@jbrowse/plugin-dotplot-view 3.7.0 → 4.0.0

package/dist/DotplotRenderer/drawDotplot.js

@@ -1,209 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawDotplot = drawDotplot;
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const colors_1 = require("@jbrowse/core/ui/colors");
-const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
-const colord_1 = require("@jbrowse/core/util/colord");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const clamp_1 = require("./clamp");
-const { parseCigar } = plugin_alignments_1.MismatchParser;
-function hashString(str) {
-    let hash = 0;
-    for (let i = 0; i < str.length; i++) {
-        const char = str.charCodeAt(i);
-        hash = (hash << 5) - hash + char;
-        hash = hash & hash;
-    }
-    return Math.abs(hash);
-}
-function getQueryColor(queryName) {
-    const hash = hashString(queryName);
-    return colors_1.category10[hash % colors_1.category10.length];
-}
-function applyAlpha(color, alpha) {
-    if (alpha === 1) {
-        return color;
-    }
-    return (0, colord_1.colord)(color).alpha(alpha).toRgbString();
-}
-async function drawDotplot(ctx, props) {
-    var _a, _b;
-    const { config, views, height, drawCigar, theme, alpha = 1, minAlignmentLength = 0, colorBy: colorByOverride, } = props;
-    const color = (0, configuration_1.readConfObject)(config, 'color');
-    const posColor = (0, configuration_1.readConfObject)(config, 'posColor');
-    const negColor = (0, configuration_1.readConfObject)(config, 'negColor');
-    const colorBy = colorByOverride !== null && colorByOverride !== void 0 ? colorByOverride : (0, configuration_1.readConfObject)(config, 'colorBy');
-    const lineWidth = (0, configuration_1.readConfObject)(config, 'lineWidth');
-    const thresholds = (0, configuration_1.readConfObject)(config, 'thresholds');
-    const palette = (0, configuration_1.readConfObject)(config, 'thresholdsPalette');
-    const isCallback = config.color.isCallback;
-    const hview = views[0];
-    const vview = views[1];
-    const db1 = (_a = hview.dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.offsetPx;
-    const db2 = (_b = vview.dynamicBlocks.contentBlocks[0]) === null || _b === void 0 ? void 0 : _b.offsetPx;
-    const warnings = [];
-    ctx.lineWidth = lineWidth;
-    const { bpPerPx: hBpPerPx } = hview;
-    const { bpPerPx: vBpPerPx } = vview;
-    const hsnap = {
-        ...(0, mobx_state_tree_1.getSnapshot)(hview),
-        staticBlocks: hview.staticBlocks,
-        width: hview.width,
-    };
-    const vsnap = {
-        ...(0, mobx_state_tree_1.getSnapshot)(vview),
-        staticBlocks: vview.staticBlocks,
-        width: vview.width,
-    };
-    const t = (0, ui_1.createJBrowseTheme)(theme);
-    const features = hview.features || [];
-    let posColorWithAlpha;
-    let negColorWithAlpha;
-    let defaultColorWithAlpha;
-    const queryColorCache = new Map();
-    const getQueryColorWithAlpha = (queryName) => {
-        if (!queryColorCache.has(queryName)) {
-            const c = getQueryColor(queryName);
-            queryColorCache.set(queryName, applyAlpha(c, alpha));
-        }
-        return queryColorCache.get(queryName);
-    };
-    if (colorBy === 'strand') {
-        posColorWithAlpha = applyAlpha(posColor, alpha);
-        negColorWithAlpha = applyAlpha(negColor, alpha);
-    }
-    else if (colorBy === 'default' && !isCallback) {
-        const c = color === '#f0f' ? t.palette.text.primary : color;
-        defaultColorWithAlpha = applyAlpha(c, alpha);
-    }
-    for (const feature of features) {
-        const strand = feature.get('strand') || 1;
-        const fStart = feature.get('start');
-        const fEnd = feature.get('end');
-        if (minAlignmentLength > 0) {
-            const alignmentLength = Math.abs(fEnd - fStart);
-            if (alignmentLength < minAlignmentLength) {
-                continue;
-            }
-        }
-        const refName = feature.get('refName');
-        const mate = feature.get('mate');
-        const mateRef = mate.refName;
-        const start = strand === 1 ? fStart : fEnd;
-        const end = strand === 1 ? fEnd : fStart;
-        let colorWithAlpha;
-        if (colorBy === 'strand') {
-            colorWithAlpha = strand === -1 ? negColorWithAlpha : posColorWithAlpha;
-        }
-        else if (colorBy === 'query') {
-            const queryName = refName;
-            colorWithAlpha = getQueryColorWithAlpha(queryName);
-        }
-        else if (colorBy === 'default' && !isCallback) {
-            colorWithAlpha = defaultColorWithAlpha;
