public override int GetHashCode()
{
int hashCode = Property.GetHashCode();
hashCode = GetCallStack().Skip(1).Aggregate(hashCode, (code, owner) => code ^ owner.GetHashCode());
if (PropertyParameters != null)
{
hashCode = PropertyParameters.Aggregate(hashCode, (hash, param) => hash ^ param.GetHashCode());
}
return(hashCode);
}
public Property(PropertyParameters parameters)
{
RawType = parameters.RawType;
RawPropertyInfo = parameters.RawPropertyInfo;
Name = parameters.Name;
Type = parameters.Type;
PropertyAccessModifier = parameters.PropertyAccessModifier;
HasSetter = parameters.HasSetter;
SetterAccessModifier = parameters.SetterAccessModifier;
RawSetMethod = parameters.RawSetMethod;
SetMethod = parameters.SetMethod;
HasGetter = parameters.HasGetter;
GetterAccessModifier = parameters.GetterAccessModifier;
RawGetMethod = parameters.RawGetMethod;
GetMethod = parameters.GetMethod;
}
/// <summary>
/// Validates the Cluster Builder 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="propParam">Property parameters</param>
/// <returns>True, if successfully validated</returns>
private bool ValidateClusterBuilderMatches(IEnumerable<Match> matches, string nodeName, PropertyParameters propParam)
{
// Validates the Cluster builder MUMs
string firstSeqOrderExpected = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustFirstSequenceMumOrderNode);
string lengthExpected = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustLengthNode);
string secondSeqOrderExpected = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustSecondSequenceMumOrderNode);
var firstSeqOrderActual = new StringBuilder();
var lengthActual = new StringBuilder();
var secondSeqOrderActual = new StringBuilder();
var cbObj = new ClusterBuilder {MinimumScore = 0};
switch (propParam)
{
case PropertyParameters.MinimumScore:
cbObj.MinimumScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MinimumScoreNode), null);
break;
case PropertyParameters.MaximumSeparation:
cbObj.MaximumSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MaximumSeparationNode), null);
break;
case PropertyParameters.FixedSeparation:
cbObj.FixedSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
case PropertyParameters.SeparationFactor:
cbObj.SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
break;
case PropertyParameters.FixedSeparationAndSeparationFactor:
cbObj.SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
cbObj.FixedSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
case PropertyParameters.MaximumFixedAndSeparationFactor:
cbObj.MaximumSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MaximumSeparationNode), null);
cbObj.SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
cbObj.FixedSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
default:
break;
}
var meObj = matches.Select(m => new MatchExtension(m)).ToList();
IEnumerable<Cluster> clusts = cbObj.BuildClusters(meObj);
foreach (MatchExtension maxMatchExtension in clusts.SelectMany(clust => clust.Matches))
{
firstSeqOrderActual.Append(maxMatchExtension.ReferenceSequenceOffset);
secondSeqOrderActual.Append(maxMatchExtension.QuerySequenceOffset);
lengthActual.Append(maxMatchExtension.Length);
}
if ((0 != string.Compare(firstSeqOrderExpected.Replace(",", ""), firstSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(lengthExpected.Replace(",", ""), lengthActual.ToString(), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(secondSeqOrderExpected.Replace(",", ""), secondSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture)))
{
ApplicationLog.WriteLine("NUCmer P1 : Cluster builder match not matching");
return false;
}
return true;
}
private void ValidateNUCmerAlignGeneralTestCases(string nodeName, bool isFilePath, bool isAlignList, AdditionalParameters addParam,
PropertyParameters propParam, bool isAmbiguous)
{
IList<ISequence> refSeqList = new List<ISequence>();
IList<ISequence> 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);
ApplicationLog.WriteLine(string.Format(null, "NUCmer P1 : Successfully validated the File Path '{0}'.", filePath));
var fastaparserobj = new FastAParser();
IEnumerable<ISequence> referenceSeqList = fastaparserobj.Parse(filePath);
foreach (ISequence seq in referenceSeqList)
{
refSeqList.Add(seq);
}
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format(null, "NUCmer P1 : Successfully validated the File Path '{0}'.", queryFilePath));
var queryParserobj = new FastAParser();
IEnumerable<ISequence> serSeqList = queryParserobj.Parse(queryFilePath);
foreach (ISequence seq in serSeqList)
{
searchSeqList.Add(seq);
}
}
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));
IAlphabet ambAlphabet = null;
if (isAmbiguous)
{
switch (seqAlphabet.Name.ToLower(CultureInfo.CurrentCulture))
{
case "dna":
case "ambiguousdna":
ambAlphabet = AmbiguousDnaAlphabet.Instance;
break;
case "rna":
case "ambiguousrna":
ambAlphabet = AmbiguousRnaAlphabet.Instance;
break;
case "protein":
case "ambiguousprotein":
ambAlphabet = AmbiguousProteinAlphabet.Instance;
break;
default:
break;
}
}
else
{
ambAlphabet = seqAlphabet;
}
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(ambAlphabet,
Encoding.ASCII.GetBytes(referenceSequences[i]));
referSeq.ID = "ref " + i;
refSeqList.Add(referSeq);
}
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(ambAlphabet,
Encoding.ASCII.GetBytes(searchSequences[i]));
searchSeq.ID = "qry " + i;
searchSeqList.Add(searchSeq);
