jebl.evolution.align.scores
Class ScoresFactory
java.lang.Object
jebl.evolution.align.scores.ScoresFactory
public class ScoresFactory
- extends java.lang.Object
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
ScoresFactory
public ScoresFactory()
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 JukesCantorval
- 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/