public static IEnumerable <Coverage> EstimateIncreasingCoverages(this IEnumerable <MatchedWith> matches, double queryLength, double trackLength, double fingerprintLength, double permittedGap)
{
var sequences = LongestIncreasingTrackSequence.FindAllIncreasingTrackSequences(matches, permittedGap);
var coverages = sequences.Select(sequence => new Coverage(sequence, queryLength, trackLength, fingerprintLength, permittedGap));
return(OverlappingRegionFilter.FilterCrossMatchedCoverages(coverages));
}
public void ShouldNotFailWithJustOneEntryAtTheInput()
{
var matches = new List <Matches> {
new Matches(TestUtilities.GetMatchedWith(new[] { 1 }, new[] { 1 }))
};
var result = OverlappingRegionFilter.MergeOverlappingSequences(matches, PermittedGap);
Assert.AreEqual(1, result.Count());
}
public void ShouldMergeOverlappingRegionsWithLongestInFront()
{
var result = OverlappingRegionFilter.MergeOverlappingSequences(
new List <Matches>
{
new Matches(TestUtilities.GetMatchedWith(new[] { 0, 1, 3, 4 }, new[] { 0, 1, 2, 3 }).ToList()),
new Matches(TestUtilities.GetMatchedWith(new[] { 2 }, new[] { 1 }).ToList())
}, PermittedGap)
.ToList();
Assert.AreEqual(1, result.Count);
CollectionAssert.AreEqual(new float[] { 0, 1, 2, 3, 4 }, result[0].Select(with => with.QueryMatchAt));
}
public void ShouldFilterOverlappingRegionsWithLongestInFront2()
{
var result = OverlappingRegionFilter.FilterOverlappingSequences(
new List <List <MatchedWith> >
{
TestUtilities.GetMatchedWith(new float[] { 0, 1, 2 }, new float[] { 0, 1, 2 }).ToList(),
TestUtilities.GetMatchedWith(new float[] { 4, 5 }, new float[] { 4, 5 }).ToList()
})
.ToList();
Assert.AreEqual(2, result.Count);
CollectionAssert.AreEqual(new float[] { 0, 1, 2 }, result[0].Select(with => with.QueryAt));
CollectionAssert.AreEqual(new float[] { 4, 5 }, result[1].Select(with => with.QueryAt));
}
public void ShouldIdentifyThatItIsContainedWithinItself()
{
// a ------------
// b ---
var a = TestUtilities.GetMatchedWith(new[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }, new[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }).EstimateCoverage(10, 10, 1, 1);
var b = TestUtilities.GetMatchedWith(new[] { 4, 5, 6 }, new[] { 4, 5, 6 }).EstimateCoverage(3, 3, 1, 1);
Assert.IsTrue(a.Contains(b));
Assert.IsFalse(b.Contains(a));
var results = OverlappingRegionFilter.FilterCrossMatchedCoverages(new[] { a, b }).ToList();
Assert.AreEqual(1, results.Count);
Assert.AreSame(a, results.First());
}
public void ShouldFilterOverlappingRegionsWithLongestInTheBack()
{
var result = OverlappingRegionFilter.MergeOverlappingSequences(
new List <Matches>
{
new Matches(TestUtilities.GetMatchedWith(new[] { 4, 6, 7, 9, 10 }, new[] { 4, 5, 6, 7, 9 }).ToList()),
new Matches(TestUtilities.GetMatchedWith(new[] { 10, 11, 17 }, new[] { 10, 11, 12 }).ToList()),
new Matches(TestUtilities.GetMatchedWith(new[] { 0, 1, 2 }, new[] { 0, 1, 2 }).ToList()),
new Matches(TestUtilities.GetMatchedWith(new[] { 5 }, new[] { 5 }).ToList()),
new Matches(TestUtilities.GetMatchedWith(new[] { 6 }, new[] { 6 }).ToList())
}, PermittedGap)
.ToList();
Assert.AreEqual(2, result.Count);
CollectionAssert.AreEqual(new float[] { 4, 5, 6, 7, 9, 10, 11, 17 }, result[0].Select(with => with.QueryMatchAt));
CollectionAssert.AreEqual(new float[] { 0, 1, 2 }, result[1].Select(with => with.QueryMatchAt));
}
