protected override async void OnStartup(StartupEventArgs e)
{
var appIcon = WpfUI.Properties.Resources.M;
var assemblyParameters = AssemblyParameters.CreateFromAssembly(typeof(App).Assembly);
var appConfig = ApplicationConfiguration.CreateFromIcon("Word Analysis System", appIcon);
await BootstrapService.StartUpAsync(assemblyParameters, appConfig);
}
/// <summary>
/// Validates the Sequences for all the general test cases.
/// </summary>
/// <param name="node">Xml Node Name</param>
/// <param name="additionalParameter">
/// Additional Parameter based
/// on which the validations are done.
/// </param>
private void ValidateComputeFeature(string node, AssemblyParameters additionalParameter)
{
// Get the parameters from Xml
string firstSequence = utilityObj.xmlUtil.GetTextValue(node, Constants.SequenceNode1);
string secondSequence = utilityObj.xmlUtil.GetTextValue(node, Constants.SequenceNode2);
string kmerLength = utilityObj.xmlUtil.GetTextValue(node, Constants.KmerLengthNode);
string expectedFeatureCount = utilityObj.xmlUtil.GetTextValue(node, Constants.FeatureCount);
string expectedFeature = utilityObj.xmlUtil.GetTextValue(node, Constants.FeatureName);
string expectedFeatureType = utilityObj.xmlUtil.GetTextValue(node, Constants.FeatureType);
string expectedStartIndex = utilityObj.xmlUtil.GetTextValue(node, Constants.StartIndexNode);
string expectedEndIndex = utilityObj.xmlUtil.GetTextValue(node, Constants.EndIndexNode);
ISequence seq1 = null;
ISequence seq2 = null;
// Create Sequences.
switch (additionalParameter)
{
case AssemblyParameters.Assemble:
var seqObj1 =
new Sequence(Alphabets.Protein, firstSequence);
var seqObj2 =
new Sequence(Alphabets.Protein, secondSequence);
seq1 = seqObj1;
seq2 = seqObj2;
break;
case AssemblyParameters.Consensus:
seq1 = new Sequence(Alphabets.DNA, firstSequence);
seq2 = new Sequence(Alphabets.DNA, secondSequence);
break;
}
var kmerBuilder = new SequenceToKmerBuilder();
KmersOfSequence kmerList =
kmerBuilder.Build(seq1, int.Parse(kmerLength, null));
List <WordMatch> nodes =
WordMatch.BuildMatchTable(
kmerList,
seq2,
int.Parse(kmerLength, null));
List <WordMatch> matchList =
WordMatch.GetMinimalList(nodes, int.Parse(kmerLength, null));
List <DifferenceNode> diffNode =
DifferenceNode.BuildDiffList(matchList, seq1, seq2);
List <DifferenceNode.CompareFeature> features =
DifferenceNode.OutputDiffList(diffNode, seq1, seq2);
// Validate difference.
Assert.AreEqual(expectedFeatureCount, features.Count.ToString((IFormatProvider)null));
Assert.AreEqual(expectedFeature, features[0].Feature);
Assert.AreEqual(expectedFeatureType, features[0].FeatureType);
Assert.AreEqual(expectedStartIndex, features[0].Start.ToString((IFormatProvider)null));
Assert.AreEqual(expectedEndIndex, features[0].End.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format(null, "Kmer P1 : Validated DifferenceNodes successfully."));
}
private static IServiceProvider CreateServiceProvider(IServiceCollection services)
{
var container = ContainerInitializationService.CreateInitializedContainer(
AssemblyParameters.CreateFromAssembly(typeof(ServiceInitialization).Assembly));
container.Populate(services);
var result = container.GetInstance <IServiceProvider>();
return(result);
}
/// <summary>
/// Validates the Sequence Assembler for all the general test cases.
/// </summary>
/// <param name="nodeName">Xml Node Name</param>
/// <param name="additionalParameter">
/// Additional Parameter based
/// on which the validations are done.
/// </param>
/// <param name="isSeqAssemblyctr">True if Default contructor is validated or else false.</param>
private void ValidateSequenceAssemblerGeneral(string nodeName,
AssemblyParameters additionalParameter, bool isSeqAssemblyctr)
{
// Get the parameters from Xml
int matchScore = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode), null);
int mismatchScore = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode), null);
int gapCost = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapCostNode), null);
double mergeThreshold = double.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MergeThresholdNode), null);
double consensusThreshold = double.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ConsensusThresholdNode),
null);
string[] sequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SequencesNode);
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string documentation = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.DocumentaionNode);
var info = new SerializationInfo(typeof(OverlapDeNovoAssembly),
new FormatterConverter());
var context = new StreamingContext(StreamingContextStates.All);
var inputs = new List <ISequence>();
switch (additionalParameter)
{
case AssemblyParameters.Consensus:
for (int i = 0; i < sequences.Length; i++)
{
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null, "SimpleConsensusMethod P1 : Sequence '{0}' used is '{1}'.", i, sequences[i]));
var seq = new Sequence(alphabet, sequences[i]);
inputs.Add(seq);
}
break;
default:
for (int i = 0; i < sequences.Length; i++)
{
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly P1 : Sequence '{0}' used is '{1}'.", i, sequences[i]));
var seq = new Sequence(alphabet, sequences[i]);
inputs.Add(seq);
}
break;
}
// here is how the above sequences should align:
// TATAAAGCGCCAA
// GCCAAAATTTAGGC
// AGGCACCCGCGGTATT <= reversed
//
// TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT
var assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new PairwiseOverlapAligner()
};
switch (additionalParameter)
{
case AssemblyParameters.DiagonalSM:
(assembler.OverlapAlgorithm).SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore, mismatchScore);
break;
case AssemblyParameters.SimilarityMatrix:
string blosumFilePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
(assembler.OverlapAlgorithm).SimilarityMatrix = new SimilarityMatrix(blosumFilePath);
break;
default:
(assembler.OverlapAlgorithm).SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore);
break;
}
(assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = false;
// Assembles all the sequences.
