@jbrowse/plugin-dotplot-view 2.6.1

package/esm/DotplotView/1dview.d.ts

@@ -0,0 +1,307 @@
+import { Instance } from 'mobx-state-tree';
+declare const Dotplot1DView: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    } & {
+        assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+         * #getter
+         */
+    }, {
+        setRefName(newRefName: string): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, {
+    features: import("@jbrowse/core/util").Feature[] | undefined;
+    volatileWidth: number;
+} & {
+    setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+    setBpPerPx(val: number): void;
+    setVolatileWidth(width: number): void;
+} & {
+    readonly width: number;
+    readonly assemblyNames: string[];
+    readonly displayedRegionsTotalPx: number;
+    readonly maxOffset: number;
+    readonly minOffset: number;
+    readonly totalBp: number;
+} & {
+    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    readonly currBp: number;
+} & {
+    pxToBp(px: number): {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    };
+    bpToPx({ refName, coord, regionNumber, }: {
+        refName: string;
+        coord: number;
+        regionNumber?: number | undefined;
+    }): number | undefined;
+} & {
+    setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+    showAllRegions(): void;
+    zoomOut(): void;
+    zoomIn(): void;
+    zoomTo(bpPerPx: number, offset?: number | undefined): number;
+    scrollTo(offsetPx: number): number;
+    centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+    scroll(distance: number): number;
+} & {
+    moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+} & {
+    /**
+     * #action
+     */
+    setScaleFactor(n: number): void;
+    /**
+     * #action
+     */
+    center(): void;
+} & {
+    /**
+     * #getter
+     * this uses padding=false and elision=false
+     */
+    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    /**
+     * #getter
+     */
+    readonly scaleFactor: number;
+    /**
+     * #getter
+     */
+    readonly maxBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly minBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly maxOffset: number;
+    /**
+     * #getter
+     */
+    readonly minOffset: number;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+declare const DotplotHView: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    } & {
+        assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+         * #getter
+         */
+    }, {
+        setRefName(newRefName: string): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, {
+    features: import("@jbrowse/core/util").Feature[] | undefined;
+    volatileWidth: number;
+} & {
+    setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+    setBpPerPx(val: number): void;
+    setVolatileWidth(width: number): void;
+} & {
+    readonly width: number;
+    readonly assemblyNames: string[];
+    readonly displayedRegionsTotalPx: number;
+    readonly maxOffset: number;
+    readonly minOffset: number;
+    readonly totalBp: number;
+} & {
+    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    readonly currBp: number;
+} & {
+    pxToBp(px: number): {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    };
+    bpToPx({ refName, coord, regionNumber, }: {
+        refName: string;
+        coord: number;
+        regionNumber?: number | undefined;
+    }): number | undefined;
+} & {
+    setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+    showAllRegions(): void;
+    zoomOut(): void;
+    zoomIn(): void;
+    zoomTo(bpPerPx: number, offset?: number | undefined): number;
+    scrollTo(offsetPx: number): number;
+    centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+    scroll(distance: number): number;
+} & {
+    moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+} & {
+    /**
+     * #action
+     */
+    setScaleFactor(n: number): void;
+    /**
+     * #action
+     */
+    center(): void;
+} & {
+    /**
+     * #getter
+     * this uses padding=false and elision=false
+     */
+    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    /**
+     * #getter
+     */
+    readonly scaleFactor: number;
+    /**
+     * #getter
+     */
+    readonly maxBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly minBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly maxOffset: number;
+    /**
+     * #getter
+     */
+    readonly minOffset: number;
+} & {
+    readonly width: any;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+declare const DotplotVView: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    } & {
+        assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+         * #getter
+         */
+    }, {
+        setRefName(newRefName: string): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, {
+    features: import("@jbrowse/core/util").Feature[] | undefined;
+    volatileWidth: number;
+} & {
+    setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+    setBpPerPx(val: number): void;
+    setVolatileWidth(width: number): void;
+} & {
+    readonly width: number;
+    readonly assemblyNames: string[];
+    readonly displayedRegionsTotalPx: number;
+    readonly maxOffset: number;
+    readonly minOffset: number;
+    readonly totalBp: number;
+} & {
+    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    readonly currBp: number;
+} & {
+    pxToBp(px: number): {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    };
+    bpToPx({ refName, coord, regionNumber, }: {
+        refName: string;
+        coord: number;
+        regionNumber?: number | undefined;
+    }): number | undefined;
+} & {
+    setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+    showAllRegions(): void;
+    zoomOut(): void;
+    zoomIn(): void;
+    zoomTo(bpPerPx: number, offset?: number | undefined): number;
+    scrollTo(offsetPx: number): number;
+    centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+    scroll(distance: number): number;
+} & {
+    moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+} & {
+    /**
+     * #action
+     */
+    setScaleFactor(n: number): void;
+    /**
+     * #action
+     */
+    center(): void;
+} & {
+    /**
+     * #getter
+     * this uses padding=false and elision=false
+     */
+    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+    /**
+     * #getter
+     */
+    readonly scaleFactor: number;
+    /**
+     * #getter
+     */
+    readonly maxBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly minBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly maxOffset: number;
+    /**
+     * #getter
+     */
+    readonly minOffset: number;
+} & {
+    readonly width: any;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export { DotplotVView, DotplotHView, Dotplot1DView };
+export type Dotplot1DViewModel = Instance<typeof Dotplot1DView>;

