Package jebl.evolution.align.scores

Class ScoresFactory

java.lang.Object
jebl.evolution.align.scores.ScoresFactory
public class ScoresFactory extends Object

  • Field Details

    • 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 Details

    • ScoresFactory

      public ScoresFactory()

  • Method Details

    • generateScores

      public static Scores generateScores(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(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(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()