/// <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="additionalParam">LIS action type enum</param>
void ValidateFindMatchSuffixGeneralTestCases(string nodeName, bool isFilePath,
AdditionalParameters additionalParam)
{
ISequence referenceSeqs;
var searchSeqList = new List<ISequence>();
if (isFilePath)
{
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
FastAParser parser = new FastAParser();
IEnumerable<ISequence> referenceSeqList = parser.Parse(filePath);
List<Byte> byteList = new List<Byte>();
foreach (ISequence seq in referenceSeqList)
{
byteList.AddRange(seq);
byteList.Add((byte)'+');
}
referenceSeqs = new Sequence(referenceSeqList.First().Alphabet.GetMummerAlphabet(), byteList.ToArray());
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
IEnumerable<ISequence> querySeqList = parser.Parse(queryFilePath);
searchSeqList.AddRange(querySeqList);
}
else
{
// Gets the reference & search sequences from the configuration file
string[] referenceSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
string[] searchSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
List<ISequence> refSeqList = referenceSequences.Select(t => new Sequence(seqAlphabet, this.encodingObj.GetBytes(t))).Cast<ISequence>().ToList();
List<Byte> byteListQuery = new List<Byte>();
foreach (ISequence seq in refSeqList)
{
byteListQuery.AddRange(seq);
byteListQuery.Add((byte)'+');
}
referenceSeqs = new Sequence(refSeqList.First().Alphabet.GetMummerAlphabet(),
byteListQuery.ToArray());
searchSeqList.AddRange(searchSequences.Select(t => new Sequence(seqAlphabet, this.encodingObj.GetBytes(t))).Cast<ISequence>());
}
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Builds the suffix for the reference sequence passed.
MultiWaySuffixTree suffixTreeBuilder = new MultiWaySuffixTree(referenceSeqs as Sequence)
{
MinLengthOfMatch = long.Parse(mumLength, null)
};
var matches = new Dictionary<ISequence, IEnumerable<Match>>();
foreach (ISequence sequence in searchSeqList)
{
matches.Add(sequence,
suffixTreeBuilder.SearchMatchesUniqueInReference(sequence));
}
List<Match> mums = new List<Match>();
foreach (var a in matches.Values)
{
mums.AddRange(a);
}
switch (additionalParam)
{
case AdditionalParameters.FindUniqueMatches:
// Validates the Unique Matches.
Assert.IsTrue(this.ValidateUniqueMatches(mums, nodeName, additionalParam, isFilePath));
break;
case AdditionalParameters.PerformClusterBuilder:
// Validates the Unique Matches.
Assert.IsTrue(this.ValidateUniqueMatches(mums, nodeName, additionalParam, isFilePath));
break;
default:
break;
}
}
void ValidateFindMatchSimpleSuffixGeneralTestCases(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 configurtion 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),
this.encodingObj.GetBytes(referenceSequence));
querySequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceNode);
seqAlp = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(seqAlp),
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 = null;
matches = suffixTreeBuilder.SearchMatchesUniqueInReference(querySeq);
// Validates the Unique Matches.
ApplicationLog.WriteLine("MUMmer BVT : Validating the Unique Matches");
Assert.IsTrue(this.ValidateUniqueMatches(matches, nodeName, LISParameters.FindUniqueMatches));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer BVT : Successfully validated the all the unique matches for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
}
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));
}
