@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.0

package/dist/LinearSyntenyDisplay/components/util.js

@@ -1,199 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawMatchSimple = drawMatchSimple;
-exports.draw = draw;
-exports.drawLocationMarkers = drawLocationMarkers;
-exports.drawBox = drawBox;
-exports.drawBezierBox = drawBezierBox;
-exports.onSynClick = onSynClick;
-exports.onSynContextClick = onSynContextClick;
-exports.getTooltip = getTooltip;
-const util_1 = require("@jbrowse/core/util");
-const drawSynteny_1 = require("../drawSynteny");
-function drawMatchSimple({ feature, ctx, offsets, level, cb, height, drawCurves, oobLimit, viewWidth, hideTiny, }) {
-    const { p11, p12, p21, p22 } = feature;
-    const x11 = p11.offsetPx - offsets[level];
-    const x12 = p12.offsetPx - offsets[level];
-    const x21 = p21.offsetPx - offsets[level + 1];
-    const x22 = p22.offsetPx - offsets[level + 1];
-    const l1 = Math.abs(x12 - x11);
-    const l2 = Math.abs(x22 - x21);
-    const y1 = 0;
-    const y2 = height;
-    const mid = (y2 - y1) / 2;
-    const minX = Math.min(x21, x22);
-    const maxX = Math.max(x21, x22);
-    if (!(0, util_1.doesIntersect2)(minX, maxX, -oobLimit, viewWidth + oobLimit)) {
-        return;
-    }
-    if (l1 <= 1 && l2 <= 1) {
-        if (!hideTiny) {
-            ctx.beginPath();
-            ctx.moveTo(x11, y1);
-            if (drawCurves) {
-                ctx.bezierCurveTo(x11, mid, x21, mid, x21, y2);
-            }
-            else {
-                ctx.lineTo(x21, y2);
-            }
-            ctx.stroke();
-        }
-    }
-    else {
-        draw(ctx, x11, x12, y1, x22, x21, y2, mid, drawCurves);
-        cb(ctx);
-    }
-}
-function draw(ctx, x1, x2, y1, x3, x4, y2, mid, drawCurves) {
-    if (drawCurves) {
-        drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid);
-    }
-    else {
-        drawBox(ctx, x1, x2, y1, x3, x4, y2);
-    }
-}
-function drawLocationMarkers(ctx, x1, x2, y1, x3, x4, y2, mid, bpPerPx1, bpPerPx2, drawCurves) {
-    const width1 = Math.abs(x2 - x1);
-    const width2 = Math.abs(x4 - x3);
-    const averageWidth = (width1 + width2) / 2;
-    if (averageWidth < 30) {
-        return;
-    }
-    const targetPixelSpacing = 20;
-    const numMarkers = Math.max(2, Math.floor(averageWidth / targetPixelSpacing) + 1);
-    const prevStrokeStyle = ctx.strokeStyle;
-    const prevLineWidth = ctx.lineWidth;
-    ctx.strokeStyle = 'rgba(0, 0, 0, 0.25)';
-    ctx.lineWidth = 0.5;
-    ctx.beginPath();
-    if (drawCurves) {
-        for (let step = 0; step < numMarkers; step++) {
-            const t = step / numMarkers;
-            const topX = x1 + (x2 - x1) * t;
-            const bottomX = x4 + (x3 - x4) * t;
-            ctx.moveTo(topX, y1);
-            ctx.bezierCurveTo(topX, mid, bottomX, mid, bottomX, y2);
-        }
-    }
-    else {
-        for (let step = 0; step < numMarkers; step++) {
-            const t = step / numMarkers;
-            const topX = x1 + (x2 - x1) * t;
-            const bottomX = x4 + (x3 - x4) * t;
-            ctx.moveTo(topX, y1);
-            ctx.lineTo(bottomX, y2);
-        }
-    }
-    ctx.stroke();
-    ctx.strokeStyle = prevStrokeStyle;
-    ctx.lineWidth = prevLineWidth;
-}
-function drawBox(ctx, x1, x2, y1, x3, x4, y2) {
-    ctx.beginPath();
-    ctx.moveTo(x1, y1);
-    ctx.lineTo(x2, y1);
-    ctx.lineTo(x3, y2);
-    ctx.lineTo(x4, y2);
-    ctx.closePath();
-}
-function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
-    const len1 = Math.abs(x1 - x2);
-    const len2 = Math.abs(x1 - x2);
-    if (len1 < 5 && len2 < 5 && x2 < x1 && Math.abs(x1 - x3) > 100) {
-        const tmp = x1;
-        x1 = x2;
-        x2 = tmp;
-    }
-    ctx.beginPath();
-    ctx.moveTo(x1, y1);
-    ctx.lineTo(x2, y1);
-    ctx.bezierCurveTo(x2, mid, x3, mid, x3, y2);
-    ctx.lineTo(x4, y2);
-    ctx.bezierCurveTo(x4, mid, x1, mid, x1, y1);
-    ctx.closePath();
-}
-function onSynClick(event, model) {
-    const view = (0, util_1.getContainingView)(model);
-    const track = (0, util_1.getContainingTrack)(model);
-    const { featPositions, numFeats, clickMapCanvas: ref1, cigarClickMapCanvas: ref2, level, } = model;
-    if (!ref1 || !ref2) {
-        return;
-    }
-    const rect = ref1.getBoundingClientRect();
-    const ctx1 = ref1.getContext('2d');
-    const ctx2 = ref2.getContext('2d');
-    if (!ctx1 || !ctx2) {
-        return;
-    }
-    const x = event.clientX - rect.left;
-    const y = event.clientY - rect.top;
-    const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data;
-    const unitMultiplier = Math.floor(drawSynteny_1.MAX_COLOR_RANGE / numFeats);
-    const id = (0, drawSynteny_1.getId)(r1, g1, b1, unitMultiplier);
-    const feat = featPositions[id];
-    if (feat) {
-        const { f } = feat;
-        model.setClickId(f.id());
-        const session = (0, util_1.getSession)(model);
-        if ((0, util_1.isSessionModelWithWidgets)(session)) {
-            session.showWidget(session.addWidget('SyntenyFeatureWidget', 'syntenyFeature', {
-                view,
-                track,
-                featureData: f.toJSON(),
-                level,
-            }));
-        }
-    }
-    return feat;
-}
-function onSynContextClick(event, model, setAnchorEl) {
-    event.preventDefault();
-    const ref1 = model.clickMapCanvas;
-    const ref2 = model.cigarClickMapCanvas;
-    if (!ref1 || !ref2) {
-        return;
-    }
-    const rect = ref1.getBoundingClientRect();
-    const ctx1 = ref1.getContext('2d');
-    const ctx2 = ref2.getContext('2d');
-    if (!ctx1 || !ctx2) {
-        return;
-    }
-    const { clientX, clientY } = event;
-    const x = clientX - rect.left;
-    const y = clientY - rect.top;
-    const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data;
-    const unitMultiplier = Math.floor(drawSynteny_1.MAX_COLOR_RANGE / model.numFeats);
-    const id = (0, drawSynteny_1.getId)(r1, g1, b1, unitMultiplier);
-    const f = model.featPositions[id];
-    if (f) {
-        model.setClickId(f.f.id());
-        setAnchorEl({
-            clientX,
-            clientY,
-            feature: f,
-        });
-    }
-}
-function getTooltip({ feature, cigarOp, cigarOpLen, }) {
-    const f1 = feature.toJSON();
-    const f2 = f1.mate;
-    const l1 = f1.end - f1.start;
-    const l2 = f2.end - f2.start;
-    const identity = f1.identity;
-    const n1 = f1.name;
-    const n2 = f2.name;
-    return [
-        `Loc1: ${(0, util_1.assembleLocString)(f1)}`,
-        `Loc2: ${(0, util_1.assembleLocString)(f2)}`,
-        `Inverted: ${f1.strand === -1}`,
-        `Query len: ${l1.toLocaleString('en-US')}`,
-        `Target len: ${l2.toLocaleString('en-US')}`,
-        identity ? `Identity: ${identity.toPrecision(2)}` : '',
-        cigarOp ? `CIGAR operator: ${(0, util_1.toLocale)(+cigarOpLen)}${cigarOp}` : '',
-        n1 ? `Name 1: ${n1}` : '',
-        n2 ? `Name 2: ${n2}` : '',
-    ]
-        .filter(f => !!f)
-        .join('<br/>');
-}

