org.biojava.nbio.structure.symmetry.core

Class UniqueSequenceList

java.lang.Object

org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

All Implemented Interfaces:

Cloneable

public class UniqueSequenceList
extends Object
implements Cloneable

Bean for a single sequence. These are intended to be unique sequences (100% id) as an imput to clustering.

Constructor Summary

Constructors

Constructor and Description
UniqueSequenceList(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, String seqResSequence)

Method Summary

Modifier and Type	Method and Description
Object	clone()
List<Integer>	getAlignment1()
List<Integer>	getAlignment2()
Atom[]	getCalphaAtoms()
String	getChainId()
int	getModelNumber()
String	getSeqResSequence()
static String	getSequenceString(Atom[] caAlphaAtoms)
int	getStructureId()
boolean	isMatch(Atom[] caAlphaAtoms) Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list
void	setAlignment1(List<Integer> alignment1)
void	setAlignment2(List<Integer> alignment2)
void	setSequenceString(String sequenceString)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

UniqueSequenceList

public UniqueSequenceList(Atom[] cAlphaAtoms,
                          String chainId,
                          int modelNumber,
                          int structureId,
                          String seqResSequence)

Method Detail

isMatch

public boolean isMatch(Atom[] caAlphaAtoms)

Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list

Parameters:

caAlphaAtoms -

Returns:

getChainId

public String getChainId()

getModelNumber

public int getModelNumber()

getStructureId

public int getStructureId()

getCalphaAtoms

public Atom[] getCalphaAtoms()

getSeqResSequence

public String getSeqResSequence()

setSequenceString

public void setSequenceString(String sequenceString)

Parameters:

sequenceString - the sequenceString to set

getAlignment1

public List<Integer> getAlignment1()

Returns:

the alignment1

setAlignment1

public void setAlignment1(List<Integer> alignment1)

Parameters:

alignment1 - the alignment1 to set

getAlignment2

public List<Integer> getAlignment2()

Returns:

the alignment2

setAlignment2

public void setAlignment2(List<Integer> alignment2)

Parameters:

alignment2 - the alignment2 to set

clone

public Object clone()

Overrides:

clone in class Object

getSequenceString

public static String getSequenceString(Atom[] caAlphaAtoms)

toString

public String toString()

Overrides:

toString in class Object