/// <summary>
/// Concat all the sequences into one sequence with special character.
/// </summary>
/// <param name="sequences">List of reference sequence.</param>
/// <returns>Concatenated sequence.</returns>
protected static ISequence ConcatSequence(IEnumerable <ISequence> sequences)
{
if (sequences == null)
{
throw new ArgumentNullException("sequences");
}
// Add the Concatenating symbol to every sequence in reference list
// Note that, as of now protein sequence is being created out
// of input sequence add concatenation character "X" to it to
// simplify implementation.
List <byte> referenceSequence = null;
foreach (ISequence sequence in sequences)
{
if (null == referenceSequence)
{
referenceSequence = new List <byte>(sequence);
}
else
{
referenceSequence.AddRange(sequence);
}
// Add concatenating symbol.
referenceSequence.Add((byte)'+');
}
return(new Sequence(AlphabetExtensions.GetMummerAlphabet(sequences.ElementAt(0).Alphabet), referenceSequence.ToArray(), false));
}
void ValidateFindMatchSuffixGeneralTestCases(string nodeName, bool isFilePath,
AdditionalParameters additionalParam)
{
ISequence referenceSeqs = null;
string[] referenceSequences = null;
string[] searchSequences = null;
List <ISequence> searchSeqList = new List <ISequence>();
if (isFilePath)
{
// Gets the reference sequence from the FastA file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Successfully validated the File Path '{0}'.", filePath));
using (FastAParser parser = new FastAParser(filePath))
{
IEnumerable <ISequence> referenceSeqList = parser.Parse();
List <Byte> byteList = new List <Byte>();
foreach (ISequence seq in referenceSeqList)
{
byteList.AddRange(seq);
byteList.Add((byte)'+');
}
referenceSeqs = new Sequence(AlphabetExtensions.GetMummerAlphabet(referenceSeqList.ElementAt(0).Alphabet),
byteList.ToArray());
// Gets the query sequence from the FastA file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Successfully validated the File Path '{0}'.", queryFilePath));
FastAParser queryParser = new FastAParser(queryFilePath);
IEnumerable <ISequence> querySeqList = queryParser.Parse();
foreach (ISequence seq in querySeqList)
{
searchSeqList.Add(seq);
}
}
}
else
{
// Gets the reference & search sequences from the configurtion file
referenceSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
searchSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
List <ISequence> refSeqList = new List <ISequence>();
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(referenceSequences[i]));
refSeqList.Add(referSeq);
}
List <Byte> byteListQuery = new List <Byte>();
foreach (ISequence seq in refSeqList)
{
byteListQuery.AddRange(seq);
byteListQuery.Add((byte)'+');
}
referenceSeqs = new Sequence(AlphabetExtensions.GetMummerAlphabet(refSeqList.ElementAt(0).Alphabet),
byteListQuery.ToArray());
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(searchSequences[i]));
searchSeqList.Add(searchSeq);
}
}
string mumLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Builds the suffix for the reference sequence passed.
MultiWaySuffixTree suffixTreeBuilder = new MultiWaySuffixTree(referenceSeqs as Sequence);
suffixTreeBuilder.MinLengthOfMatch = long.Parse(mumLength, null);
Dictionary <ISequence, IEnumerable <Match> > matches =
new Dictionary <ISequence, IEnumerable <Match> >();
for (int i = 0; i < searchSeqList.Count; i++)
{
matches.Add(searchSeqList[i],
suffixTreeBuilder.SearchMatchesUniqueInReference(searchSeqList[i]));
}
List <Match> mums = new List <Match>();
foreach (var a in matches.Values)
{
mums.AddRange(a);
}
switch (additionalParam)
{
case AdditionalParameters.FindUniqueMatches:
// Validates the Unique Matches.
ApplicationLog.WriteLine("NUCmer BVT : Validating the Unique Matches");
Assert.IsTrue(ValidateUniqueMatches(mums, nodeName, additionalParam, isFilePath));
Console.WriteLine(
"NUCmer BVT : Successfully validated the all the unique matches for the sequences.");
break;
case AdditionalParameters.PerformClusterBuilder:
// Validates the Unique Matches.
ApplicationLog.WriteLine(
"NUCmer BVT : Validating the Unique Matches using Cluster Builder");
Assert.IsTrue(ValidateUniqueMatches(mums, nodeName, additionalParam, isFilePath));
Console.WriteLine(
"NUCmer BVT : Successfully validated the all the cluster builder matches for the sequences.");
break;
default:
break;
}
ApplicationLog.WriteLine(
"NUCmer BVT : Successfully validated the all the unique matches for the sequences.");
}
