public void TestStreamingInSegmentedSequence()
{
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);
ISuffixTreeBuilder kurtzSuffixTreeBuilder = new KurtzSuffixTreeBuilder();
ApplicationLog.WriteLine("Begin SuffixTree Test for string '{0}'", segmentedSequece.ToString());
SequenceSuffixTree kurtzSuffixTree = kurtzSuffixTreeBuilder.BuildSuffixTree(segmentedSequece);
string queryString = "AATTNANAGGC";
Sequence querySequence = new Sequence(Alphabets.Protein, queryString);
ApplicationLog.WriteLine("Query string : {0}. Minimum Length of MUM : 3.", queryString);
ApplicationLog.WriteTime("Start Time.", DateTime.Now.ToString());
IList <MaxUniqueMatch> MUMs = kurtzSuffixTreeBuilder.FindMatches(kurtzSuffixTree, querySequence, 3);
ApplicationLog.WriteTime("End Time.", DateTime.Now.ToString());
// Verify the count of MUMs found
Assert.AreEqual(3, MUMs.Count);
}
public void ValidateWriteTimeParamForValidLogFile()
{
string output = utilityObj.xmlUtil.GetTextValue(
Constants.ApplicationLogNode, Constants.ExpectedOutputNode);
string[] args = utilityObj.xmlUtil.GetTextValue(
Constants.ApplicationLogNode, Constants.AdditionalArgumentsNode).Split(';');
//// Open the file for write.
string[] expectedOutput = ApplicationLog.WriteTime(output, args).Split(':');
Assert.AreEqual(4, expectedOutput.Length);
Assert.AreEqual(output.Trim(), expectedOutput[3].Trim());
ApplicationLog.WriteLine(string.Concat(
"ApplicationLog BVT: Validation of WriteTime method for File completed successfully."));
}
public void TestSequence()
{
string sequenceString = "BANANA";
Sequence sequence = new Sequence(Alphabets.Protein, sequenceString);
ISuffixTreeBuilder kurtzSuffixTreeBuilder = new KurtzSuffixTreeBuilder();
ApplicationLog.WriteLine("Begin SuffixTree Test for string '{0}'", sequenceString);
ApplicationLog.WriteTime("Start Time.", DateTime.Now.ToString());
SequenceSuffixTree kurtzSuffixTree = kurtzSuffixTreeBuilder.BuildSuffixTree(sequence);
ApplicationLog.WriteTime("End Time.", DateTime.Now.ToString());
// Verify the edges in Suffix Tree
Assert.AreEqual(10, kurtzSuffixTree.Edges.Count);
// Verify the sequence in Suffix Tree
Assert.AreEqual(kurtzSuffixTree.Sequence.ToString(), sequenceString);
}
