jebl.evolution.align.scores
Class ScoresFactory

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

public class ScoresFactory
extends Object

Constructor Summary

ScoresFactory()

Method Summary

static 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 matrices
static AminoAcidScores[]	getAvailableAminoAcidScores()
static NucleotideScores[]	getAvailableNucleotideScores()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ScoresFactory

public ScoresFactory()

Method Detail

generateScores

public static Scores generateScores(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(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(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()