jebl.evolution.align.scores
Class ScoresFactory

java.lang.Object
  extended by jebl.evolution.align.scores.ScoresFactory

public class ScoresFactory
extends java.lang.Object


Field Summary
static AminoAcidScores AMINO_ACID_IDENTITY
           
static Blosum45 BLOSUM_45
           
static Blosum50 BLOSUM_50
           
static Blosum55 BLOSUM_55
           
static Blosum60 BLOSUM_60
           
static Blosum62 BLOSUM_62
           
static Blosum65 BLOSUM_65
           
static Blosum70 BLOSUM_70
           
static Blosum75 BLOSUM_75
           
static Blosum80 BLOSUM_80
           
static Blosum85 BLOSUM_85
           
static Blosum90 BLOSUM_90
           
static NucleotideScores NUCLEOTIDE_51_PERCENT_SIMILARITY
           
static NucleotideScores NUCLEOTIDE_65_PERCENT_SIMILARITY
           
static NucleotideScores NUCLEOTIDE_70_PERCENT_SIMILARITY
           
static NucleotideScores NUCLEOTIDE_93_PERCENT_SIMILARITY
           
static Pam100 PAM_100
           
static Pam110 PAM_110
           
static Pam120 PAM_120
           
static Pam130 PAM_130
           
static Pam140 PAM_140
           
static Pam150 PAM_150
           
static Pam160 PAM_160
           
static Pam170 PAM_170
           
static Pam180 PAM_180
           
static Pam190 PAM_190
           
static Pam200 PAM_200
           
static Pam210 PAM_210
           
static Pam220 PAM_220
           
static Pam230 PAM_230
           
static Pam240 PAM_240
           
static Pam250 PAM_250
           
 
Constructor Summary
ScoresFactory()
           
 
Method Summary
static Scores generateScores(java.lang.String nameVal)
          For any matrix.
static Scores generateScores(java.lang.String name, float val)
          For calculated nucleotide matrices.
static Scores generateScores(java.lang.String name, int val)
          For Blosum and Pam matrices
static AminoAcidScores[] getAvailableAminoAcidScores()
           
static NucleotideScores[] getAvailableNucleotideScores()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

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()


http://code.google.com/p/jebl2/