public class ScoresFactory
extends java.lang.Object
Modifier and Type | Field and 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 |
Constructor and Description |
---|
ScoresFactory() |
Modifier and Type | Method and 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 matrices
|
static AminoAcidScores[] |
getAvailableAminoAcidScores() |
static NucleotideScores[] |
getAvailableNucleotideScores() |
public static final Blosum45 BLOSUM_45
public static final Blosum50 BLOSUM_50
public static final Blosum55 BLOSUM_55
public static final Blosum60 BLOSUM_60
public static final Blosum62 BLOSUM_62
public static final Blosum65 BLOSUM_65
public static final Blosum70 BLOSUM_70
public static final Blosum75 BLOSUM_75
public static final Blosum80 BLOSUM_80
public static final Blosum85 BLOSUM_85
public static final Blosum90 BLOSUM_90
public static final Pam100 PAM_100
public static final Pam110 PAM_110
public static final Pam120 PAM_120
public static final Pam130 PAM_130
public static final Pam140 PAM_140
public static final Pam150 PAM_150
public static final Pam160 PAM_160
public static final Pam170 PAM_170
public static final Pam180 PAM_180
public static final Pam190 PAM_190
public static final Pam200 PAM_200
public static final Pam210 PAM_210
public static final Pam220 PAM_220
public static final Pam230 PAM_230
public static final Pam240 PAM_240
public static final Pam250 PAM_250
public static final AminoAcidScores AMINO_ACID_IDENTITY
public static final NucleotideScores NUCLEOTIDE_51_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_65_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_70_PERCENT_SIMILARITY
public static final NucleotideScores NUCLEOTIDE_93_PERCENT_SIMILARITY
public static Scores generateScores(java.lang.String nameVal)
nameVal
- name and value of the matrix in String form. (eg Blosum45).public static Scores generateScores(java.lang.String name, int val)
name
- "Blosum" or "Pam"val
- currently 45 - 90 or 100 - 250public static Scores generateScores(java.lang.String name, float val)
name
- Currently only JukesCantorval
- val used to calculate matrix. eg. evolutionary distance d.public static AminoAcidScores[] getAvailableAminoAcidScores()
public static NucleotideScores[] getAvailableNucleotideScores()
http://code.google.com/p/jebl2/