/// <summary>
/// Build Suffix Tree using reference sequence
/// </summary>
/// <param name="referenceSequence">sequence to build SuffixTree</param>
/// <returns>Suffix Tree</returns>
protected override ISuffixTree BuildSuffixTree(ISequence referenceSequence)
{
ISuffixTreeBuilder suffixTreeBuilder = Factory.CreateNew(referenceSequence);
ISuffixTree suffixTree = suffixTreeBuilder.BuildSuffixTree(referenceSequence);
return(suffixTree);
}
/// <summary>
/// Traverse the suffix tree using query sequence and return list of MUMs
/// </summary>
/// <param name="suffixTree">Suffix tree</param>
/// <param name="referenceSequence">Reference sequence</param>
/// <param name="sequence">Query sequence</param>
/// <param name="lengthOfMUM">Minimum length of MUM</param>
/// <returns>List of MUMs</returns>
protected override IList <MaxUniqueMatch> Streaming(
ISuffixTree suffixTree,
ISequence referenceSequence,
ISequence sequence,
long lengthOfMUM)
{
ISuffixTreeBuilder suffixTreeBuilder = Factory.CreateNew(referenceSequence);
return(suffixTreeBuilder.FindMatches(suffixTree, sequence, lengthOfMUM));
}
public void TestFindMaximumMatchInSequence()
{
string sequenceString = "BANANA";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
using (SimpleSuffixTreeBuilder simpleSuffixTreebldr = new SimpleSuffixTreeBuilder())
{
ISuffixTreeBuilder simpleSuffixTreeBuilder = simpleSuffixTreebldr;
ISuffixTree simpleSuffixTree = simpleSuffixTreeBuilder.BuildSuffixTree(sequence);
string queryString = "ANA";
Sequence querySequence = new Sequence(Alphabets.Protein, queryString);
IList <MaxUniqueMatch> MUMs = simpleSuffixTreeBuilder.FindMaximumMatches(simpleSuffixTree, querySequence, 3);
// Verify the count of MUMs found
Assert.AreEqual(1, MUMs.Count);
simpleSuffixTreeBuilder = null;
}
}
