/// <summary>
/// Initializes a new instance of the NUCmerAttributes class.
/// </summary>
public NUCmerAttributes()
{
AlignmentInfo alignmentAttribute;
alignmentAttribute = new AlignmentInfo(
Properties.Resource.FIXED_SEPARATION_NAME,
Properties.Resource.FIXED_SEPARATION_DESCRIPTION,
true,
ClusterBuilder.DefaultFixedSeparation.ToString(CultureInfo.InvariantCulture),
AlignmentInfo.IntType,
null);
Attributes.Add(FixedSeparation, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.MAXIMUM_SEPARATION_NAME,
Properties.Resource.MAXIMUM_SEPARATION_DESCRIPTION,
true,
ClusterBuilder.DefaultMaximumSeparation.ToString(CultureInfo.InvariantCulture),
AlignmentInfo.IntType,
null);
Attributes.Add(MaximumSeparation, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.MINIMUM_SCORE_NAME,
Properties.Resource.MINIMUM_SCORE_DESCRIPTION,
true,
ClusterBuilder.DefaultMinimumScore.ToString(CultureInfo.InvariantCulture),
AlignmentInfo.IntType,
null);
Attributes.Add(MinimumScore, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.SEPARATION_FACTOR_NAME,
Properties.Resource.SEPARATION_FACTOR_DESCRIPTION,
true,
ClusterBuilder.DefaultSeparationFactor.ToString(CultureInfo.InvariantCulture),
AlignmentInfo.FloatType,
null);
Attributes.Add(SeparationFactor, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.BREAK_LENGTH_NAME,
Properties.Resource.BREAK_LENGTH_DESCRIPTION,
true,
NUCmerAligner.DefaultBreakLength.ToString(CultureInfo.InvariantCulture),
AlignmentInfo.IntType,
null);
Attributes.Add(BreakLength, alignmentAttribute);
}
/// <summary>
/// Initializes a new instance of the PairwiseAlignmentAttributes class.
/// </summary>
public PairwiseAlignmentAttributes()
{
attributes = new Dictionary <string, AlignmentInfo>();
StringListValidator similarityMatrixList = new StringListValidator(
Properties.Resource.SimilarityMatrix_DiagonalSM,
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SM.StandardSimilarityMatrix.Blosum45.ToString(),
SM.StandardSimilarityMatrix.Blosum50.ToString(),
SM.StandardSimilarityMatrix.Blosum62.ToString(),
SM.StandardSimilarityMatrix.Blosum80.ToString(),
SM.StandardSimilarityMatrix.Blosum90.ToString(),
SM.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
SM.StandardSimilarityMatrix.Pam250.ToString(),
SM.StandardSimilarityMatrix.Pam30.ToString(),
SM.StandardSimilarityMatrix.Pam70.ToString());
AlignmentInfo alignmentAttribute = new AlignmentInfo(
Properties.Resource.SIMILARITY_MATRIX_NAME,
Properties.Resource.SIMILARITY_MATRIX_DESCRIPTION,
true,
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
AlignmentInfo.StringListType,
similarityMatrixList);
attributes.Add(SimilarityMatrix, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.GAP_COST_NAME,
Properties.Resource.GAP_COST_DESCRIPTION,
true,
"-8",
AlignmentInfo.IntType,
null);
attributes.Add(GapOpenCost, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.GAP_EXTENSION_COST_NAME,
Properties.Resource.GAP_EXTENSION_COST_DESCRIPTION,
true,
"-8",
AlignmentInfo.IntType,
null);
attributes.Add(GapExtensionCost, alignmentAttribute);
}
