/// <summary>
/// User will typically choose their own parameters, these defaults are reasonable for many cases.
/// </summary>
private void SetDefaults()
{
_nucmerAligner = new ModifiedSmithWaterman();
// Set the default Similarity Matrix
SimilarityMatrix = new SimilarityMatrix(
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix);
// Set the defaults
GapOpenCost = DefaultGapOpenCost;
GapExtensionCost = DefaultGapExtensionCost;
LengthOfMUM = DefaultLengthOfMUM;
// Set the ClusterBuilder properties to defaults
FixedSeparation = ClusterBuilder.DefaultFixedSeparation;
MaximumSeparation = ClusterBuilder.DefaultMaximumSeparation;
MinimumScore = ClusterBuilder.DefaultMinimumScore;
SeparationFactor = ClusterBuilder.DefaultSeparationFactor;
BreakLength = ModifiedSmithWaterman.DefaultBreakLength;
ScoreMethod = ClusterScoreMethod.MatchLength;
}
/// <summary>
/// Initializes a new instance of the NUCmer class.
/// </summary>
public NUCmer()
{
// User will typically choose their own parameters, these
// defaults are reasonable for many cases.
nucmerAligner = new ModifiedSmithWaterman();
// Set the default Similarity Matrix
SimilarityMatrix = new SimilarityMatrix(
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix);
// Set the defaults
GapOpenCost = DefaultGapOpenCost;
GapExtensionCost = DefaultGapExtensionCost;
LengthOfMUM = DefaultLengthOfMUM;
// Set the ClusterBuilder properties to defaults
FixedSeparation = ClusterBuilder.DefaultFixedSeparation;
MaximumSeparation = ClusterBuilder.DefaultMaximumSeparation;
MinimumScore = ClusterBuilder.DefaultMinimumScore;
SeparationFactor = ClusterBuilder.DefaultSeparationFactor;
BreakLength = ModifiedSmithWaterman.DefaultBreakLength;
}
/// <summary>
/// User will typically choose their own parameters, these defaults are reasonable for many cases.
/// </summary>
private void SetDefaults()
{
_nucmerAligner = new ModifiedSmithWaterman();
// Set the default Similarity Matrix
SimilarityMatrix = new SimilarityMatrix(
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix);
// Set the defaults
GapOpenCost = DefaultGapOpenCost;
GapExtensionCost = DefaultGapExtensionCost;
LengthOfMUM = DefaultLengthOfMUM;
// Set the ClusterBuilder properties to defaults
FixedSeparation = ClusterBuilder.DefaultFixedSeparation;
MaximumSeparation = ClusterBuilder.DefaultMaximumSeparation;
MinimumScore = ClusterBuilder.DefaultMinimumScore;
SeparationFactor = ClusterBuilder.DefaultSeparationFactor;
BreakLength = ModifiedSmithWaterman.DefaultBreakLength;
ScoreMethod = ClusterScoreMethod.MatchLength;
}
