roi.js

/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2016-2017 The Regents of the University of California
 * Author: Jim Robinson
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
import FeatureSource from './feature/featureSource.js'
import IGVGraphics from "./igv-canvas.js";

var defaultHighlightColor = "rgba(68, 134, 247, 0.25)";

const ROI = function (config, genome) {
    this.config = config;
    this.name = config.name;
    this.roiSource = new FeatureSource(config, genome);
    this.color = config.color || defaultHighlightColor;
};

ROI.prototype.getFeatures = function (chr, start, end) {

    return this.roiSource.getFeatures(chr, start, end);
};

ROI.prototype.draw = function (drawConfiguration) {

    var endBP,
        region,
        coord,
        regions,
        len;

    regions = drawConfiguration.features;
    if (!regions) {
        return;
    }

    endBP = drawConfiguration.bpStart + (drawConfiguration.pixelWidth * drawConfiguration.bpPerPixel + 1);
    for (var i = 0, len = regions.length; i < len; i++) {

        region = regions[i];
        if (region.end < drawConfiguration.bpStart) {
            continue;
        }

        if (region.start > endBP) {
            break;
        }

        coord = coordinates(region, drawConfiguration.bpStart, drawConfiguration.bpPerPixel);
        IGVGraphics.fillRect(drawConfiguration.context, coord.x, 0, coord.width, drawConfiguration.pixelHeight, {fillStyle: this.color});
    }


};

function coordinates(region, startBP, bpp) {

    var ss,
        ee,
        width;

    ss = Math.round((region.start - startBP) / bpp);
    ee = Math.round((region.end - startBP) / bpp);
    width = ee - ss;

    if (width < 3) {
        width = 3;
        ss -= 1;
    }

    return {x: ss, width: width};
}

export default ROI