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()