-        }
-        else {
-            let r = 'black';
-            if (colorBy === 'identity') {
-                const identity = feature.get('identity');
-                for (let i = 0; i < thresholds.length; i++) {
-                    if (identity > +thresholds[i]) {
-                        r = palette[i] || 'black';
-                        break;
-                    }
-                }
-            }
-            else if (colorBy === 'meanQueryIdentity') {
-                r = `hsl(${feature.get('meanScore') * 200},100%,40%)`;
-            }
-            else if (colorBy === 'mappingQuality') {
-                r = `hsl(${feature.get('mappingQual')},100%,40%)`;
-            }
-            else if (colorBy === 'default' && isCallback) {
-                r = (0, configuration_1.readConfObject)(config, 'color', { feature });
-            }
-            colorWithAlpha = applyAlpha(r, alpha);
-        }
-        ctx.fillStyle = colorWithAlpha;
-        ctx.strokeStyle = colorWithAlpha;
-        const b10 = (0, Base1DUtils_1.bpToPx)({ self: hsnap, refName, coord: start });
-        const b20 = (0, Base1DUtils_1.bpToPx)({ self: hsnap, refName, coord: end });
-        const e10 = (0, Base1DUtils_1.bpToPx)({ self: vsnap, refName: mateRef, coord: mate.start });
-        const e20 = (0, Base1DUtils_1.bpToPx)({ self: vsnap, refName: mateRef, coord: mate.end });
-        if (b10 !== undefined &&
-            b20 !== undefined &&
-            e10 !== undefined &&
-            e20 !== undefined) {
-            const b1 = b10.offsetPx - db1;
-            const b2 = b20.offsetPx - db1;
-            const e1 = e10.offsetPx - db2;
-            const e2 = e20.offsetPx - db2;
-            if (Math.abs(b1 - b2) <= 4 && Math.abs(e1 - e2) <= 4) {
-                ctx.beginPath();
-                ctx.arc(b1, height - e1, lineWidth / 2, 0, 2 * Math.PI);
-                ctx.fill();
-            }
-            else {
-                let currX = b1;
-                let currY = e1;
-                const cigar = feature.get('CIGAR');
-                if (drawCigar && cigar) {
-                    const cigarOps = parseCigar(cigar);
-                    ctx.beginPath();
-                    ctx.moveTo(currX, height - currY);
-                    let lastDrawnX = currX;
-                    let lastDrawnY = currX;
-                    for (let i = 0; i < cigarOps.length; i += 2) {
-                        const val = +cigarOps[i];
-                        const op = cigarOps[i + 1];
-                        if (op === 'M' || op === '=' || op === 'X') {
-                            currX += (val / hBpPerPx) * strand;
-                            currY += val / vBpPerPx;
-                        }
-                        else if (op === 'D' || op === 'N') {
-                            currX += (val / hBpPerPx) * strand;
-                        }
-                        else if (op === 'I') {
-                            currY += val / vBpPerPx;
-                        }
-                        currX = (0, clamp_1.clampWithWarnX)(currX, b1, b2, feature, warnings);
-                        currY = (0, clamp_1.clampWithWarnY)(currY, e1, e2, feature, warnings);
-                        if (Math.abs(currX - lastDrawnX) > 0.5 ||
-                            Math.abs(currY - lastDrawnY) > 0.5) {
-                            ctx.lineTo(currX, height - currY);
-                            lastDrawnX = currX;
-                            lastDrawnY = currY;
-                        }
-                    }
-                    ctx.stroke();
-                }
-                else {
-                    ctx.beginPath();
-                    ctx.moveTo(b1, height - e1);
-                    ctx.lineTo(b2, height - e2);
-                    ctx.stroke();
-                }
-            }
-        }
-        else {
-            if (warnings.length <= 5) {
-                if (b10 === undefined || b20 === undefined) {
-                    warnings.push({
-                        message: `feature at (X-coord: ${refName}:${start}-${end}) not plotted, fell outside of range`,
-                        effect: 'feature not rendered',
-                    });
-                }
-                else {
-                    warnings.push({
-                        message: `feature at (Y-coord: ${mateRef}:${mate.start}-${mate.end}) not plotted, fell outside of range`,
-                        effect: 'feature not rendered',
-                    });
-                }
-            }
-        }
-    }
-    return { warnings };
-}

