com.hfg.bio.seq.alignment

Class MultipleSequenceAlignment<T extends BioSequence>

java.lang.Object

com.hfg.bio.seq.alignment.MultipleSequenceAlignment<T>

All Implemented Interfaces:

Cloneable

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

Container for aligned sequences.

Constructor Summary

Constructors

Constructor and Description
MultipleSequenceAlignment()
MultipleSequenceAlignment(Collection<T> inAlignedSeqs)

Method Summary

Modifier and Type	Method and Description
void	addInsert(int inIndex)
void	addSequence(T inSeq)
void	clearAttributes()
void	clearCachedData()
MultipleSequenceAlignment<T>	clone()
Object	getAttribute(String inName)
Collection<String>	getAttributeNames()
BioSequenceType	getBioSequenceType()
DataTable	getDataTable()
DistanceMatrix	getDistanceMatrix(DistanceMatrixModel inAlgorithm) Returns a distance matrix using the specified model.
String	getId()
SparseMatrix<String,String,Float>	getPctIdentityMatrix() Returns a percent identity matrix adjusted for any terminal gaps.
PositionalFrequencyMatrix<T>	getPositionFreqMatrix()
PositionalFrequencyMatrix<T>	getPositionFreqMatrix(PositionalFrequencyMatrix.Flag[] inFlags)
List<Character>	getPositionResidues(int inPosition)
Set<Character>	getPositionResidueSet(int inPosition)
T	getSequence(String inSeqId)
List<T>	getSequences()
String	getTitle()
boolean	hasAttribute(String inName)
int	length()
void	orderByDistanceTo(String inSeqID)
Object	removeAttribute(String inName)
void	removeSequence(T inSeq)
void	setAttribute(String inName, Object inValue)
MultipleSequenceAlignment<T>	setDataTable(DataTable inValue)
MultipleSequenceAlignment<T>	setId(String inValue)
protected void	setLength(int inValue)
MultipleSequenceAlignment<T>	setTitle(String inValue)
int	size()
MultipleSequenceAlignment<T>	subset(Collection<String> inSeqIds)

Methods inherited from class java.lang.Object

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

Constructor Detail

MultipleSequenceAlignment

public MultipleSequenceAlignment()

MultipleSequenceAlignment

public MultipleSequenceAlignment(Collection<T> inAlignedSeqs)

Method Detail

setId

public MultipleSequenceAlignment<T> setId(String inValue)

getId

public String getId()

setTitle

public MultipleSequenceAlignment<T> setTitle(String inValue)

getTitle

public String getTitle()

setDataTable

public MultipleSequenceAlignment<T> setDataTable(DataTable inValue)

getDataTable

public DataTable getDataTable()

clone

public MultipleSequenceAlignment<T> clone()

Overrides:

clone in class Object

clearCachedData

public void clearCachedData()

subset

public MultipleSequenceAlignment<T> subset(Collection<String> inSeqIds)

addSequence

public void addSequence(T inSeq)

getSequences

public List<T> getSequences()

getSequence

public T getSequence(String inSeqId)

removeSequence

public void removeSequence(T inSeq)

addInsert

public void addInsert(int inIndex)

size

public int size()

getBioSequenceType

public BioSequenceType getBioSequenceType()

length

public int length()

getPositionFreqMatrix

public PositionalFrequencyMatrix<T> getPositionFreqMatrix()

getPositionFreqMatrix

public PositionalFrequencyMatrix<T> getPositionFreqMatrix(PositionalFrequencyMatrix.Flag[] inFlags)

getPctIdentityMatrix

public SparseMatrix<String,String,Float> getPctIdentityMatrix()

Returns a percent identity matrix adjusted for any terminal gaps.

Returns:

the generated percent identity matrix

getDistanceMatrix

public DistanceMatrix getDistanceMatrix(DistanceMatrixModel inAlgorithm)

Returns a distance matrix using the specified model. For a simple distance matrix based on mismatches and without any evolutionary compensation, use the UncorrectedModel.

Parameters:

inAlgorithm - the distance matrix mode to use when calculating the distance matrix

Returns:

the generated DistanceMatrix

orderByDistanceTo

public void orderByDistanceTo(String inSeqID)

getPositionResidues

public List<Character> getPositionResidues(int inPosition)

getPositionResidueSet

public Set<Character> getPositionResidueSet(int inPosition)

setAttribute

public void setAttribute(String inName,
                         Object inValue)

hasAttribute

public boolean hasAttribute(String inName)

getAttribute

public Object getAttribute(String inName)

getAttributeNames

public Collection<String> getAttributeNames()

clearAttributes

public void clearAttributes()

removeAttribute

public Object removeAttribute(String inName)

setLength

protected void setLength(int inValue)