/// <summary>
/// This method when passed the algorithm name instantiates
/// the framework class which implements.
/// </summary>
/// <param name="algorithmName">Name of the algorithm.</param>
/// <returns>Class which instantiates the algorithm.</returns>
private static ISequenceAligner ChooseAlgorithm(string algorithmName)
{
foreach (ISequenceAligner aligner in SequenceAligners.All)
{
if (aligner.Name.Equals(algorithmName))
{
IPairwiseSequenceAligner pairWise = aligner as IPairwiseSequenceAligner;
if (pairWise != null)
{
return(pairWise);
}
}
}
return(null);
}
/// <summary>
/// Logs results to current Application log
/// </summary>
/// <param name="psa"></param>
/// <param name="result"></param>
public static void LogResult(IPairwiseSequenceAligner psa, IEnumerable <IPairwiseSequenceAlignment> result)
{
ApplicationLog.WriteLine("{0}, Matrix {1}; GapOpenCost {2}, GapExtensionCost {3}", psa.Name, psa.SimilarityMatrix.Name, psa.GapOpenCost, psa.GapExtensionCost);
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine("Input 0 {0}", sequenceResult.FirstSequence);
ApplicationLog.WriteLine("Input 1 {0}", sequenceResult.SecondSequence);
int count = 1;
foreach (var oneResult in sequenceResult.PairwiseAlignedSequences)
{
ApplicationLog.WriteLine(" #" + count++);
ApplicationLog.WriteLine(" Score {0}", oneResult.Score);
ApplicationLog.WriteLine(" Result 0 {0}", oneResult.FirstSequence);
ApplicationLog.WriteLine(" Result 1 {0}", oneResult.SecondSequence);
ApplicationLog.WriteLine(" Offset 0 {0}", oneResult.FirstOffset);
ApplicationLog.WriteLine(" Offset 1 {0}", oneResult.SecondOffset);
ApplicationLog.WriteLine(" Consensus {0}", oneResult.Consensus);
}
}
}
/// <summary>
/// Logs results to current Application log
/// </summary>
/// <param name="psa"></param>
/// <param name="result"></param>
public static void LogResult(IPairwiseSequenceAligner psa, IEnumerable<IPairwiseSequenceAlignment> result)
{
ApplicationLog.WriteLine("{0}, Matrix {1}; GapOpenCost {2}, GapExtensionCost {3}", psa.Name, psa.SimilarityMatrix.Name, psa.GapOpenCost, psa.GapExtensionCost);
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine("Input 0 {0}", sequenceResult.FirstSequence);
ApplicationLog.WriteLine("Input 1 {0}", sequenceResult.SecondSequence);
int count = 1;
foreach (var oneResult in sequenceResult.PairwiseAlignedSequences)
{
ApplicationLog.WriteLine(" #" + count++);
ApplicationLog.WriteLine(" Score {0}", oneResult.Score);
ApplicationLog.WriteLine(" Result 0 {0}", oneResult.FirstSequence);
ApplicationLog.WriteLine(" Result 1 {0}", oneResult.SecondSequence);
ApplicationLog.WriteLine(" Offset 0 {0}", oneResult.FirstOffset);
ApplicationLog.WriteLine(" Offset 1 {0}", oneResult.SecondOffset);
ApplicationLog.WriteLine(" Consensus {0}", oneResult.Consensus);
}
}
}
