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[ignore] | ||
.*node_modules/flow-bin.* | ||
.*node_modules/jsxhint.* | ||
.*build.* | ||
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[include] | ||
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/* @flow */ | ||
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var Interval = require('./Interval'); | ||
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/** | ||
* Class representing a closed interval on the genome: contig:start-stop. | ||
* | ||
* The contig may be either a string ("chr22") or a number (in case the contigs | ||
* are indexed, for example). | ||
*/ | ||
class ContigInterval { | ||
contig: string|number; | ||
interval: Interval; | ||
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constructor(contig: string|number, start: number, stop: number) { | ||
this.contig = contig; | ||
this.interval = new Interval(start, stop); | ||
} | ||
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// TODO: make these getter methods & switch to Babel. | ||
start(): number { | ||
return this.interval.start; | ||
} | ||
stop(): number { | ||
return this.interval.stop; | ||
} | ||
length(): number { | ||
return this.interval.length(); | ||
} | ||
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intersects(other: ContigInterval): boolean { | ||
return (this.contig === other.contig && | ||
this.interval.intersects(other.interval)); | ||
} | ||
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toString(): string { | ||
return `${this.contig}:${this.start()}-${this.stop()}`; | ||
} | ||
} | ||
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module.exports = ContigInterval; |
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/** | ||
* Class representing a closed numeric interval, [start, stop]. | ||
* | ||
* @flow | ||
*/ | ||
class Interval { | ||
start: number; | ||
stop: number; | ||
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// Represents [start, stop] -- both ends are inclusive. | ||
// If stop < start, then this is an empty interval. | ||
constructor(start: number, stop: number) { | ||
this.start = start; | ||
this.stop = stop; | ||
} | ||
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// TODO: make this a getter method & switch to Babel. | ||
length(): number { | ||
return Math.max(0, this.stop - this.start + 1); | ||
} | ||
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intersect(other: Interval): Interval { | ||
return new Interval(Math.max(this.start, other.start), | ||
Math.min(this.stop, other.stop)); | ||
} | ||
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intersects(other: Interval): boolean { | ||
return this.start <= other.stop && other.start <= this.stop; | ||
} | ||
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contains(value: number): boolean { | ||
return value >= this.start && value <= this.stop; | ||
} | ||
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clone(): Interval { | ||
return new Interval(this.start, this.stop); | ||
} | ||
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static intersectAll(intervals: Array<Interval>): Interval { | ||
if (!intervals.length) { | ||
throw new Error('Tried to intersect zero intervals'); | ||
} | ||
var result = intervals[0].clone(); | ||
intervals.slice(1).forEach(function({start, stop}) { | ||
result.start = Math.max(start, result.start); | ||
result.stop = Math.min(stop, result.stop); | ||
}); | ||
return result; | ||
} | ||
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// Returns an interval which contains all the given intervals. | ||
static boundingInterval(intervals: Array<Interval>): Interval { | ||
if (!intervals.length) { | ||
throw new Error('Tried to bound zero intervals'); | ||
} | ||
var result = intervals[0].clone(); | ||
intervals.slice(1).forEach(function({start, stop}) { | ||
result.start = Math.min(start, result.start); | ||
result.stop = Math.max(stop, result.stop); | ||
}); | ||
return result; | ||
} | ||
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toString(): string { | ||