package/dist/DotplotRenderer/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function DotplotRendererF(pluginManager: PluginManager): void;

package/dist/DotplotRenderer/index.js

@@ -1,17 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = DotplotRendererF;
-const DotplotRenderer_1 = __importDefault(require("./DotplotRenderer"));
-const DotplotRendering_1 = __importDefault(require("./components/DotplotRendering"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function DotplotRendererF(pluginManager) {
-    pluginManager.addRendererType(() => new DotplotRenderer_1.default({
-        name: 'DotplotRenderer',
-        configSchema: configSchema_1.default,
-        ReactComponent: DotplotRendering_1.default,
-        pluginManager,
-    }));
-}

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

@@ -1,199 +0,0 @@
-import type { 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").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-    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: undefined | import("@jbrowse/core/util").Feature[];
-    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;
-    }): number | undefined;
-} & {
-    setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
-    showAllRegions(): void;
-    zoomOut(): void;
-    zoomIn(): void;
-    zoomTo(bpPerPx: number, offset?: number): 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, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
-} & {
-    setScaleFactor(n: number): void;
-    center(): void;
-} & {
-    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-    readonly scaleFactor: number;
-    readonly maxBpPerPx: number;
-    readonly minBpPerPx: number;
-    readonly maxOffset: number;
-    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").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-    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: undefined | import("@jbrowse/core/util").Feature[];
-    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;
-    }): number | undefined;
-} & {
-    setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
-    showAllRegions(): void;
-    zoomOut(): void;
-    zoomIn(): void;
-    zoomTo(bpPerPx: number, offset?: number): 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, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
-} & {
-    setScaleFactor(n: number): void;
-    center(): void;
-} & {
-    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-    readonly scaleFactor: number;
-    readonly maxBpPerPx: number;
-    readonly minBpPerPx: number;
-    readonly maxOffset: number;
-    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").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-    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: undefined | import("@jbrowse/core/util").Feature[];
-    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;
-    }): number | undefined;
-} & {
-    setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
-    showAllRegions(): void;
-    zoomOut(): void;
-    zoomIn(): void;
-    zoomTo(bpPerPx: number, offset?: number): 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, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
-} & {
-    setScaleFactor(n: number): void;
-    center(): void;
-} & {
-    readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
-    readonly scaleFactor: number;
-    readonly maxBpPerPx: number;
-    readonly minBpPerPx: number;
-    readonly maxOffset: number;
-    readonly minOffset: number;
-} & {
-    readonly width: any;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export { Dotplot1DView, DotplotHView, DotplotVView };
-export type Dotplot1DViewModel = Instance<typeof Dotplot1DView>;

