Package jebl.evolution.align.scores
Class ScoresFactory
- java.lang.Object
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- jebl.evolution.align.scores.ScoresFactory
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public class ScoresFactory extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description 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
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Constructor Summary
Constructors Constructor Description ScoresFactory()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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 matricesstatic AminoAcidScores[]
getAvailableAminoAcidScores()
static NucleotideScores[]
getAvailableNucleotideScores()
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Field Detail
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BLOSUM_45
public static final Blosum45 BLOSUM_45
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BLOSUM_50
public static final Blosum50 BLOSUM_50
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BLOSUM_55
public static final Blosum55 BLOSUM_55
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BLOSUM_60
public static final Blosum60 BLOSUM_60
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BLOSUM_62
public static final Blosum62 BLOSUM_62
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BLOSUM_65
public static final Blosum65 BLOSUM_65
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BLOSUM_70
public static final Blosum70 BLOSUM_70
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BLOSUM_75
public static final Blosum75 BLOSUM_75
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BLOSUM_80
public static final Blosum80 BLOSUM_80
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BLOSUM_85
public static final Blosum85 BLOSUM_85
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BLOSUM_90
public static final Blosum90 BLOSUM_90
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PAM_100
public static final Pam100 PAM_100
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PAM_110
public static final Pam110 PAM_110
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PAM_120
public static final Pam120 PAM_120
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PAM_130
public static final Pam130 PAM_130
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PAM_140
public static final Pam140 PAM_140
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PAM_150
public static final Pam150 PAM_150
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PAM_160
public static final Pam160 PAM_160
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PAM_170
public static final Pam170 PAM_170
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PAM_180
public static final Pam180 PAM_180
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PAM_190
public static final Pam190 PAM_190
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PAM_200
public static final Pam200 PAM_200
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PAM_210
public static final Pam210 PAM_210
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PAM_220
public static final Pam220 PAM_220
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PAM_230
public static final Pam230 PAM_230
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PAM_240
public static final Pam240 PAM_240
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PAM_250
public static final Pam250 PAM_250
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AMINO_ACID_IDENTITY
public static final AminoAcidScores AMINO_ACID_IDENTITY
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NUCLEOTIDE_51_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_51_PERCENT_SIMILARITY
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NUCLEOTIDE_65_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_65_PERCENT_SIMILARITY
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NUCLEOTIDE_70_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_70_PERCENT_SIMILARITY
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NUCLEOTIDE_93_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_93_PERCENT_SIMILARITY
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Method Detail
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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.
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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.
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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.
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getAvailableAminoAcidScores
public static AminoAcidScores[] getAvailableAminoAcidScores()
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getAvailableNucleotideScores
public static NucleotideScores[] getAvailableNucleotideScores()
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