public void TestStreamingPersistentSegmentedSequence()
{
string sequenceString = "AAATTGGC";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
SegmentedSequence segmentedSequece = new SegmentedSequence(sequence);
sequenceString = "ANANA";
sequence = new Sequence(Alphabets.Protein, sequenceString);
segmentedSequece.Sequences.Add(sequence);
using (SimpleSuffixTreeBuilder simpleSuffixTreeBuilder = new SimpleSuffixTreeBuilder())
{
simpleSuffixTreeBuilder.PersistenceThreshold = 0;
ISuffixTree persistentSuffixTree = simpleSuffixTreeBuilder.BuildSuffixTree(segmentedSequece);
string queryString = "AATTNANAGGC";
Sequence querySequence = new Sequence(Alphabets.Protein, queryString);
IList <MaxUniqueMatch> MUMs = simpleSuffixTreeBuilder.FindMatches(persistentSuffixTree, querySequence, 3);
// Verify the count of MUMs found
Assert.AreEqual(3, MUMs.Count);
}
}
public void TestInMemorySimpleSequence()
{
string sequenceString = "BANANA";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
using (SimpleSuffixTreeBuilder simpleSuffixTreeBuilder = new SimpleSuffixTreeBuilder())
{
IMultiWaySuffixTree inMemorySuffixTree = simpleSuffixTreeBuilder.BuildSuffixTree(sequence) as IMultiWaySuffixTree;
// Verify the edges in Suffix Tree
Assert.AreEqual(7, inMemorySuffixTree.Count);
// Verify the sequence in Suffix Tree
Assert.AreEqual(inMemorySuffixTree.Sequence.ToString(), sequenceString);
}
}
public void TestStreamingInMemorySimpleSequence()
{
string sequenceString = "AGTATGCCCCCCCCCCTGCCG";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
using (SimpleSuffixTreeBuilder simpleSuffixTreeBuilder = new SimpleSuffixTreeBuilder())
{
ISuffixTree inMemorySuffixTree = simpleSuffixTreeBuilder.BuildSuffixTree(sequence);
string queryString = "CCCCCCCCTATG";
Sequence querySequence = new Sequence(Alphabets.Protein, queryString);
IList <MaxUniqueMatch> MUMs = simpleSuffixTreeBuilder.FindMatches(inMemorySuffixTree, querySequence, 3);
// Verify the count of MUMs found
Assert.AreEqual(2, MUMs.Count);
}
}
public void TestPersistentSimpleSequence()
{
string sequenceString = "BANANA";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
using (SimpleSuffixTreeBuilder simpleSuffixTreeBuilder = new SimpleSuffixTreeBuilder())
{
simpleSuffixTreeBuilder.PersistenceThreshold = 0;
IMultiWaySuffixTree persistentSuffixTree = simpleSuffixTreeBuilder.BuildSuffixTree(sequence) as IMultiWaySuffixTree;
// Verify the edges in Suffix Tree
Assert.AreEqual(7, persistentSuffixTree.Count);
// Verify the sequence in Suffix Tree
Assert.AreEqual(persistentSuffixTree.Sequence.ToString(), sequenceString);
}
}
public void TestFindMaximumMatchPersistentInSequence()
{
string sequenceString = "BANANA";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
using (SimpleSuffixTreeBuilder simpleSuffixTreeBuilder = new SimpleSuffixTreeBuilder())
{
simpleSuffixTreeBuilder.PersistenceThreshold = 0;
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);
}
}
