com.hfg.bio.seq

Class PositionalFrequencyMatrix<T extends BioSequence>

java.lang.Object

com.hfg.bio.seq.PositionalFrequencyMatrix<T>

All Implemented Interfaces:

Cloneable

public class PositionalFrequencyMatrix<T extends BioSequence>
extends Object
implements Cloneable

Positional frequency matrix.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PositionalFrequencyMatrix.Flag

Constructor Summary

Constructors

Constructor and Description
PositionalFrequencyMatrix(MultipleSequenceAlignment<T> inMSA)
PositionalFrequencyMatrix(MultipleSequenceAlignment<T> inMSA, PositionalFrequencyMatrix.Flag... inFlags)

Method Summary

Modifier and Type	Method and Description
void	addSequence(T inSequence)
PositionalFrequencyMatrix<T>	clone()
int	getCount(Character inResidue, Integer inPosition)
Set<PositionalFrequencyMatrix.Flag>	getFlags()
float	getFraction(Character inResidue, Integer inPosition)
float	getFractionIncludingGaps(Character inResidue, Integer inPosition)
int	getGapCount(Integer inPosition)
int	getGapExtCount(Integer inPosition)
int	getGapOpenCount(Integer inPosition)
Set<Character>	getHighestFreqResidues(Integer inPosition) Returns the residue with the highest frequency at the specified position or multiple residues if they share the highest frequency value.
Set<Integer>	getPositionKeys()
int	getPositionTotal(Integer inPosition) Returns the number of sequences with a residue and not a gap at the specified position.
Set<Character>	getResidueKeys()
Set<Character>	getResidues(Integer inPosition)
Set<Character>	getResidues(Integer inPosition, Float inMinFraction) Retrieves the residues at the specified position that are represented above the specified minimum fraction.
void	insertGapAtPosition(int inPosition)

Methods inherited from class java.lang.Object

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

Constructor Detail

PositionalFrequencyMatrix

public PositionalFrequencyMatrix(MultipleSequenceAlignment<T> inMSA)

PositionalFrequencyMatrix

public PositionalFrequencyMatrix(MultipleSequenceAlignment<T> inMSA,
                                 PositionalFrequencyMatrix.Flag... inFlags)

Method Detail

clone

public PositionalFrequencyMatrix<T> clone()

Overrides:

clone in class Object

addSequence

public void addSequence(T inSequence)

getResidueKeys

public Set<Character> getResidueKeys()

getPositionKeys

public Set<Integer> getPositionKeys()

insertGapAtPosition

public void insertGapAtPosition(int inPosition)

getCount

public int getCount(Character inResidue,
                    Integer inPosition)

getGapCount

public int getGapCount(Integer inPosition)

getGapOpenCount

public int getGapOpenCount(Integer inPosition)

getGapExtCount

public int getGapExtCount(Integer inPosition)

getHighestFreqResidues

public Set<Character> getHighestFreqResidues(Integer inPosition)

Returns the residue with the highest frequency at the specified position or multiple residues if they share the highest frequency value.

Parameters:

inPosition - the (1-based) position to evaluate

Returns:

the residue with the highest frequency at the specified position or multiple residues if they share the highest frequency value

getResidues

public Set<Character> getResidues(Integer inPosition)

getResidues

public Set<Character> getResidues(Integer inPosition,
                                  Float inMinFraction)

Retrieves the residues at the specified position that are represented above the specified minimum fraction.

Parameters:

inPosition - the aligned sequence position

inMinFraction - the minimum fraction for residues to return. Null returns residues that are present in at least one sequence.

Returns:

a Set of residue characters from the specified position

getFraction

public float getFraction(Character inResidue,
                         Integer inPosition)

getFractionIncludingGaps

public float getFractionIncludingGaps(Character inResidue,
                                      Integer inPosition)

getPositionTotal

public int getPositionTotal(Integer inPosition)

Returns the number of sequences with a residue and not a gap at the specified position.

Parameters:

inPosition - the 1-based position in the matrix being queried

Returns:

the number of sequences with a residue and not a gap at the specified position

getFlags

public Set<PositionalFrequencyMatrix.Flag> getFlags()