react-msaview 1.3.1 → 2.0.0

package/bundle/layout.js

@@ -1,53 +0,0 @@
-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

@@ -1,364 +0,0 @@
-/// <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>;