return `[${this.start}, ${this.stop}]`; | ||
} | ||
} | ||
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module.exports = Interval; |
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/** | ||
* Grab-bag of utility functions. | ||
* @flow | ||
*/ | ||
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// Compare two tuples of equal length. Is t1 <= t2? | ||
// TODO: make this tupleLessOrEqual<T> -- it works with strings or booleans, too. | ||
function tupleLessOrEqual(t1: Array<number>, t2: Array<number>): boolean { | ||
if (t1.length != t2.length) throw new Error('Comparing non-equal length tuples'); | ||
for (var i = 0; i < t1.length; i++) { | ||
if (t1[i] > t2[i]) { | ||
return false; | ||
} else if (t1[i] < t2[i]) { | ||
return true; | ||
} | ||
} | ||
return true; | ||
} | ||
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// Do two ranges of tuples overlap? | ||
// TODO: make this tupleRangeOverlaps<T> -- it works with strings or booleans, too. | ||
function tupleRangeOverlaps(tupleRange1: Array<Array<number>>, | ||
tupleRange2: Array<Array<number>>): boolean { | ||
return ( | ||
// Are the ranges overlapping? | ||
tupleLessOrEqual(tupleRange1[0], tupleRange2[1]) && | ||
tupleLessOrEqual(tupleRange2[0], tupleRange1[1]) && | ||
// ... and non-empty? | ||
tupleLessOrEqual(tupleRange1[0], tupleRange1[1]) && | ||
tupleLessOrEqual(tupleRange2[0], tupleRange2[1])); | ||
} | ||
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module.exports = {tupleLessOrEqual, tupleRangeOverlaps}; |
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var chai = require('chai'); | ||
var expect = chai.expect; | ||
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var ContigInterval = require('../src/ContigInterval'); | ||
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describe('ContigInterval', function() { | ||
it('should have basic accessors', function() { | ||
var tp53 = new ContigInterval(10, 7512444, 7531643); | ||
expect(tp53.toString()).to.equal('10:7512444-7531643'); | ||
expect(tp53.contig).to.equal(10); | ||
expect(tp53.start()).to.equal(7512444); | ||
expect(tp53.stop()).to.equal(7531643); | ||
expect(tp53.length()).to.equal(19200); | ||
}); | ||
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it('should determine intersections', function() { | ||
var tp53 = new ContigInterval(10, 7512444, 7531643); | ||
var other = new ContigInterval(10, 7512444, 7531642); | ||
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expect(tp53.intersects(other)).to.be.true; | ||
}); | ||
}); |
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var chai = require('chai'); | ||
var expect = chai.expect; | ||
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var Interval = require('../src/Interval'); | ||
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describe('Interval', function() { | ||
it('should have start/stop/length', function() { | ||
var x = new Interval(10, 20); | ||
expect(x.start).to.equal(10); | ||
expect(x.stop).to.equal(20); | ||
expect(x.length()).to.equal(11); | ||
expect(x.toString()).to.equal('[10, 20]'); | ||
}); | ||
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it('should determine containment', function() { | ||
var x = new Interval(-10, 10); | ||
expect(x.contains(0)).to.be.true; | ||
expect(x.contains(-10)).to.be.true; | ||
expect(x.contains(+10)).to.be.true; | ||
expect(x.contains(+11)).to.be.false; | ||
expect(x.contains(-11)).to.be.false; | ||
}); | ||
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it('should work with empty intervals', function() { | ||
var empty = new Interval(5, 0), | ||
other = new Interval(-10, 10); | ||
expect(empty.contains(0)).to.be.false; | ||
expect(empty.length()).to.equal(0); | ||
expect(empty.intersect(other).length()).to.equal(0); | ||
}); | ||
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it('should determine intersections', function() { | ||
var tp53 = new Interval(7512444, 7531643); | ||
var other = new Interval(7512444, 7531642); | ||
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expect(tp53.intersects(other)).to.be.true; | ||
