/// <summary>
/// Gets the list of alignment argument based on the algorithm selected
/// </summary>
/// <returns>Alignment arguments</returns>
private IAlignmentAttributes GetAlignmentAttribute(string algo)
{
IAlignmentAttributes alignmentAttributes = null;
ISequenceAligner sequenceAligner = ChooseAlgorithm(algo);
if (sequenceAligner is NucmerPairwiseAligner)
{
alignmentAttributes = new NUCmerAttributes();
}
else if (sequenceAligner is MUMmerAligner)
{
alignmentAttributes = new MUMmerAttributes();
}
else if ((sequenceAligner is SmithWatermanAligner) ||
(sequenceAligner is NeedlemanWunschAligner) ||
(sequenceAligner is PairwiseOverlapAligner))
{
alignmentAttributes = new PairwiseAlignmentAttributes();
}
else if (sequenceAligner is PAMSAMMultipleSequenceAligner)
{
alignmentAttributes = new PamsamAlignmentAttributes();
}
return(alignmentAttributes);
}
/// <summary>
/// Gets the list of alignment argument based on the algorithm selected
/// </summary>
/// <param name="algoName">Name of the algorithm used</param>
/// <returns>Alignment arguments</returns>
private IAlignmentAttributes GetAlignmentAttribute(string algoName)
{
IAlignmentAttributes alignmentAttributes = null;
ISequenceAligner sequenceAligner = ChooseAlgorithm(algoName);
this.Aligner = sequenceAligner;
if (sequenceAligner is NUCmer3)
{
alignmentAttributes = new NUCmerAttributes();
}
else if (sequenceAligner is MUMmer3)
{
alignmentAttributes = new MUMmerAttributes();
}
else if ((sequenceAligner is SmithWatermanAligner) ||
(sequenceAligner is NeedlemanWunschAligner) ||
(sequenceAligner is PairwiseOverlapAligner))
{
alignmentAttributes = new PairwiseAlignmentAttributes();
}
return(alignmentAttributes);
}