Package jebl.evolution.align.scores
Class ScoresFactory
java.lang.Object
jebl.evolution.align.scores.ScoresFactory
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final AminoAcidScores
static final Blosum45
static final Blosum50
static final Blosum55
static final Blosum60
static final Blosum62
static final Blosum65
static final Blosum70
static final Blosum75
static final Blosum80
static final Blosum85
static final Blosum90
static final NucleotideScores
static final NucleotideScores
static final NucleotideScores
static final NucleotideScores
static final Pam100
static final Pam110
static final Pam120
static final Pam130
static final Pam140
static final Pam150
static final Pam160
static final Pam170
static final Pam180
static final Pam190
static final Pam200
static final Pam210
static final Pam220
static final Pam230
static final Pam240
static final Pam250
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Scores
generateScores
(String nameVal) For any matrix.static Scores
generateScores
(String name, float val) For calculated nucleotide matrices.static Scores
generateScores
(String name, int val) For Blosum and Pam matricesstatic AminoAcidScores[]
static NucleotideScores[]
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Field Details
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BLOSUM_45
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BLOSUM_50
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BLOSUM_55
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BLOSUM_60
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BLOSUM_62
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BLOSUM_65
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BLOSUM_70
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BLOSUM_75
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BLOSUM_80
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BLOSUM_85
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BLOSUM_90
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PAM_100
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PAM_110
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PAM_120
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PAM_130
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PAM_140
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PAM_150
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PAM_160
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PAM_170
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PAM_180
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PAM_190
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PAM_200
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PAM_210
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PAM_220
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PAM_230
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PAM_240
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PAM_250
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AMINO_ACID_IDENTITY
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NUCLEOTIDE_51_PERCENT_SIMILARITY
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NUCLEOTIDE_65_PERCENT_SIMILARITY
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NUCLEOTIDE_70_PERCENT_SIMILARITY
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NUCLEOTIDE_93_PERCENT_SIMILARITY
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Constructor Details
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ScoresFactory
public ScoresFactory()
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Method Details
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generateScores
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
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
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
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getAvailableNucleotideScores
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