/// <summary>
/// Method that finds the index of the 2 strings that have the maximum overlap
/// </summary>
/// <returns>The index of 2 strings with max overlap and the merged string of the 2 fragments</returns>
public Tuple <int, int, string> FindMaxOverlap()
{
//nested loop to grab all unique fragment pairs to find overlap for
for (int i = 0; i < fragmentCollection.Count; i++)
{
for (int j = i + 1; j < fragmentCollection.Count; j++)
{
OverlapFinder finder = new OverlapFinder(fragmentCollection[i], fragmentCollection[j]);
var overlapResults = finder.FindOverlap();
//As we interate through each permutation, check if the current overlap is more than the previous max overlap
//Overwrite the old overlap details if the current overlap is longer
if (overlapResults.Item1 > maxOverlap)
{
maxOverlap = overlapResults.Item1;
index1 = i;
index2 = j;
mergedFragment = overlapResults.Item2;
}
}
}
return(Tuple.Create(index1, index2, mergedFragment));
}
public void OverlapFinder_BothWayMatchEqually()
{
//Arrange
string firstString = "abxy";
string secondString = "xyab";
int expectedOverlap = 2;
string expectedMergedString = "abxyab";
//Act
GenomeSequencing.OverlapFinder finder = new GenomeSequencing.OverlapFinder(firstString, secondString);
var result = finder.FindOverlap();
//Assert
Assert.AreEqual(expectedOverlap, result.Item1);
Assert.AreEqual(expectedMergedString, result.Item2);
}
public void OverlapFinder_SecondStringContainsFirstString()
{
//Arrange
string firstString = "ell";
string secondString = "s well tha";
int expectedOverlap = 3;
string expectedMergedString = "s well tha";
//Act
GenomeSequencing.OverlapFinder finder = new GenomeSequencing.OverlapFinder(firstString, secondString);
var result = finder.FindOverlap();
//Assert
Assert.AreEqual(expectedOverlap, result.Item1);
Assert.AreEqual(expectedMergedString, result.Item2);
}
public void NoMatchTest()
{
//Arrange
string firstString = "abc";
string secondString = "xyz";
int expectedOverlap = 0;
string expectedMergedString = "abcxyz";
//Act
GenomeSequencing.OverlapFinder finder = new GenomeSequencing.OverlapFinder(firstString, secondString);
var result = finder.FindOverlap();
//Assert
Assert.AreEqual(expectedOverlap, result.Item1);
Assert.AreEqual(expectedMergedString, result.Item2);
}
public void OverlapFinder_SecondStringOneCharLongMiddleMatch()
{
//Arrange
string firstString = "abc";
string secondString = "b";
int expectedOverlap = 1;
string expectedMergedString = "abc";
//Act
GenomeSequencing.OverlapFinder finder = new GenomeSequencing.OverlapFinder(firstString, secondString);
var result = finder.FindOverlap();
//Assert
Assert.AreEqual(expectedOverlap, result.Item1);
Assert.AreEqual(expectedMergedString, result.Item2);
}
public void OverlapFinder_PostfixMatchesPrefix()
{
//Arrange
string firstString = "abij";
string secondString = "ijxy";
int expectedOverlap = 2;
string expectedMergedString = "abijxy";
//Act
GenomeSequencing.OverlapFinder finder = new GenomeSequencing.OverlapFinder(firstString, secondString);
var result = finder.FindOverlap();
//Assert
Assert.AreEqual(expectedOverlap, result.Item1);
Assert.AreEqual(expectedMergedString, result.Item2);
}