Class ScoresFactory


  • public class ScoresFactory
    extends java.lang.Object
    • Field Detail

      • BLOSUM_45

        public static final Blosum45 BLOSUM_45
      • BLOSUM_50

        public static final Blosum50 BLOSUM_50
      • BLOSUM_55

        public static final Blosum55 BLOSUM_55
      • BLOSUM_60

        public static final Blosum60 BLOSUM_60
      • BLOSUM_62

        public static final Blosum62 BLOSUM_62
      • BLOSUM_65

        public static final Blosum65 BLOSUM_65
      • BLOSUM_70

        public static final Blosum70 BLOSUM_70
      • BLOSUM_75

        public static final Blosum75 BLOSUM_75
      • BLOSUM_80

        public static final Blosum80 BLOSUM_80
      • BLOSUM_85

        public static final Blosum85 BLOSUM_85
      • BLOSUM_90

        public static final Blosum90 BLOSUM_90
      • PAM_100

        public static final Pam100 PAM_100
      • PAM_110

        public static final Pam110 PAM_110
      • PAM_120

        public static final Pam120 PAM_120
      • PAM_130

        public static final Pam130 PAM_130
      • PAM_140

        public static final Pam140 PAM_140
      • PAM_150

        public static final Pam150 PAM_150
      • PAM_160

        public static final Pam160 PAM_160
      • PAM_170

        public static final Pam170 PAM_170
      • PAM_180

        public static final Pam180 PAM_180
      • PAM_190

        public static final Pam190 PAM_190
      • PAM_200

        public static final Pam200 PAM_200
      • PAM_210

        public static final Pam210 PAM_210
      • PAM_220

        public static final Pam220 PAM_220
      • PAM_230

        public static final Pam230 PAM_230
      • PAM_240

        public static final Pam240 PAM_240
      • PAM_250

        public static final Pam250 PAM_250
      • AMINO_ACID_IDENTITY

        public static final AminoAcidScores AMINO_ACID_IDENTITY
      • NUCLEOTIDE_51_PERCENT_SIMILARITY

        public static final NucleotideScores NUCLEOTIDE_51_PERCENT_SIMILARITY
      • NUCLEOTIDE_65_PERCENT_SIMILARITY

        public static final NucleotideScores NUCLEOTIDE_65_PERCENT_SIMILARITY
      • NUCLEOTIDE_70_PERCENT_SIMILARITY

        public static final NucleotideScores NUCLEOTIDE_70_PERCENT_SIMILARITY
      • NUCLEOTIDE_93_PERCENT_SIMILARITY

        public static final NucleotideScores NUCLEOTIDE_93_PERCENT_SIMILARITY
    • Constructor Detail

      • ScoresFactory

        public ScoresFactory()
    • Method Detail

      • generateScores

        public static Scores generateScores​(java.lang.String nameVal)
        For any matrix.
        Parameters:
        nameVal - name and value of the matrix in String form. (eg Blosum45).
        Returns:
        substitution matrix of given name.
      • generateScores

        public static Scores generateScores​(java.lang.String name,
                                            int val)
        For Blosum and Pam matrices
        Parameters:
        name - "Blosum" or "Pam"
        val - currently 45 - 90 or 100 - 250
        Returns:
        substitution matrix given by name and val.
      • generateScores

        public static Scores generateScores​(java.lang.String name,
                                            float val)
        For calculated nucleotide matrices.
        Parameters:
        name - Currently only JukesCantor
        val - val used to calculate matrix. eg. evolutionary distance d.
        Returns:
        substitution matrix calculated using val.
      • getAvailableAminoAcidScores

        public static AminoAcidScores[] getAvailableAminoAcidScores()
      • getAvailableNucleotideScores

        public static NucleotideScores[] getAvailableNucleotideScores()