/// <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="LISActionType">LIS action type enum</param>
static void ValidateFindMatchSuffixGeneralTestCases(string nodeName, bool isFilePath,
LISParameters LISActionType)
{
ISequence referenceSeq = null;
ISequence querySeq = null;
string referenceSequence = string.Empty;
string querySequence = string.Empty;
if (isFilePath)
{
// Gets the reference sequence from the configurtion file
string filePath = Utility._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();
IList <ISequence> referenceSeqs = parser.Parse(filePath);
referenceSeq = referenceSeqs[0];
referenceSequence = referenceSeq.ToString();
// Gets the reference sequence from the configurtion file
string queryFilePath = Utility._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();
IList <ISequence> querySeqs = queryParser.Parse(queryFilePath);
querySeq = querySeqs[0];
querySequence = querySeq.ToString();
}
else
{
// Gets the reference sequence from the configurtion file
referenceSequence = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SequenceNode);
string seqAlp = Utility._xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(seqAlp),
referenceSequence);
querySequence = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceNode);
seqAlp = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(seqAlp),
querySequence);
}
string mumLength = Utility._xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Builds the suffix for the reference sequence passed.
ISuffixTreeBuilder suffixTreeBuilder = new KurtzSuffixTreeBuilder();
SequenceSuffixTree suffixTree = suffixTreeBuilder.BuildSuffixTree(referenceSeq);
IList <MaxUniqueMatch> matches = suffixTreeBuilder.FindMatches(suffixTree, querySeq,
long.Parse(mumLength, null));
switch (LISActionType)
{
case LISParameters.FindUniqueMatches:
// Validates the Unique Matches.
ApplicationLog.WriteLine("MUMmer BVT : Validating the Unique Matches");
Assert.IsTrue(ValidateUniqueMatches(matches, nodeName, LISActionType));
break;
case LISParameters.PerformLIS:
// Validates the Unique Matches.
ApplicationLog.WriteLine("MUMmer BVT : Validating the Unique Matches using LIS");
LongestIncreasingSubsequence lisObj = new LongestIncreasingSubsequence();
IList <MaxUniqueMatch> lisMatches = lisObj.GetLongestSequence(matches);
Assert.IsTrue(ValidateUniqueMatches(lisMatches, nodeName, LISActionType));
break;
default:
break;
}
Console.WriteLine(string.Format(null,
"MUMmer BVT : Successfully validated the all the unique matches for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
ApplicationLog.WriteLine(string.Format(null,
"MUMmer BVT : Successfully validated the all the unique matches for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
}
/// <summary>
/// Validates the Unique Matches for the input provided.
/// </summary>
/// <param name="matches">Max Unique Match list</param>
/// <param name="nodeName">Node name to be read from xml</param>
/// <param name="LISActionType">Unique Match/Sub level LIS/LIS</param>
/// <returns>True, if successfully validated</returns>
static bool ValidateUniqueMatches(IList <MaxUniqueMatch> matches,
string nodeName, LISParameters LISActionType)
{
// Gets all the unique matches properties to be validated as in xml.
string[] firstSeqOrder = null;
string[] firstSeqStart = null;
string[] length = null;
string[] secondSeqOrder = null;
string[] secondSeqStart = null;
switch (LISActionType)
{
case LISParameters.PerformLIS:
firstSeqOrder = Utility._xmlUtil.GetTextValue(nodeName,
Constants.LisFirstSequenceMumOrderNode).Split(',');
firstSeqStart = Utility._xmlUtil.GetTextValue(nodeName,
Constants.LisFirstSequenceStartNode).Split(',');
length = Utility._xmlUtil.GetTextValue(nodeName, Constants.LisLengthNode).Split(',');
secondSeqOrder = Utility._xmlUtil.GetTextValue(nodeName,
Constants.LisSecondSequenceMumOrderNode).Split(',');
secondSeqStart = Utility._xmlUtil.GetTextValue(nodeName,
Constants.LisSecondSequenceStartNode).Split(',');
break;
case LISParameters.FindUniqueMatches:
firstSeqOrder = Utility._xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
firstSeqStart = Utility._xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceStartNode).Split(',');
length = Utility._xmlUtil.GetTextValue(nodeName, Constants.LengthNode).Split(',');
secondSeqOrder = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
secondSeqStart = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceStartNode).Split(',');
break;
default:
break;
}
int i = 0;
// Loops through all the matches and validates the same.
foreach (MaxUniqueMatch match in matches)
{
if ((0 != string.Compare(firstSeqOrder[i],
match.FirstSequenceMumOrder.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(firstSeqStart[i],
match.FirstSequenceStart.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(length[i],
match.Length.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(secondSeqOrder[i],
match.SecondSequenceMumOrder.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(secondSeqStart[i],
match.SecondSequenceStart.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture)))
{
Console.WriteLine(string.Format(null,
"MUMmer BVT : Unique match not matching at index '{0}'", i.ToString()));
ApplicationLog.WriteLine(string.Format(null,
"MUMmer BVT : Unique match not matching at index '{0}'", i.ToString()));
return(false);
}
i++;
}
return(true);
}
/// <summary>
/// Validates the Unique Matches for the input provided.
/// </summary>
/// <param name="matches">Max Unique Match list</param>
/// <param name="nodeName">Node name to be read from xml</param>
/// <param name="lisActionType"></param>
/// <returns>True, if successfully validated</returns>
bool ValidateUniqueMatches(IEnumerable<Match> matches, string nodeName, LISParameters lisActionType)
{
// Gets all the unique matches properties to be validated as in xml.
string[] firstSeqStart = null;
string[] length = null;
string[] secondSeqStart = null;
switch (lisActionType)
{
case LISParameters.PerformLIS:
firstSeqStart = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LisFirstSequenceStartNode).Split(',');
length = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.LisLengthNode).Split(',');
secondSeqStart = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LisSecondSequenceStartNode).Split(',');
break;
case LISParameters.FindUniqueMatches:
firstSeqStart = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceStartNode).Split(',');
length = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.LengthNode).Split(',');
secondSeqStart = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceStartNode).Split(',');
break;
default:
break;
}
int i = 0;
// Loops through all the matches and validates the same.
foreach (Match match in matches)
{
if ((0 != string.Compare(firstSeqStart[i],
match.ReferenceSequenceOffset.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(length[i],
match.Length.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(secondSeqStart[i],
match.QuerySequenceOffset.ToString((IFormatProvider)null), true, CultureInfo.CurrentCulture)))
{
ApplicationLog.WriteLine(string.Format("MUMmer BVT : Unique match not matching at index '{0}'", i.ToString((IFormatProvider)null)));
return false;
}
i++;
}
return true;
}
