org.biojava.nbio.protmod.structure

Class ModifiedCompoundImpl

java.lang.Object

org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

All Implemented Interfaces:

Serializable, Comparable<ModifiedCompound>, ModifiedCompound

public class ModifiedCompoundImpl
extends Object
implements ModifiedCompound, Serializable, Comparable<ModifiedCompound>

Since:

3.0

Author:

Jianjiong Gao

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	newline

Constructor Summary

Constructors

Constructor and Description
ModifiedCompoundImpl()
ModifiedCompoundImpl(ProteinModification modification, Collection<StructureAtomLinkage> linkages)
ModifiedCompoundImpl(ProteinModification modification, StructureGroup modifiedResidue) Create a ModifiedCompoundImpl that has only one involved component.

Method Summary

Modifier and Type	Method and Description
boolean	addAtomLinkage(StructureAtomLinkage linkage) Add a linkage.
void	addAtomLinkages(Collection<StructureAtomLinkage> linkages) Add a collections of linkages.
int	compareTo(ModifiedCompound compound)
boolean	crossChains()
boolean	equals(Object obj)
Set<StructureAtomLinkage>	getAtomLinkages()
String	getDescription() return a description of this compound
Set<StructureGroup>	getGroups()
Set<StructureGroup>	getGroups(boolean isAminoAcid)
ProteinModification	getModification()
String	getOriginalModificationId() Deprecated. use getModification().getId()
int	hashCode()
void	setAtomLinkages(Set<StructureAtomLinkage> linkages) Set atom linkages
void	setDescription(String desc)
void	setGroups(Set<StructureGroup> groups)
void	setModification(ProteinModification protmod)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

newline

public static final String newline

Constructor Detail

ModifiedCompoundImpl

public ModifiedCompoundImpl()

ModifiedCompoundImpl

public ModifiedCompoundImpl(ProteinModification modification,
                            StructureGroup modifiedResidue)

Create a ModifiedCompoundImpl that has only one involved component. Use this constructor for a modified residue.

Parameters:

modification - ProteinModification.

modifiedResidue - modified group.

Throws:

IllegalArgumentException - if either argument is null.

ModifiedCompoundImpl

public ModifiedCompoundImpl(ProteinModification modification,
                            Collection<StructureAtomLinkage> linkages)

Parameters:

modification - ProteinModification.

linkages - a collection of atom linkages.

See Also:

ProteinModification, StructureAtomLinkage

Method Detail

setModification

public void setModification(ProteinModification protmod)

Specified by:

setModification in interface ModifiedCompound

getModification

public ProteinModification getModification()

Specified by:

getModification in interface ModifiedCompound

Returns:

ProteinModificationBean occurred on the residue.

getOriginalModificationId

@Deprecated
public String getOriginalModificationId()

Deprecated. use getModification().getId()

Returns:

the original modification ID.

getGroups

public Set<StructureGroup> getGroups()

Specified by:

getGroups in interface ModifiedCompound

Returns:

a set of involved group.

getGroups

public Set<StructureGroup> getGroups(boolean isAminoAcid)

Specified by:

getGroups in interface ModifiedCompound

Parameters:

isAminoAcid - true if amino acids.

Returns:

a set of involved group of the type.

setGroups

public void setGroups(Set<StructureGroup> groups)

Specified by:

setGroups in interface ModifiedCompound

getAtomLinkages

public Set<StructureAtomLinkage> getAtomLinkages()

Specified by:

getAtomLinkages in interface ModifiedCompound

Returns:

a set of atom linkages.

See Also:

#getLinkedGroupPairs, StructureAtomLinkage

setAtomLinkages

public void setAtomLinkages(Set<StructureAtomLinkage> linkages)

Description copied from interface: ModifiedCompound

Set atom linkages

Specified by:

setAtomLinkages in interface ModifiedCompound

addAtomLinkage

public boolean addAtomLinkage(StructureAtomLinkage linkage)

Description copied from interface: ModifiedCompound

Add a linkage. Add new the involved groups first using addGroup.

Specified by:

addAtomLinkage in interface ModifiedCompound

Parameters:

linkage - an atom linkage.

Returns:

true if this linkage was not already contained.

See Also:

StructureAtomLinkage

addAtomLinkages

public void addAtomLinkages(Collection<StructureAtomLinkage> linkages)

Description copied from interface: ModifiedCompound

Add a collections of linkages.

Specified by:

addAtomLinkages in interface ModifiedCompound

Parameters:

linkages - an atom linkage.

crossChains

public boolean crossChains()

Specified by:

crossChains in interface ModifiedCompound

Returns:

true if groups from multiple chains were involved

toString

public String toString()

Overrides:

toString in class Object

getDescription

public String getDescription()

Description copied from interface: ModifiedCompound

return a description of this compound

Specified by:

getDescription in interface ModifiedCompound

Returns:

a description

setDescription

public void setDescription(String desc)

Specified by:

setDescription in interface ModifiedCompound

compareTo

public int compareTo(ModifiedCompound compound)

Specified by:

compareTo in interface Comparable<ModifiedCompound>

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

Returns:

true if same modification and same components; false, otherwise.

hashCode

public int hashCode()

Overrides:

hashCode in class Object