com.hfg.bio.seq.alignment.matrix

Class PSSM

java.lang.Object

com.hfg.bio.seq.alignment.matrix.PSSM

public class PSSM
extends Object

Container for a Position-Specific Scoring Matrix (PSSM). Also known as a Position-Weighted Matrix.

See http://en.wikipedia.org/wiki/Position_weight_matrix

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PSSM.Flag

Constructor Summary

Constructors

Constructor and Description
PSSM(MultipleSequenceAlignment inMSA, AminoAcidFreqTable inBackgroundAAFreq, PSSM.Flag... inFlags) Constructs a PSSM from a multiple sequence alignment.
PSSM(MultipleSequenceAlignment inMSA, PSSM.Flag... inFlags) Constructs a PSSM from a multiple sequence alignment.
PSSM(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
float	getGapExtScore(int inPosition)
float	getGapOpenScore(int inPosition)
float[]	getGapOpenScores()
String	getName()
int	length()
float	score(int inPosition, char inResidue)
PSSM	setName(String inValue)
String	showScoring(Collection<BioSequence> inSeqs)
XMLTag	toXMLTag()

Methods inherited from class java.lang.Object

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

Constructor Detail

PSSM

public PSSM(MultipleSequenceAlignment inMSA,
            PSSM.Flag... inFlags)

Constructs a PSSM from a multiple sequence alignment.

Parameters:

inMSA - source multiple sequence alignment

inFlags - flag(s) to apply to the PSSM

PSSM

public PSSM(MultipleSequenceAlignment inMSA,
            AminoAcidFreqTable inBackgroundAAFreq,
            PSSM.Flag... inFlags)

Constructs a PSSM from a multiple sequence alignment.

Parameters:

inMSA - source multiple sequence alignment

inBackgroundAAFreq - optional background amino acid frequency table. If null, an equal residue probability is used.

inFlags - flag(s) to apply to the PSSM

PSSM

public PSSM(XMLTag inXMLTag)

Method Detail

score

public float score(int inPosition,
                   char inResidue)

getGapOpenScore

public float getGapOpenScore(int inPosition)

getGapOpenScores

public float[] getGapOpenScores()

getGapExtScore

public float getGapExtScore(int inPosition)

showScoring

public String showScoring(Collection<BioSequence> inSeqs)

getName

public String getName()

setName

public PSSM setName(String inValue)

length

public int length()

toXMLTag

public XMLTag toXMLTag()