/// <summary>
/// Works out the SCS of the string collection passed into the object
/// </summary>
/// <returns>The string that represents the Shortest Common Superstring</returns>
public string GetGreedySCS()
{
//while there is more than 1 string in the collection we match and merge.
//when there is 1 string left in the collection, that is Shortest Common Superstring
while (fragmentCollection.Count > 1)
{
MaxOverlapFinder maxFinder = new MaxOverlapFinder(fragmentCollection);
var result = maxFinder.FindMaxOverlap();
try
{
//delete item2 first because it will always be higher index that item1
//else get bug where item1 deleted then the indexes of the list change and deleting index item2
//is not the right index anymore because the indexes have changed after the first item removal
fragmentCollection.RemoveAt(result.Item2);
fragmentCollection.RemoveAt(result.Item1);
fragmentCollection.Add(result.Item3);
}
catch (IndexOutOfRangeException e)
{
Console.WriteLine("Error removing or adding from the collection. " + e.Message);
}
}
//FIXME better way of doing this?
return(string.Join(" ", fragmentCollection.ToArray()));
}
public void FindMaxOverlapTest()
{
//Arrange
string[] input = { "all is well", "ell that en", "hat end", "t ends well" };
List <string> collection = new List <string>(input);
int expectedIndex1 = 1;
int expectedIndex2 = 2;
string expectedMergedString = "ell that end";
//Act
GenomeSequencing.MaxOverlapFinder maxFinder = new GenomeSequencing.MaxOverlapFinder(collection);
var result = maxFinder.FindMaxOverlap();
//Assert
Assert.AreEqual(expectedIndex1, result.Item1);
Assert.AreEqual(expectedIndex2, result.Item2);
Assert.AreEqual(expectedMergedString, result.Item3);
}
