void ValidateMUMsGeneralTestCases(string nodeName, bool isFilePath)
{
ISequence referenceSeq = null;
ISequence querySeq = null;
IEnumerable<ISequence> querySeqs = null;
string referenceSequence = string.Empty;
string querySequence = string.Empty;
IEnumerable<ISequence> referenceSeqs = null;
if (isFilePath)
{
// Gets the reference sequence from the configurtion file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastAParser parser = new FastAParser();
parser.Alphabet = Alphabets.DNA;
referenceSeqs = parser.Parse(filePath);
referenceSeq = referenceSeqs.ElementAt(0);
referenceSequence = new string(referenceSeq.Select(a => (char)a).ToArray());
// Gets the reference sequence from the configuration file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer BVT : Successfully validated the Search File Path '{0}'.", queryFilePath));
querySeqs = parser.Parse(queryFilePath);
querySeq = querySeqs.ElementAt(0);
querySequence = new string(querySeq.Select(a => (char)a).ToArray());
}
else
{
// Gets the reference sequence from the configurtion file
referenceSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SequenceNode);
string referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet),
this.encodingObj.GetBytes(referenceSequence));
querySequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceNode);
referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet),
this.encodingObj.GetBytes(querySequence));
querySeqs = new List<ISequence>() { querySeq };
}
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
Bio.Algorithms.MUMmer.MUMmer mum = new Bio.Algorithms.MUMmer.MUMmer(referenceSeq as Sequence);
mum.LengthOfMUM = long.Parse(mumLength, null);
IEnumerable<Match> actualResult = null;
actualResult = mum.GetMatchesUniqueInReference(querySeqs.ElementAt(0));
// Validate MUMs output.
Assert.IsTrue(this.ValidateMums(nodeName, actualResult));
ApplicationLog.WriteLine("MUMmer BVT : Successfully validated the Mumms.");
}
/// <summary>
/// Validates Longest Increasing sequences.
/// </summary>
/// <param name="nodeName">Node name which needs to be read for execution.</param>
/// <param name="isFilePath">Is File Path?</param>
void ValidateLongestIncreasingSubsequenceTestCases(string nodeName, bool isFilePath)
{
ISequence referenceSeq = null;
ISequence querySeq = null;
string referenceSequence = string.Empty;
string querySequence = string.Empty;
IEnumerable<ISequence> referenceSeqs = null;
if (isFilePath)
{
// Gets the reference sequence from the configurtion file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastAParser parser = new FastAParser();
referenceSeqs = parser.Parse(filePath);
referenceSeq = referenceSeqs.ElementAt(0);
referenceSequence = new string(referenceSeq.Select(a => (char)a).ToArray());
// Gets the reference sequence from the configuration file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer BVT : Successfully validated the Search File Path '{0}'.", queryFilePath));
IEnumerable<ISequence> querySeqs = null;
querySeqs = parser.Parse(queryFilePath);
querySeq = querySeqs.ElementAt(0);
querySequence = new string(querySeq.Select(a => (char)a).ToArray());
}
else
{
// Gets the reference sequence from the configuration file
referenceSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SequenceNode);
string seqAlp = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(seqAlp),
referenceSequence);
querySequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceNode);
seqAlp = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(seqAlp),
querySequence);
}
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
IEnumerable<Match> matches;
Bio.Algorithms.MUMmer.MUMmer mum = new Bio.Algorithms.MUMmer.MUMmer(referenceSeq as Sequence);
mum.LengthOfMUM = long.Parse(mumLength);
matches = mum.GetMatchesUniqueInReference(querySeq);
// Validates the Unique Matches.
ApplicationLog.WriteLine("MUMmer BVT : Validating the Unique Matches using LIS");
LongestIncreasingSubsequence lisObj = new LongestIncreasingSubsequence();
List<Match> listMatch = new List<Match>();
foreach (Match mtch in matches)
{
listMatch.Add(mtch);
}
IList<Match> lisSorted = null, actualLis = null;
lisSorted = lisObj.SortMum(listMatch);
actualLis = lisObj.GetLongestSequence(lisSorted);
Assert.IsTrue(this.ValidateUniqueMatches(actualLis, nodeName, LISParameters.PerformLIS));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer BVT : Successfully validated the all the unique matches for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
}
public void ValidateGetMumsWithMaxMatchWithOneLineSequence()
{
// Gets the reference sequence from the configurtion file
string referenceSequence = this.utilityObj.xmlUtil.GetTextValue(Constants.OneLineSequenceNodeName,
Constants.SequenceNode);
string referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(Constants.OneLineSequenceNodeName,
Constants.AlphabetNameNode);
ISequence referenceSeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet),
this.encodingObj.GetBytes(referenceSequence));
string querySequence = this.utilityObj.xmlUtil.GetTextValue(Constants.OneLineSequenceNodeName,
Constants.SearchSequenceNode);
referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(Constants.OneLineSequenceNodeName,
Constants.SearchSequenceAlphabetNode);
ISequence querySeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet),
this.encodingObj.GetBytes(querySequence));
string mumLength = this.utilityObj.xmlUtil.GetTextValue(Constants.OneLineSequenceNodeName, Constants.MUMLengthNode);
Bio.Algorithms.MUMmer.MUMmer mum = new Bio.Algorithms.MUMmer.MUMmer(referenceSeq as Sequence);
mum.LengthOfMUM = long.Parse(mumLength, null);
IEnumerable<Match> actualResult = null;
actualResult = mum.GetMatches(querySeq);
// Validate MUMs output.
Assert.IsTrue(this.ValidateMums(Constants.OneLineSequenceNodeName, actualResult));
ApplicationLog.WriteLine("MUMmer BVT : Successfully validated the Mumms.");
}