}); | ||
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it('should clone', function() { | ||
var x = new Interval(0, 5), | ||
y = x.clone(); | ||
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y.start = 1; | ||
expect(x.start).to.equal(0); | ||
expect(y.start).to.equal(1); | ||
}); | ||
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it('should intersect many intervals', function() { | ||
var ivs = [ | ||
new Interval(0, 10), | ||
new Interval(5, 15), | ||
new Interval(-5, 5) | ||
]; | ||
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var intAll = Interval.intersectAll; | ||
expect(intAll( ivs ).toString()).to.equal('[5, 5]'); | ||
expect(intAll([ivs[0], ivs[1]]).toString()).to.equal('[5, 10]'); | ||
expect(intAll([ivs[0], ivs[2]]).toString()).to.equal('[0, 5]'); | ||
expect(intAll([ivs[0] ]).toString()).to.equal('[0, 10]'); | ||
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expect(() => intAll([])).to.throw(/intersect zero intervals/); | ||
}); | ||
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it('should construct bounding intervals', function() { | ||
var ivs = [ | ||
new Interval(0, 10), | ||
new Interval(5, 15), | ||
new Interval(-5, 5) | ||
]; | ||
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var bound = Interval.boundingInterval; | ||
expect(bound( ivs ).toString()).to.equal('[-5, 15]'); | ||
expect(bound([ivs[0], ivs[1]]).toString()).to.equal('[0, 15]'); | ||
expect(bound([ivs[0], ivs[2]]).toString()).to.equal('[-5, 10]'); | ||
expect(bound([ivs[0] ]).toString()).to.equal('[0, 10]'); | ||
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expect(() => bound([])).to.throw(/bound zero intervals/); | ||
}); | ||
}); |
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var chai = require('chai'); | ||
var expect = chai.expect; | ||
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var utils = require('../src/utils'); | ||
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describe('utils', function() { | ||
describe('tupleLessOrEqual', function() { | ||
var lessEqual = utils.tupleLessOrEqual; | ||
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it('should work on 1-tuples', function() { | ||
expect(lessEqual([0], [1])).to.be.true; | ||
expect(lessEqual([1], [0])).to.be.false; | ||
expect(lessEqual([0], [0])).to.be.true; | ||
}); | ||
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it('should work on 2-tuples', function() { | ||
expect(lessEqual([0, 1], [0, 2])).to.be.true; | ||
expect(lessEqual([0, 1], [0, 0])).to.be.false; | ||
expect(lessEqual([0, 1], [1, 0])).to.be.true; | ||
}); | ||
}); | ||
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describe('tupleRangeOverlaps', function() { | ||
var overlap = utils.tupleRangeOverlaps; | ||
it('should work on 1-tuples', function() { | ||
var ivs = [ | ||
[[0], [10]], | ||
[[5], [15]], | ||
[[-5], [5]], | ||
[[-5], [4]] | ||
]; | ||
var empty = [[4], [3]]; | ||
expect(overlap(ivs[0], ivs[1])).to.be.true; | ||
expect(overlap(ivs[0], ivs[2])).to.be.true | ||
expect(overlap(ivs[1], ivs[3])).to.be.false | ||
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expect(overlap(ivs[0], empty)).to.be.false | ||
expect(overlap(ivs[1], empty)).to.be.false | ||
expect(overlap(ivs[2], empty)).to.be.false | ||
expect(overlap(ivs[3], empty)).to.be.false | ||
}); | ||
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it('should work on 2-tuples', function() { | ||
expect(overlap([[0, 0], [0, 10]], | ||
[[0, 5], [0, 15]])).to.be.true; | ||
expect(overlap([[0, 0], [0, 10]], | ||
[[-1, 15], [0, 0]])).to.be.true; | ||
expect(overlap([[0, 0], [0, 10]], | ||
[[-1, 15], [1, -15]])).to.be.true; | ||
expect(overlap([[0, 0], [0, 10]], | ||
[[-1, 15], [0, -1]])).to.be.false; | ||
expect(overlap([[0, 0], [0, 10]], | ||
[[-1, 15], [0, 0]])).to.be.true; | ||
expect(overlap([[0, 0], [0, 10]], | ||
[[0, 10], [0, 11]])).to.be.true; | ||
expect(overlap([[1, 0], [3, 10]], | ||
[[-1, 10], [2, 1]])).to.be.true; | ||
expect(overlap([[3, 0], [3, 10]], | ||
[[-1, 10], [2, 1]])).to.be.false; | ||
}); | ||
}); | ||
}); |