+    }
+    /**
+     * @returns top position for the rect, or Null if laying
+     *  out the rect would exceed maxHeighe
+     */
+    Layout.prototype.addRect = function (id, left, right, height, data) {
+        // add to rbush
+        var existingRecord = this.rectangles.get(id);
+        if (existingRecord) {
+            return existingRecord.minY;
+        }
+        var currHeight = 0;
+        while (this.rbush.collides({
+            minX: left,
+            minY: currHeight,
+            maxX: right,
+            maxY: currHeight + height,
+        }) &&
+            currHeight <= this.maxHeight) {
+            currHeight += 1;
+        }
+        var record = {
+            minX: left,
+            minY: currHeight,
+            maxX: right,
+            maxY: currHeight + height,
+            id: id,
+            data: data,
+        };
+        this.rbush.insert(record);
+        this.rectangles.set(id, record);
+        this.pTotalHeight = Math.max(this.pTotalHeight, currHeight);
+        return currHeight;
+    };
+    Object.defineProperty(Layout.prototype, "totalHeight", {
+        get: function () {
+            return this.pTotalHeight;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    return Layout;
+}());
+export default Layout;

package/bundle/model.d.ts

@@ -0,0 +1,364 @@
+/// <reference types="react" />
+import { Instance, SnapshotIn } from 'mobx-state-tree';
+import { HierarchyNode } from 'd3-hierarchy';
+import { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
+import ClustalMSA from './parsers/ClustalMSA';
+import StockholmMSA from './parsers/StockholmMSA';
+import FastaMSA from './parsers/FastaMSA';
+interface BasicTrackModel {
+    id: string;
+    name: string;
+    associatedRowName?: string;
+    height: number;
+}
+export interface TextTrackModel extends BasicTrackModel {
+    customColorScheme?: {
+        [key: string]: string;
+    };
+    data: string;
+}
+export interface BoxTrackModel extends BasicTrackModel {
+    features: {
+        start: number;
+        end: number;
+    }[];
+}
+export interface TextTrack {
+    ReactComponent: React.FC<any>;
+    model: TextTrackModel;
+}
+export interface BoxTrack {
+    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>;
+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>>;
+} & {
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"MsaView">;
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    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]>;
+    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>;
+    resizeHandleWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
+    blockSize: import("mobx-state-tree").IType<number | undefined, number, number>;
+    mouseRow: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    mouseCol: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    selectedStructures: import("mobx-state-tree").IArrayType<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>>;
+    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
+    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    bgColor: 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>;
+    highResScaleFactor: import("mobx-state-tree").IType<number | undefined, number, number>;
+    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
+    treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        uri: string;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        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<{
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }>> | import("mobx-state-tree").ModelInstanceTypeProps<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelInstanceTypeProps<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>>>;
+    msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        uri: string;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        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<{
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }>> | import("mobx-state-tree").ModelInstanceTypeProps<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelInstanceTypeProps<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>>>;
+    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>>;
+    boxTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        id: import("mobx-state-tree").ISimpleType<string>;
+        accession: import("mobx-state-tree").ISimpleType<string>;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        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;
+    } & {
+        setError(error: Error): void;
+        setData(data: string): void;
+    } & {
+        afterCreate(): void;
+    } & {
+        readonly loading: boolean;
+        readonly features: {
+            seq_id: string;
+            source: string;
+            type: string;
+            start: number;
+            end: number;
+            score: number;
+            strand: string;
+            phase: string;
+        }[] | undefined;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    annotatedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        attributes: import("mobx-state-tree").IType<Record<string, string[]>, Record<string, string[]>, Record<string, string[]>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    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>>;
+    }, {
+        setTree(tree?: string | undefined): void;