package/dist/LinearSyntenyDisplay/configSchemaF.d.ts

@@ -1,12 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    trackIds: {
-        type: string;
-        defaultValue: never[];
-    };
-    middle: {
-        type: string;
-        defaultValue: boolean;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
-export default configSchemaFactory;

package/dist/LinearSyntenyDisplay/configSchemaF.js

@@ -1,23 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const configSchemaF_1 = __importDefault(require("../LinearComparativeDisplay/configSchemaF"));
-function configSchemaFactory(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LinearSyntenyDisplay', {
-        trackIds: {
-            type: 'stringArray',
-            defaultValue: [],
-        },
-        middle: {
-            type: 'boolean',
-            defaultValue: true,
-        },
-    }, {
-        baseConfiguration: (0, configSchemaF_1.default)(pluginManager),
-        explicitlyTyped: true,
-    });
-}
-exports.default = configSchemaFactory;

package/dist/LinearSyntenyDisplay/drawSynteny.d.ts

@@ -1,6 +0,0 @@
-import type { LinearSyntenyDisplayModel } from './model';
-export declare const MAX_COLOR_RANGE: number;
-export declare function getId(r: number, g: number, b: number, unitMultiplier: number): number;
-export declare function drawCigarClickMap(model: LinearSyntenyDisplayModel, cigarClickMapCanvas: CanvasRenderingContext2D): void;
-export declare function drawRef(model: LinearSyntenyDisplayModel, mainCanvas: CanvasRenderingContext2D): void;
-export declare function drawMouseoverClickMap(model: LinearSyntenyDisplayModel): void;