}
}
// Gets the mum length from the xml
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
var nucmerObj = new NucmerPairwiseAligner();
// Check for additional parameters and update the object accordingly
switch (addParam)
{
case AdditionalParameters.AlignSimilarityMatrix:
nucmerObj.SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
break;
default:
break;
}
// Update other values for NUCmer object
nucmerObj.MaximumSeparation = 0;
nucmerObj.MinimumScore = 2;
nucmerObj.SeparationFactor = 0.12f;
nucmerObj.BreakLength = 2;
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
switch (propParam)
{
case PropertyParameters.MinimumScore:
nucmerObj.MinimumScore = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MinimumScoreNode), null);
break;
case PropertyParameters.MaximumSeparation:
nucmerObj.MaximumSeparation = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MaximumSeparationNode), null);
break;
case PropertyParameters.FixedSeparation:
nucmerObj.FixedSeparation = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
case PropertyParameters.SeparationFactor:
nucmerObj.SeparationFactor = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
break;
case PropertyParameters.FixedSeparationAndSeparationFactor:
nucmerObj.SeparationFactor = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
nucmerObj.FixedSeparation = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
case PropertyParameters.MaximumFixedAndSeparationFactor:
nucmerObj.MaximumSeparation = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MaximumSeparationNode), null);
nucmerObj.SeparationFactor = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
nucmerObj.FixedSeparation = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
default:
break;
}
IList<ISequenceAlignment> align = null;
if (isAlignList)
{
var listOfSeq = new List<ISequence> {refSeqList.ElementAt(0), searchSeqList.ElementAt(0)};
align = nucmerObj.Align(listOfSeq);
}
else
{
align = nucmerObj.Align(refSeqList, searchSeqList);
}
string expectedSequences = isFilePath
? this.utilityObj.xmlUtil.GetFileTextValue(nodeName, Constants.ExpectedSequencesNode)
: this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
// Gets all the aligned sequences in comma separated format
foreach (IPairwiseSequenceAlignment seqAlignment in align)
{
foreach (PairwiseAlignedSequence alignedSeq in seqAlignment)
{
var actualStr = alignedSeq.FirstSequence.ConvertToString();
Assert.IsTrue(expSeqArray.Contains(actualStr));
actualStr = alignedSeq.SecondSequence.ConvertToString();
Assert.IsTrue(expSeqArray.Contains(actualStr));
}
}
ApplicationLog.WriteLine("NUCmer P1 : Successfully validated all the aligned sequences.");
}
private void ValidateFindMatchSuffixGeneralTestCases(string nodeName, bool isFilePath,
AdditionalParameters additionalParam,
PropertyParameters propParam)
{
ISequence referenceSeq;
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);
ApplicationLog.WriteLine(string.Format(null, "NUCmer P1 : Successfully validated the File Path '{0}'.", filePath));
var parser = new FastAParser();
IEnumerable<ISequence> referenceSeqList = parser.Parse(filePath);
var byteList = new List<Byte>();
foreach (ISequence seq in referenceSeqList)
{
byteList.AddRange(seq);
byteList.Add((byte) '+');
}
referenceSeq = 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);
ApplicationLog.WriteLine(string.Format(null, "NUCmer P1 : Successfully validated the File Path '{0}'.", queryFilePath));
var queryParserObj = new FastAParser();
IEnumerable<ISequence> querySeqList = queryParserObj.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));
var refSeqList = referenceSequences.Select(t => new Sequence(seqAlphabet, Encoding.ASCII.GetBytes(t))).Cast<ISequence>().ToList();
var byteList = new List<Byte>();
foreach (ISequence seq in refSeqList)
{
byteList.AddRange(seq);
byteList.Add((byte) '+');
}
referenceSeq = new Sequence(refSeqList.First().Alphabet.GetMummerAlphabet(), byteList.ToArray());
searchSeqList.AddRange(searchSequences.Select(t => new Sequence(seqAlphabet, Encoding.ASCII.GetBytes(t))));
}
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Builds the suffix for the reference sequence passed.
var suffixTreeBuilder = new MultiWaySuffixTree(referenceSeq as Sequence)
{
MinLengthOfMatch =
long.Parse(mumLength, null)
};
var matches = searchSeqList.ToDictionary(t => t, suffixTreeBuilder.SearchMatchesUniqueInReference);
var 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 P1 : Validating the Unique Matches");
Assert.IsTrue(this.ValidateUniqueMatches(mums, nodeName, isFilePath));
ApplicationLog.WriteLine("NUCmer P1 : Successfully validated the all the unique matches for the sequences.");
break;
case AdditionalParameters.PerformClusterBuilder:
// Validates the Unique Matches.
ApplicationLog.WriteLine(
"NUCmer P1 : Validating the Unique Matches using Cluster Builder");
Assert.IsTrue(this.ValidateClusterBuilderMatches(mums, nodeName, propParam));
ApplicationLog.WriteLine("NUCmer P1 : Successfully validated the all the cluster builder matches for the sequences.");
break;
default:
break;
}
ApplicationLog.WriteLine("NUCmer P1 : Successfully validated the all the unique matches for the sequences.");
}
public IPropertyGroup Create()
{
var properties = PropertyParameters.Select(p => _propertyFactory(p[0], (uint)p[1])).ToList();
return(new MonopolyPropertyGroup(Indices, _rentStrategy, properties));
}
