void ValidateFindMatchSuffixGeneralTestCases(string nodeName, bool isFilePath,
bool isMultiSequenceSearchFile, PhaseOneAmbiguityParameters isAmbiguousCharacter)
{
ISequence referenceSeq;
ISequence querySeq;
string referenceSequence = string.Empty;
string querySequence = string.Empty;
IEnumerable<ISequence> referenceSeqs;
IEnumerable<ISequence> querySeqs = null;
if (isFilePath)
{
// Gets the reference sequence from the configuration file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format(null, "MUMmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastAParser parser = new FastAParser();
switch (isAmbiguousCharacter)
{
case PhaseOneAmbiguityParameters.Dna:
parser.Alphabet = AmbiguousDnaAlphabet.Instance;
break;
case PhaseOneAmbiguityParameters.Rna:
parser.Alphabet = AmbiguousRnaAlphabet.Instance;
break;
default:
break;
}
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(null, "MUMmer BVT : Successfully validated the Search File Path '{0}'.", queryFilePath));
FastAParser queryParser = new FastAParser();
switch (isAmbiguousCharacter)
{
case PhaseOneAmbiguityParameters.Dna:
queryParser.Alphabet = AmbiguousDnaAlphabet.Instance;
break;
case PhaseOneAmbiguityParameters.Rna:
queryParser.Alphabet = AmbiguousRnaAlphabet.Instance;
break;
default:
break;
}
querySeqs = queryParser.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 referenceAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(referenceAlphabet),
this.encodingObj.GetBytes(referenceSequence));
querySequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceNode);
referenceAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(referenceAlphabet),
this.encodingObj.GetBytes(querySequence));
}
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Builds the suffix for the reference sequence passed.
MultiWaySuffixTree suffixTreeBuilder = new MultiWaySuffixTree(referenceSeq as Sequence);
suffixTreeBuilder.MinLengthOfMatch = long.Parse(mumLength, null);
IEnumerable<Match> matches = suffixTreeBuilder.SearchMatchesUniqueInReference(querySeq);
// For multi sequence query file validate all the sequences with the reference sequence
if (isMultiSequenceSearchFile)
{
matches = suffixTreeBuilder.SearchMatchesUniqueInReference(querySeqs.ElementAt(0));
Assert.IsTrue(this.ValidateUniqueMatches(matches, nodeName));
matches = suffixTreeBuilder.SearchMatchesUniqueInReference(querySeqs.ElementAt(1));
Assert.IsTrue(this.ValidateUniqueMatches(matches, nodeName));
}
else
{
matches = suffixTreeBuilder.SearchMatchesUniqueInReference(querySeq);
Assert.IsTrue(this.ValidateUniqueMatches(matches, nodeName));
}
ApplicationLog.WriteLine(string.Format(null, "MUMmer P1 : Successfully validated the all the unique matches for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
}
/// <summary>
/// Validates most of the find matches suffix tree test cases with varying parameters.
/// </summary>
/// <param name="nodeName">Node name which needs to be read for execution.</param>
/// <param name="isFilePath">Is File Path?</param>
/// <param name="isAmbiguousCharacter"></param>
void ValidateFindMatchSuffixGeneralTestCases(string nodeName,
bool isFilePath, PhaseOneAmbiguityParameters isAmbiguousCharacter)
{
this.ValidateFindMatchSuffixGeneralTestCases(nodeName, isFilePath, false, isAmbiguousCharacter);
}
