/// <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; }