+        setMSA(msa?: string | undefined): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+}, {
+    width: number;
+} & {
+    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    setDisplayName(name: string): void;
+    setWidth(newWidth: number): void;
+} & {
+    error: Error | undefined;
+    margin: {
+        left: number;
+        top: number;
+    };
+    DialogComponent: import("react").FC<any> | undefined;
+    DialogProps: any;
+    annotPos: {
+        left: number;
+        right: number;
+    } | undefined;
+} & {
+    setDialogComponent(dlg: React.FC<any> | undefined, props: any): void;
+    setHeight(height: number): void;
+    addStructureToSelection(elt: SnapshotIn<typeof StructureModel>): void;
+    removeStructureFromSelection(elt: SnapshotIn<typeof StructureModel>): void;
+    toggleStructureSelection(elt: {
+        id: string;
+        structure: {
+            startPos: number;
+            endPos: number;
+            pdb: string;
+        };
+    }): void;
+    clearSelectedStructures(): void;
+    setError(error?: Error | undefined): void;
+    setMousePos(col?: number | undefined, row?: number | undefined): void;
+    setRowHeight(n: number): void;
+    setColWidth(n: number): void;
+    setColorSchemeName(name: string): void;
+    setScrollY(n: number): void;
+    setScrollX(n: number): void;
+    setTreeAreaWidth(n: number): void;
+    setTreeWidth(n: number): void;
+    setCurrentAlignment(n: number): void;
+    toggleLabelsAlignRight(): void;
+    toggleDrawTree(): void;
+    toggleCollapsed(node: string): void;
+    setShowOnly(node: string | undefined): void;
+    toggleBranchLen(): void;
+    toggleBgColor(): void;
+    toggleNodeBubbles(): void;
+    setData(data: {
+        msa?: string;
+        tree?: string;
+    }): void;
+    setMSAFilehandle(msaFilehandle?: FileLocationType | undefined): Promise<void>;
+    setTreeFilehandle(treeFilehandle?: FileLocationType | undefined): Promise<void>;
+    setMSA(result: string): void;
+    setTree(result: string): void;
+    afterCreate(): void;
+} & {
+    readonly initialized: boolean | "" | undefined;
+    readonly blocksX: number[];
+    readonly blocksY: number[];
+} & {
+    readonly blocks2d: number[][];
+    readonly done: string | false | undefined;
+    readonly colorScheme: {
+        [key: string]: string;
+    };
+    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 numColumns: number;
+    readonly tree: any;
+    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 inverseStructures: any;
+    readonly msaAreaWidth: number;
+    readonly blanks: number[];
+    readonly rows: string[][];
+    readonly columns: Record<string, string>;
+    readonly columns2d: string[];
+    readonly colStats: {
+        [key: string]: number;
+    }[];
+    readonly hierarchy: HierarchyNode<any>;
+    readonly totalHeight: number;
+} & {
+    addUniprotTrack(node: {
+        name: string;
+        accession: string;
+    }): void;
+    doScrollY(deltaY: number): void;
+    doScrollX(deltaX: number): void;
+    setMouseoveredColumn(n: number, chain: string, file: string): void;
+    toggleTrack(id: string): void;
+} & {
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly conservation: string[];
+    readonly tracks: BasicTrack[];
+    readonly turnedOnTracks: BasicTrack[];
+    pxToBp(coord: number): number;
+    rowSpecificBpToPx(rowName: string, position: number): number;
+    globalBpToPx(position: number): number;
+    relativePxToBp(rowName: string, position: number): number;
+    getPos(pos: number): number;
+} & {
+    addAnnotation(start: number, end: number, attributes: {
+        [key: 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;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    resizeHandleWidth: number;
+    blockSize: number;
+    mouseRow: number | undefined;
+    mouseCol: number | undefined;
+    selectedStructures: import("mobx-state-tree").ModelSnapshotType<{
+        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>>;
+    }>[];
+    labelsAlignRight: boolean;
+    colWidth: number;
+    showBranchLen: boolean;
+    bgColor: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    highResScaleFactor: number;
+    colorSchemeName: string;
+    treeFilehandle: {
+        uri: string;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | undefined;
+    msaFilehandle: {
+        uri: string;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | undefined;
+    currentAlignment: number;
+    collapsed: string[];
+    showOnly: string | undefined;
+    boxTracks: import("mobx-state-tree").ModelSnapshotType<{
+        id: import("mobx-state-tree").ISimpleType<string>;
+        accession: import("mobx-state-tree").ISimpleType<string>;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        associatedRowName: import("mobx-state-tree").ISimpleType<string>;
+        height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }>[];
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    annotatedRegions: import("mobx-state-tree").ModelSnapshotType<{
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        attributes: import("mobx-state-tree").IType<Record<string, string[]>, Record<string, string[]>, Record<string, string[]>>;
+    }>[];
+    data: {
+        msa?: string | undefined;
+        tree?: string | undefined;
+    };
+}>;
+export default model;
+export declare type MsaViewStateModel = typeof model;
+export declare type MsaViewModel = Instance<MsaViewStateModel>;