com.hfg.bio.seq.alignment.matrix

Class SubstitutionMatrix

java.lang.Object

com.hfg.bio.seq.alignment.matrix.SubstitutionMatrix

public class SubstitutionMatrix
extends Object

Substitution matrix for use with pairwise sequence alignments.

Field Summary

Fields

Modifier and Type	Field and Description
static SubstitutionMatrix	BLOSUM62
static SubstitutionMatrix	BLOSUM90
static SubstitutionMatrix	BLOSUM90_GAP
static SubstitutionMatrix	IDENTITY
static SubstitutionMatrix	IDENTITY_GAP
static SubstitutionMatrix	NUCLEOTIDE
static SubstitutionMatrix	PAM10
static SubstitutionMatrix	PAM100
static SubstitutionMatrix	PAM120
static SubstitutionMatrix	PAM250

Constructor Summary

Constructors

Constructor and Description
SubstitutionMatrix(String inName, BufferedReader inReader) Constructor using a BufferedReader.

Method Summary

Modifier and Type	Method and Description
boolean	contains(char inResidue) Returns whether or not this substitution matrix supports the specified character.
float[][]	getRawMatrix()
int	getResidueIndex(char inResidue)
int[]	getResidueIndicesForSequence(String inSequence)
String	name()
float	score(char inResidue1, char inResidue2)
float	scoreCaseInsensitive(char inResidue1, char inResidue2)
String	toString()
static Collection<SubstitutionMatrix>	values()

Methods inherited from class java.lang.Object

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

Field Detail

IDENTITY

public static final SubstitutionMatrix IDENTITY

IDENTITY_GAP

public static final SubstitutionMatrix IDENTITY_GAP

NUCLEOTIDE

public static final SubstitutionMatrix NUCLEOTIDE

PAM10

public static final SubstitutionMatrix PAM10

PAM100

public static final SubstitutionMatrix PAM100

PAM120

public static final SubstitutionMatrix PAM120

PAM250

public static final SubstitutionMatrix PAM250

BLOSUM62

public static final SubstitutionMatrix BLOSUM62

BLOSUM90

public static final SubstitutionMatrix BLOSUM90

BLOSUM90_GAP

public static final SubstitutionMatrix BLOSUM90_GAP

Constructor Detail

SubstitutionMatrix

public SubstitutionMatrix(String inName,
                          BufferedReader inReader)
                   throws IOException

Constructor using a BufferedReader.

Parameters:

inName - the name to use for the substitution matrix

inReader - reader containing the substitution matrix data

Throws:

IOException - if a problem is encountered reading from the specified Reader

Method Detail

name

public String name()

toString

public String toString()

Overrides:

toString in class Object

contains

public boolean contains(char inResidue)

Returns whether or not this substitution matrix supports the specified character.

Parameters:

inResidue - the character to be checked for inclusion in this matrix

Returns:

whether or not this substitution matrix supports the specified character

getResidueIndex

public int getResidueIndex(char inResidue)

getResidueIndicesForSequence

public int[] getResidueIndicesForSequence(String inSequence)

score

public float score(char inResidue1,
                   char inResidue2)

scoreCaseInsensitive

public float scoreCaseInsensitive(char inResidue1,
                                  char inResidue2)

getRawMatrix

public float[][] getRawMatrix()

values

public static Collection<SubstitutionMatrix> values()