package/esm/DotplotView/1dview.js

@@ -0,0 +1,87 @@
+import { getParent } from 'mobx-state-tree';
+import { observable } from 'mobx';
+import Base1DView from '@jbrowse/core/util/Base1DViewModel';
+import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
+/**
+ * #stateModel Dotplot1DView
+ * ref https://mobx-state-tree.js.org/concepts/volatiles on volatile state used here
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const Dotplot1DView = Base1DView.extend(self => {
+    const scaleFactor = observable.box(1);
+    return {
+        views: {
+            /**
+             * #getter
+             * this uses padding=false and elision=false
+             */
+            get dynamicBlocks() {
+                return calculateDynamicBlocks(self, false, false);
+            },
+            /**
+             * #getter
+             */
+            get scaleFactor() {
+                return scaleFactor.get();
+            },
+            /**
+             * #getter
+             */
+            get maxBpPerPx() {
+                return self.totalBp / (self.width - 50);
+            },
+            /**
+             * #getter
+             */
+            get minBpPerPx() {
+                return 1 / 50;
+            },
+            /**
+             * #getter
+             */
+            get maxOffset() {
+                return self.displayedRegionsTotalPx - self.width * 0.2;
+            },
+            /**
+             * #getter
+             */
+            get minOffset() {
+                return -self.width * 0.8;
+            },
+        },
+        actions: {
+            /**
+             * #action
+             */
+            setScaleFactor(n) {
+                scaleFactor.set(n);
+            },
+            /**
+             * #action
+             */
+            center() {
+                const centerBp = self.totalBp / 2;
+                const centerPx = centerBp / self.bpPerPx;
+                self.scrollTo(centerPx - self.width / 2);
+            },
+        },
+    };
+});
+const DotplotHView = Dotplot1DView.extend(self => ({
+    views: {
+        get width() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return getParent(self).viewWidth;
+        },
+    },
+}));
+const DotplotVView = Dotplot1DView.extend(self => ({
+    views: {
+        get width() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return getParent(self).viewHeight;
+        },
+    },
+}));
+export { DotplotVView, DotplotHView, Dotplot1DView };
+//# sourceMappingURL=1dview.js.map

package/esm/DotplotView/1dview.js.map

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package/esm/DotplotView/blockTypes.d.ts

@@ -0,0 +1,61 @@
+type Func<T> = (value: BaseBlock, index: number, array: BaseBlock[]) => T;
+export declare class BlockSet {
+    blocks: BaseBlock[];
+    constructor(blocks?: BaseBlock[]);
+    push(block: BaseBlock): void;
+    getBlocks(): BaseBlock[];
+    map<T, U = this>(func: Func<T>, thisarg?: U): T[];
+    forEach<T, U = this>(func: Func<T>, thisarg?: U): void;
+    get length(): number;
+    get totalWidthPx(): number;
+    get offsetPx(): number;
+    get contentBlocks(): BaseBlock[];
+}
+export declare class BaseBlock {
+    reversed?: boolean;
+    refName: string;
+    start: number;
+    end: number;
+    assemblyName: string;
+    key: string;
+    widthPx: number;
+    offsetPx: number;
+    /**
+     * a block that should be shown as filled with data
+     */
+    constructor(data: any);
+    /**
+     * rename the reference sequence of this block and return a new one
+     *
+     * @param refName -
+     * @returns either a new block with a renamed reference sequence,
+     * or the same block, if the ref name is not actually different
+     */
+    renameReference(refName: string): any;
+    toRegion(): {
+        refName: string;
+        start: number;
+        end: number;
+        assemblyName: string;
+        reversed: boolean | undefined;
+    };
+}
+export declare class ContentBlock extends BaseBlock {
+}
+/**
+ * marker block representing one or more blocks that are
+ * too small to be shown at the current zoom level
+ */
+export declare class ElidedBlock extends BaseBlock {
+    widthPx: number;
+    elidedBlockCount: number;
+    constructor(data: Record<string, any>);
+    push(otherBlock: ElidedBlock): void;
+}
+/**
+ * marker block that sits between two different displayed regions
+ * and provides a thick border between them
+ */
+export declare class InterRegionPaddingBlock extends BaseBlock {
+}
+export {};

