/// <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); }