package/dist/DotplotView/1dview.js

@@ -1,65 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.DotplotVView = exports.DotplotHView = exports.Dotplot1DView = void 0;
-const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
-const calculateDynamicBlocks_1 = __importDefault(require("@jbrowse/core/util/calculateDynamicBlocks"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const Dotplot1DView = Base1DViewModel_1.default.extend(self => {
-    const scaleFactor = mobx_1.observable.box(1);
-    return {
-        views: {
-            get dynamicBlocks() {
-                return (0, calculateDynamicBlocks_1.default)(self, false, false);
-            },
-            get scaleFactor() {
-                return scaleFactor.get();
-            },
-            get maxBpPerPx() {
-                return self.totalBp / (self.width * 0.9);
-            },
-            get minBpPerPx() {
-                return 1 / 50;
-            },
-            get maxOffset() {
-                const leftPadding = 10;
-                return self.displayedRegionsTotalPx - leftPadding;
-            },
-            get minOffset() {
-                const rightPadding = 30;
-                return -self.width + rightPadding;
-            },
-        },
-        actions: {
-            setScaleFactor(n) {
-                scaleFactor.set(n);
-            },
-            center() {
-                const centerBp = self.totalBp / 2;
-                const centerPx = centerBp / self.bpPerPx;
-                self.scrollTo(centerPx - self.width / 2);
-            },
-        },
-    };
-});
-exports.Dotplot1DView = Dotplot1DView;
-const DotplotHView = Dotplot1DView.extend(self => ({
-    views: {
-        get width() {
-            return (0, mobx_state_tree_1.getParent)(self).viewWidth;
-        },
-    },
-}));
-exports.DotplotHView = DotplotHView;
-const DotplotVView = Dotplot1DView.extend(self => ({
-    views: {
-        get width() {
-            return (0, mobx_state_tree_1.getParent)(self).viewHeight;
-        },
-    },
-}));
-exports.DotplotVView = DotplotVView;

package/dist/DotplotView/components/Axes.d.ts

@@ -1,13 +0,0 @@
-import type { DotplotViewModel } from '../model';
-export declare const HorizontalAxis: ({ model, }: {
-    model: DotplotViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export declare const HorizontalAxisRaw: ({ model, }: {
-    model: DotplotViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export declare const VerticalAxis: ({ model, }: {
-    model: DotplotViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export declare const VerticalAxisRaw: ({ model, }: {
-    model: DotplotViewModel;
-}) => import("react/jsx-runtime").JSX.Element;