IOverlapDeNovoAssembly assembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
// Set Documentation property.
assembly.Documentation = documentation;
// Get the parameters from Xml in general
int contigSequencesCount = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigSequencesCountNode), null);
string contigConsensus = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigConsensusNode);
switch (additionalParameter)
{
case AssemblyParameters.Consensus:
// Read the contig from Contig method.
Contig contigReadForConsensus = assembly.Contigs[0];
contigReadForConsensus.Consensus = null;
var simpleSeqAssembler = new OverlapDeNovoAssembler
{
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold)
};
simpleSeqAssembler.MakeConsensus(alphabet, contigReadForConsensus);
// Log the required info.
ApplicationLog.WriteLine(string.Format(null, "SimpleConsensusMethod BVT : Consensus read is '{0}'.", contigReadForConsensus.Consensus));
Assert.AreEqual(contigConsensus, new String(contigReadForConsensus.Consensus.Select(a => (char)a).ToArray()));
break;
default:
// Get the parameters from Xml for Assemble() method test cases.
int unMergedCount = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.UnMergedSequencesCountNode),
null);
int contigsCount = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ContigsCountNode), null);
Assert.AreEqual(unMergedCount, assembly.UnmergedSequences.Count);
Assert.AreEqual(contigsCount, assembly.Contigs.Count);
Assert.AreEqual(documentation, assembly.Documentation);
Contig contigRead = assembly.Contigs[0];
// Logs the consensus
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Un Merged Sequences Count is '{0}'.", assembly.UnmergedSequences.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Contigs Count is '{0}'.", assembly.Contigs.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Contig Sequences Count is '{0}'.", contigRead.Sequences.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Consensus read is '{0}'.", contigRead.Consensus));
Assert.AreEqual(contigConsensus, new String(contigRead.Consensus.Select(a => (char)a).ToArray()));
Assert.AreEqual(contigSequencesCount, contigRead.Sequences.Count);
break;
}
}
/// <summary>
/// Validates the Sequences for all the general test cases.
/// </summary>
/// <param name="node">Xml Node Name</param>
/// <param name="additionalParameter">
/// Additional Parameter based
/// on which the validations are done.
/// </param>
private void ValidateComputeFeature(string node, AssemblyParameters additionalParameter)
{
// Get the parameters from Xml
string firstSequence = this.utilityObj.xmlUtil.GetTextValue(node, Constants.SequenceNode1);
string secondSequence = this.utilityObj.xmlUtil.GetTextValue(node, Constants.SequenceNode2);
string kmerLength = this.utilityObj.xmlUtil.GetTextValue(node, Constants.KmerLengthNode);
string expectedFeatureCount = this.utilityObj.xmlUtil.GetTextValue(node, Constants.FeatureCount);
string expectedFeature = this.utilityObj.xmlUtil.GetTextValue(node, Constants.FeatureName);
string expectedFeatureType = this.utilityObj.xmlUtil.GetTextValue(node, Constants.FeatureType);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(node, Constants.StartIndexNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(node, Constants.EndIndexNode);
ISequence seq1 = null;
ISequence seq2 = null;
// Create Sequences.
switch (additionalParameter)
{
case AssemblyParameters.Assemble:
var seqObj1 =
new Sequence(Alphabets.Protein, firstSequence);
var seqObj2 =
new Sequence(Alphabets.Protein, secondSequence);
seq1 = seqObj1;
seq2 = seqObj2;
break;
case AssemblyParameters.Consensus:
seq1 = new Sequence(Alphabets.DNA, firstSequence);
seq2 = new Sequence(Alphabets.DNA, secondSequence);
break;
}
var kmerBuilder = new SequenceToKmerBuilder();
KmersOfSequence kmerList =
kmerBuilder.Build(seq1, int.Parse(kmerLength, null));
List<WordMatch> nodes =
WordMatch.BuildMatchTable(
kmerList,
seq2,
int.Parse(kmerLength, null));
List<WordMatch> matchList =
WordMatch.GetMinimalList(nodes, int.Parse(kmerLength, null));
List<DifferenceNode> diffNode =
DifferenceNode.BuildDiffList(matchList, seq1, seq2);
List<DifferenceNode.CompareFeature> features =
DifferenceNode.OutputDiffList(diffNode, seq1, seq2);
// Validate difference.