package/esm/DotplotView/blockTypes.js

@@ -0,0 +1,109 @@
+export class BlockSet {
+    constructor(blocks = []) {
+        this.blocks = blocks;
+    }
+    push(block) {
+        if (block instanceof ElidedBlock && this.blocks.length > 0) {
+            const lastBlock = this.blocks.at(-1);
+            if (lastBlock instanceof ElidedBlock) {
+                lastBlock.push(block);
+                return;
+            }
+        }
+        this.blocks.push(block);
+    }
+    getBlocks() {
+        return this.blocks;
+    }
+    map(func, thisarg) {
+        // eslint-disable-next-line unicorn/no-array-method-this-argument
+        return this.blocks.map(func, thisarg);
+    }
+    forEach(func, thisarg) {
+        // eslint-disable-next-line unicorn/no-array-method-this-argument
+        return this.blocks.forEach(func, thisarg);
+    }
+    get length() {
+        return this.blocks.length;
+    }
+    get totalWidthPx() {
+        return this.blocks.length
+            ? this.blocks.map(blocks => blocks.widthPx).reduce((a, b) => a + b)
+            : 0;
+    }
+    get offsetPx() {
+        return this.blocks.length ? this.blocks[0].offsetPx : 0;
+    }
+    get contentBlocks() {
+        return this.blocks.filter(block => block instanceof ContentBlock);
+    }
+}
+export class BaseBlock {
+    /**
+     * a block that should be shown as filled with data
+     */
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    constructor(data) {
+        this.widthPx = 0;
+        this.offsetPx = 0;
+        Object.assign(this, data);
+        this.assemblyName = data.assemblyName;
+        this.refName = data.refName;
+        this.start = data.start;
+        this.end = data.end;
+        this.key = data.key;
+    }
+    /**
+     * rename the reference sequence of this block and return a new one
+     *
+     * @param refName -
+     * @returns either a new block with a renamed reference sequence,
+     * or the same block, if the ref name is not actually different
+     */
+    renameReference(refName) {
+        if (this.refName && refName !== this.refName) {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return new this.constructor({ ...this, refName });
+        }
+        return this;
+    }
+    toRegion() {
+        return {
+            refName: this.refName,
+            start: this.start,
+            end: this.end,
+            assemblyName: this.assemblyName,
+            reversed: this.reversed,
+        };
+    }
+}
+export class ContentBlock extends BaseBlock {
+}
+/**
+ * marker block representing one or more blocks that are
+ * too small to be shown at the current zoom level
+ */
+export class ElidedBlock extends BaseBlock {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    constructor(data) {
+        super(data);
+        this.elidedBlockCount = 0;
+        this.widthPx = data.widthPx;
+    }
+    push(otherBlock) {
+        this.elidedBlockCount += 1;
+        if (otherBlock) {
+            this.refName = '';
+            this.start = 0;
+            this.end = 0;
+            this.widthPx += otherBlock.widthPx;
+        }
+    }
+}
+/**
+ * marker block that sits between two different displayed regions
+ * and provides a thick border between them
+ */
+export class InterRegionPaddingBlock extends BaseBlock {
+}
+//# sourceMappingURL=blockTypes.js.map

package/esm/DotplotView/blockTypes.js.map

@@ -0,0 +1 @@
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package/esm/DotplotView/components/Axes.d.ts

@@ -0,0 +1,14 @@
+import React from 'react';
+import { DotplotViewModel } from '../model';
+export declare const HorizontalAxis: ({ model, }: {
+    model: DotplotViewModel;
+}) => React.JSX.Element;
+export declare const HorizontalAxisRaw: ({ model, }: {
+    model: DotplotViewModel;
+}) => React.JSX.Element;
+export declare const VerticalAxis: ({ model, }: {
+    model: DotplotViewModel;
+}) => React.JSX.Element;
+export declare const VerticalAxisRaw: ({ model, }: {
+    model: DotplotViewModel;
+}) => React.JSX.Element;