/// <summary>
/// Construct a progressive aligner
/// </summary>
/// <param name="profileAlignerName">ProfileAlignerNames member</param>
/// <param name="similarityMatrix">similarity matrix</param>
/// <param name="gapOpenPenalty">negative gapOpenPenalty</param>
/// <param name="gapExtendPenalty">negative gapExtendPenalty</param>
public ProgressiveAligner(ProfileAlignerNames profileAlignerName,
SimilarityMatrix similarityMatrix,
int gapOpenPenalty,
int gapExtendPenalty)
{
// Get ProfileAligner ready
switch (profileAlignerName)
{
case (ProfileAlignerNames.NeedlemanWunschProfileAligner):
_profileAligner = new NeedlemanWunschProfileAlignerSerial();
break;
case (ProfileAlignerNames.SmithWatermanProfileAligner):
_profileAligner = new SmithWatermanProfileAlignerSerial();
break;
default:
throw new Exception("Invalid profile aligner name");
}
_profileAligner.SimilarityMatrix = similarityMatrix;
_profileAligner.GapOpenCost = gapOpenPenalty;
_profileAligner.GapExtensionCost = gapExtendPenalty;
_alignedSequences = new List<ISequence>();
}
/// <summary>
/// Read from xml config and initialize all member variables
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="expectedScoreNode">Expected score node</param>
private void Initialize(string nodeName, string expectedScoreNode)
{
// Read all the input sequences from xml config file
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string sequenceString1 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence1);
string sequenceString2 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence2);
string sequenceString3 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence3);
string sequenceString4 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence4);
string sequenceString5 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence5);
string sequenceString6 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence6);
string sequenceString7 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Sequence7);
string sequenceString8 = null;
string sequenceString9 = null;
// Get all the input sequence object
lstSequences = new List<ISequence>();
ISequence seq1 = new Sequence(alphabet, sequenceString1);
ISequence seq2 = new Sequence(alphabet, sequenceString2);
ISequence seq3 = new Sequence(alphabet, sequenceString3);
ISequence seq4 = new Sequence(alphabet, sequenceString4);
ISequence seq5 = new Sequence(alphabet, sequenceString5);
ISequence seq6 = new Sequence(alphabet, sequenceString6);
ISequence seq7 = new Sequence(alphabet, sequenceString7);
ISequence seq8 = null;
ISequence seq9 = null;
// Add all sequences to list.
lstSequences.Add(seq1);
lstSequences.Add(seq2);
lstSequences.Add(seq3);
lstSequences.Add(seq4);
lstSequences.Add(seq5);
lstSequences.Add(seq6);
lstSequences.Add(seq7);
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
profileAligner = new NeedlemanWunschProfileAlignerParallel(similarityMatrix,
ProfileScoreFunctionNames.InnerProduct,
gapOpenPenalty, gapExtendPenalty,
Environment.ProcessorCount);
// Read all expected Sequences
sequenceString1 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode1);
sequenceString2 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode2);
sequenceString3 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode3);
sequenceString4 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode4);
sequenceString5 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode5);
sequenceString6 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode6);
sequenceString7 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode7);
sequenceString8 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode8);
sequenceString9 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode9);
seq1 = new Sequence(alphabet, sequenceString1);
seq2 = new Sequence(alphabet, sequenceString2);
seq3 = new Sequence(alphabet, sequenceString3);
seq4 = new Sequence(alphabet, sequenceString4);
seq5 = new Sequence(alphabet, sequenceString5);
seq6 = new Sequence(alphabet, sequenceString6);
seq7 = new Sequence(alphabet, sequenceString7);
seq8 = new Sequence(alphabet, sequenceString8);
seq9 = new Sequence(alphabet, sequenceString9);
// Add all sequences to list.
expectedSequences = new List<ISequence>();
expectedSequences.Add(seq1);
expectedSequences.Add(seq2);
expectedSequences.Add(seq3);
expectedSequences.Add(seq4);
expectedSequences.Add(seq5);
expectedSequences.Add(seq6);
expectedSequences.Add(seq7);
expectedSequences.Add(seq8);
expectedSequences.Add(seq9);
expectedScore = utilityObj.xmlUtil.GetTextValue(nodeName, expectedScoreNode);
// Parallel Option will only get set if the PAMSAMMultipleSequenceAligner is getting called
// To test separately distance matrix, binary tree etc..
// Set the parallel option using below ctor.
var msa = new PAMSAMMultipleSequenceAligner(lstSequences,
kmerLength, DistanceFunctionTypes.EuclideanDistance,
UpdateDistanceMethodsTypes.Average,
ProfileAlignerNames.NeedlemanWunschProfileAligner,
ProfileScoreFunctionNames.InnerProduct, similarityMatrix,
gapOpenPenalty, gapExtendPenalty, 2, 2);
ApplicationLog.WriteLine(String.Format(null,
"Initialization of all variables successfully completed for xml node {0}",
nodeName));
}
/// <summary>
/// Construct a progressive aligner with a default profile aligner
/// </summary>
/// <param name="profileAligner">profile aligner interface that aligns two profiles</param>
public ProgressiveAligner(IProfileAligner profileAligner)
{
// Get ProfileAligner ready
_profileAligner = profileAligner;
_alignedSequences = new List<ISequence>();
}
