@gmod/jbrowse/src/JBrowse/Model/Range.js

JBrowse - client-side genome browser

define( [
            'dojo/_base/declare'
        ],
        function( declare ) {
var Range = declare( null,
/**
 * @lends JBrowse.Model.Range.prototype
 */
{

    /**
     * Adapted from a combination of Range and _Compound in the
     * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
     */
    constructor: function() {
        this._ranges =
            arguments.length == 2 ? [ { min: arguments[0], max: arguments[1] } ] :
            0 in arguments[0]     ? dojo.clone( arguments[0] )                   :
                                    [ arguments[0] ];
    },

    min: function() {
        return this._ranges[0].min;
    },

    max: function() {
        return this._ranges[this._ranges.length - 1].max;
    },

    contains: function(pos) {
        for (var s = 0; s < this._ranges.length; ++s) {
            var r = this._ranges[s];
            if ( r.min <= pos && r.max >= pos ) {
                return true;
            }
        }
        return false;
    },

    isContiguous: function() {
        return this._ranges.length > 1;
    },

    ranges: function() {
        return this._ranges.map( function(r) {
            return new Range( r.min, r.max );
        });
    },

    toString: function() {
        return this._ranges
            .map(function(r) { return '['+r.min+'-'+r.max+']'; })
            .join(',');
    },

    union: function(s1) {
        var s0 = this;
        var ranges = s0.ranges().concat(s1.ranges()).sort( this.rangeOrder );
        var oranges = [];
        var current = ranges[0];

        for (var i = 1; i < ranges.length; ++i) {
            var nxt = ranges[i];
            if (nxt.min() > (current.max() + 1)) {
                oranges.push(current);
                current = nxt;
            } else {
                if (nxt.max() > current.max()) {
                    current = new Range(current.min(), nxt.max());
                }
            }
        }
        oranges.push(current);

        if (oranges.length == 1) {
            return oranges[0];
        } else {
            return new Range(oranges);
        }
    },

    intersection: function( s1 ) {
        var s0 = this;
        var r0 = s0.ranges();
        var r1 = s1.ranges();
        var l0 = r0.length, l1 = r1.length;
        var i0 = 0, i1 = 0;
        var or = [];

        while (i0 < l0 && i1 < l1) {
            var s0 = r0[i0], s1 = r1[i1];
            var lapMin = Math.max(s0.min(), s1.min());
            var lapMax = Math.min(s0.max(), s1.max());
            if (lapMax >= lapMin) {
                or.push(new Range(lapMin, lapMax));
            }
            if (s0.max() > s1.max()) {
                ++i1;
            } else {
                ++i0;
            }
        }

        if (or.length == 0) {
            return null; // FIXME
        } else if (or.length == 1) {
            return or[0];
        } else {
            return new Range(or);
        }
    },

    coverage: function() {
        var tot = 0;
        var rl = this.ranges();
        for (var ri = 0; ri < rl.length; ++ri) {
            var r = rl[ri];
            tot += (r.max() - r.min() + 1);
        }
        return tot;
    },

    rangeOrder: function( a, b ) {
        if( arguments.length < 2 ) {
            b = a;
            a = this;
        }

        if (a.min() < b.min()) {
            return -1;
        } else if (a.min() > b.min()) {
            return 1;
        } else if (a.max() < b.max()) {
            return -1;
        } else if (b.max() > a.max()) {
            return 1;
        } else {
            return 0;
        }
    }
});

return Range;
});