Assert.AreEqual(expectedFeatureCount, features.Count.ToString((IFormatProvider) null));
Assert.AreEqual(expectedFeature, features[0].Feature);
Assert.AreEqual(expectedFeatureType, features[0].FeatureType);
Assert.AreEqual(expectedStartIndex, features[0].Start.ToString((IFormatProvider) null));
Assert.AreEqual(expectedEndIndex, features[0].End.ToString((IFormatProvider) null));
ApplicationLog.WriteLine(string.Format(null, "Kmer P1 : Validated DifferenceNodes successfully."));
}
/// <summary>
/// Validates the Sequence Assembler for all the general test cases.
/// </summary>
/// <param name="nodeName">Xml Node Name</param>
/// <param name="additionalParameter">
/// Additional Parameter based
/// on which the validations are done.
/// </param>
/// <param name="isSeqAssemblyctr">True if Default contructor is validated or else false.</param>
private void ValidateSequenceAssemblerGeneral(string nodeName,
AssemblyParameters additionalParameter, bool isSeqAssemblyctr)
{
// Get the parameters from Xml
int matchScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode), null);
int mismatchScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode), null);
int gapCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapCostNode), null);
double mergeThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MergeThresholdNode), null);
double consensusThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ConsensusThresholdNode),
null);
string[] sequences = this.utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SequencesNode);
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string documentation = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.DocumentaionNode);
var info = new SerializationInfo(typeof (OverlapDeNovoAssembly),
new FormatterConverter());
var context = new StreamingContext(StreamingContextStates.All);
var inputs = new List<ISequence>();
switch (additionalParameter)
{
case AssemblyParameters.Consensus:
for (int i = 0; i < sequences.Length; i++)
{
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null, "SimpleConsensusMethod P1 : Sequence '{0}' used is '{1}'.", i, sequences[i]));
var seq = new Sequence(alphabet, sequences[i]);
inputs.Add(seq);
}
break;
default:
for (int i = 0; i < sequences.Length; i++)
{
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly P1 : Sequence '{0}' used is '{1}'.", i, sequences[i]));
var seq = new Sequence(alphabet, sequences[i]);
inputs.Add(seq);
}
break;
}
// here is how the above sequences should align:
// TATAAAGCGCCAA
// GCCAAAATTTAGGC
// AGGCACCCGCGGTATT <= reversed
//
// TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT
var assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new PairwiseOverlapAligner()
};
switch (additionalParameter)
{
case AssemblyParameters.DiagonalSM:
(assembler.OverlapAlgorithm).SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore, mismatchScore);
break;
case AssemblyParameters.SimilarityMatrix:
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
(assembler.OverlapAlgorithm).SimilarityMatrix = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
default:
(assembler.OverlapAlgorithm).SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore);
break;
}
(assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = false;
// Assembles all the sequences.
IOverlapDeNovoAssembly assembly = (IOverlapDeNovoAssembly) assembler.Assemble(inputs);
// Set Documentation property.
assembly.Documentation = documentation;
// Get the parameters from Xml in general
int contigSequencesCount = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigSequencesCountNode), null);
string contigConsensus = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigConsensusNode);
switch (additionalParameter)
{
case AssemblyParameters.Consensus:
// Read the contig from Contig method.
Contig contigReadForConsensus = assembly.Contigs[0];
contigReadForConsensus.Consensus = null;
var simpleSeqAssembler = new OverlapDeNovoAssembler
{
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold)
};
simpleSeqAssembler.MakeConsensus(alphabet, contigReadForConsensus);
// Log the required info.
ApplicationLog.WriteLine(string.Format(null, "SimpleConsensusMethod BVT : Consensus read is '{0}'.", contigReadForConsensus.Consensus));
Assert.AreEqual(contigConsensus, new String(contigReadForConsensus.Consensus.Select(a => (char) a).ToArray()));
break;
default:
// Get the parameters from Xml for Assemble() method test cases.
int unMergedCount = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.UnMergedSequencesCountNode),
null);
int contigsCount = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ContigsCountNode), null);
Assert.AreEqual(unMergedCount, assembly.UnmergedSequences.Count);
Assert.AreEqual(contigsCount, assembly.Contigs.Count);
Assert.AreEqual(documentation, assembly.Documentation);
Contig contigRead = assembly.Contigs[0];
// Logs the consensus
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Un Merged Sequences Count is '{0}'.", assembly.UnmergedSequences.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Contigs Count is '{0}'.", assembly.Contigs.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Contig Sequences Count is '{0}'.", contigRead.Sequences.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Consensus read is '{0}'.", contigRead.Consensus));
Assert.AreEqual(contigConsensus, new String(contigRead.Consensus.Select(a => (char) a).ToArray()));
Assert.AreEqual(contigSequencesCount, contigRead.Sequences.Count);
break;
}
}