package/dist/DotplotView/components/Axes.js

@@ -1,107 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.VerticalAxisRaw = exports.VerticalAxis = exports.HorizontalAxisRaw = exports.HorizontalAxis = void 0;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-const util_2 = require("./util");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
-    vtext: {
-        gridColumn: '1/2',
-        gridRow: '1/2',
-        pointerEvents: 'none',
-        userSelect: 'none',
-    },
-    htext: {
-        gridColumn: '2/2',
-        gridRow: '2/2',
-        pointerEvents: 'none',
-        userSelect: 'none',
-    },
-}));
-exports.HorizontalAxis = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { viewWidth, borderY } = model;
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsx)("svg", { width: viewWidth, height: borderY, className: classes.htext, children: (0, jsx_runtime_1.jsx)(exports.HorizontalAxisRaw, { model: model }) }));
-});
-exports.HorizontalAxisRaw = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { viewWidth, borderX, borderY, hview, htextRotation, hticks } = model;
-    const { offsetPx, width, dynamicBlocks, bpPerPx } = hview;
-    const dblocks = dynamicBlocks.contentBlocks;
-    const hide = (0, util_2.getBlockLabelKeysToHide)(dblocks, viewWidth, offsetPx);
-    const theme = (0, material_1.useTheme)();
-    const hviewSnap = {
-        ...(0, mobx_state_tree_1.getSnapshot)(hview),
-        width,
-        staticBlocks: hview.staticBlocks,
-    };
-    const ticks = hticks
-        .map(tick => {
-        var _a;
-        return [
-            tick,
-            (_a = (0, Base1DUtils_1.bpToPx)({
-                refName: tick.refName,
-                coord: tick.base,
-                self: hviewSnap,
-            })) === null || _a === void 0 ? void 0 : _a.offsetPx,
-        ];
-    })
-        .filter(f => f[1] !== undefined)
-        .map(f => [f[0], f[1] - offsetPx]);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [dblocks
-                .filter(region => !hide.has(region.key))
-                .map(region => {
-                const x = region.offsetPx;
-                const y = 0;
-                const xoff = Math.floor(x - hview.offsetPx);
-                return ((0, jsx_runtime_1.jsx)("text", { transform: `rotate(${htextRotation},${xoff},${y})`, x: xoff, y: y + 1, fontSize: 11, dominantBaseline: "hanging", textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary), children: region.refName }, JSON.stringify(region)));
-            }), ticks.map(([tick, x]) => x > 0 && x < width ? ((0, jsx_runtime_1.jsx)("line", { x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, `line-${JSON.stringify(tick)}`)) : null), ticks
-                .filter(t => t[0].type === 'major')
-                .map(([tick, x]) => x > 10 && x < width ? ((0, jsx_runtime_1.jsx)("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},0)`, fontSize: 11, dominantBaseline: "middle", textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary), children: (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx) }, `text-${JSON.stringify(tick)}`)) : null), (0, jsx_runtime_1.jsx)("text", { y: borderY - 12, x: (viewWidth - borderX) / 2, textAnchor: "middle", fontSize: 11, dominantBaseline: "hanging", ...(0, util_1.getFillProps)(theme.palette.text.primary), children: hview.assemblyNames.join(',') })] }));
-});
-exports.VerticalAxis = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { borderX, viewHeight } = model;
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsx)("svg", { className: classes.vtext, width: borderX, height: viewHeight, children: (0, jsx_runtime_1.jsx)(exports.VerticalAxisRaw, { model: model }) }));
-});
-exports.VerticalAxisRaw = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { viewHeight, borderX, borderY, vview, vtextRotation, vticks } = model;
-    const { offsetPx, width, dynamicBlocks, bpPerPx } = vview;
-    const dblocks = dynamicBlocks.contentBlocks;
-    const hide = (0, util_2.getBlockLabelKeysToHide)(dblocks, viewHeight, offsetPx);
-    const theme = (0, material_1.useTheme)();
-    const vviewSnap = {
-        ...(0, mobx_state_tree_1.getSnapshot)(vview),
-        width,
-        staticBlocks: vview.staticBlocks,
-    };
-    const ticks = vticks
-        .map(tick => {
-        var _a;
-        return [
-            tick,
-            (_a = (0, Base1DUtils_1.bpToPx)({
-                refName: tick.refName,
-                coord: tick.base,
-                self: vviewSnap,
-            })) === null || _a === void 0 ? void 0 : _a.offsetPx,
-        ];
-    })
-        .filter(f => f[1] !== undefined)
-        .map(f => [f[0], f[1] - offsetPx]);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [dblocks
-                .filter(region => !hide.has(region.key))
-                .map(region => {
-                const y = region.offsetPx;
-                const x = borderX;
-                const yoff = Math.floor(viewHeight - y + offsetPx);
-                return ((0, jsx_runtime_1.jsx)("text", { transform: `rotate(${vtextRotation},${x},${y})`, x: x, y: yoff, fontSize: 11, textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary), children: region.refName }, JSON.stringify(region)));
-            }), ticks.map(([tick, y]) => y > 0 ? ((0, jsx_runtime_1.jsx)("line", { y1: viewHeight - y, y2: viewHeight - y, x1: borderX, x2: borderX - (tick.type === 'major' ? 6 : 4), strokeWidth: 1, ...(0, util_1.getStrokeProps)(theme.palette.grey[400]) }, `line-${JSON.stringify(tick)}`)) : null), ticks
-                .filter(t => t[0].type === 'major')
-                .map(([tick, y]) => y > 10 && y < viewHeight ? ((0, jsx_runtime_1.jsx)("text", { y: viewHeight - y - 3, x: borderX - 7, textAnchor: "end", dominantBaseline: "hanging", fontSize: 11, ...(0, util_1.getFillProps)(theme.palette.text.primary), children: (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx) }, `text-${JSON.stringify(tick)}`)) : null), (0, jsx_runtime_1.jsx)("text", { y: (viewHeight - borderY) / 2, x: 12, transform: `rotate(-90,12,${(viewHeight - borderY) / 2})`, textAnchor: "middle", fontSize: 11, ...(0, util_1.getFillProps)(theme.palette.text.primary), children: vview.assemblyNames.join(',') })] }));
-});

package/dist/DotplotView/components/ColorBySelector.d.ts

@@ -1,5 +0,0 @@
-import type { DotplotViewModel } from '../model';
-declare const ColorBySelector: ({ model, }: {
-    model: DotplotViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ColorBySelector;