org.biojava.nbio.structure.symmetry.core

Class SequenceAlignmentCluster

java.lang.Object

org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

All Implemented Interfaces:

Cloneable

public class SequenceAlignmentCluster
extends Object
implements Cloneable

Represents a cluster of equivalent sequences

Constructor Summary

Constructors

Constructor and Description
SequenceAlignmentCluster(QuatSymmetryParameters parameters)

Method Summary

Modifier and Type	Method and Description
void	addUniqueSequenceList(UniqueSequenceList sequenceList)
Object	clone()
List<Atom[]>	getAlignedCalphaAtoms()
List<String>	getChainIds()
double	getMaxSequenceIdentity()
double	getMinSequenceIdentity()
List<Integer>	getModelNumbers()
PairwiseAlignment	getPairwiseAlignment(SequenceAlignmentCluster other)
int	getSequenceAlignmentLength()
int	getSequenceCount()
List<Integer>	getStructureIds()
List<UniqueSequenceList>	getUniqueSequenceList()
boolean	identityMatch(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, String sequence) Match a sequence to this cluster at 100% identity.
boolean	isPseudoStoichiometric()
void	setMaxSequenceIdentity(double maxSequenceIdentity)
void	setMinSequenceIdentity(double minSequenceIdentity)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceAlignmentCluster

public SequenceAlignmentCluster(QuatSymmetryParameters parameters)

Method Detail

isPseudoStoichiometric

public boolean isPseudoStoichiometric()

getMinSequenceIdentity

public double getMinSequenceIdentity()

setMinSequenceIdentity

public void setMinSequenceIdentity(double minSequenceIdentity)

getMaxSequenceIdentity

public double getMaxSequenceIdentity()

setMaxSequenceIdentity

public void setMaxSequenceIdentity(double maxSequenceIdentity)

addUniqueSequenceList

public void addUniqueSequenceList(UniqueSequenceList sequenceList)

getSequenceCount

public int getSequenceCount()

Returns:

the number of sequences which have been added to this cluster

getSequenceAlignmentLength

public int getSequenceAlignmentLength()

getUniqueSequenceList

public List<UniqueSequenceList> getUniqueSequenceList()

getChainIds

public List<String> getChainIds()

getModelNumbers

public List<Integer> getModelNumbers()

getStructureIds

public List<Integer> getStructureIds()

getAlignedCalphaAtoms

public List<Atom[]> getAlignedCalphaAtoms()

identityMatch

public boolean identityMatch(Atom[] cAlphaAtoms,
                             String chainId,
                             int modelNumber,
                             int structureId,
                             String sequence)

Match a sequence to this cluster at 100% identity. If the given sequence matches the cluster seed (100%), then performs an alignment to the seed and adds it to the unique sequence list.

Parameters:

cAlphaAtoms -

chainId -

modelNumber -

structureId -

sequence -

Returns:

getPairwiseAlignment

public PairwiseAlignment getPairwiseAlignment(SequenceAlignmentCluster other)

clone

public Object clone()

Overrides:

clone in class Object

toString

public String toString()

Overrides:

toString in class Object