Class ModifiedCompoundImpl
- java.lang.Object
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- org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
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- 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
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Constructor Summary
Constructors Constructor Description ModifiedCompoundImpl()
ModifiedCompoundImpl(ProteinModification modification, Collection<StructureAtomLinkage> linkages)
ModifiedCompoundImpl(ProteinModification modification, StructureGroup modifiedResidue)
Create a ModifiedCompoundImpl that has only one involved component.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 compoundSet<StructureGroup>
getGroups()
Set<StructureGroup>
getGroups(boolean isAminoAcid)
ProteinModification
getModification()
int
hashCode()
void
setAtomLinkages(Set<StructureAtomLinkage> linkages)
Set atom linkagesvoid
setDescription(String desc)
void
setGroups(Set<StructureGroup> groups)
void
setModification(ProteinModification protmod)
String
toString()
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Constructor Detail
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ModifiedCompoundImpl
public ModifiedCompoundImpl()
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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.
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ModifiedCompoundImpl
public ModifiedCompoundImpl(ProteinModification modification, Collection<StructureAtomLinkage> linkages)
- Parameters:
modification
- ProteinModification.linkages
- a collection of atom linkages.- See Also:
ProteinModification
,StructureAtomLinkage
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Method Detail
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setModification
public void setModification(ProteinModification protmod)
- Specified by:
setModification
in interfaceModifiedCompound
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getModification
public ProteinModification getModification()
- Specified by:
getModification
in interfaceModifiedCompound
- Returns:
ProteinModificationBean
occurred on the residue.
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getGroups
public Set<StructureGroup> getGroups()
- Specified by:
getGroups
in interfaceModifiedCompound
- Returns:
- a set of involved group.
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getGroups
public Set<StructureGroup> getGroups(boolean isAminoAcid)
- Specified by:
getGroups
in interfaceModifiedCompound
- Parameters:
isAminoAcid
- true if amino acids.- Returns:
- a set of involved group of the type.
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setGroups
public void setGroups(Set<StructureGroup> groups)
- Specified by:
setGroups
in interfaceModifiedCompound
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getAtomLinkages
public Set<StructureAtomLinkage> getAtomLinkages()
- Specified by:
getAtomLinkages
in interfaceModifiedCompound
- Returns:
- a set of atom linkages.
- See Also:
#getLinkedGroupPairs
,StructureAtomLinkage
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setAtomLinkages
public void setAtomLinkages(Set<StructureAtomLinkage> linkages)
Description copied from interface:ModifiedCompound
Set atom linkages- Specified by:
setAtomLinkages
in interfaceModifiedCompound
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addAtomLinkage
public boolean addAtomLinkage(StructureAtomLinkage linkage)
Description copied from interface:ModifiedCompound
Add a linkage. Add new the involved groups first usingaddGroup
.- Specified by:
addAtomLinkage
in interfaceModifiedCompound
- Parameters:
linkage
- an atom linkage.- Returns:
- true if this linkage was not already contained.
- See Also:
StructureAtomLinkage
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addAtomLinkages
public void addAtomLinkages(Collection<StructureAtomLinkage> linkages)
Description copied from interface:ModifiedCompound
Add a collections of linkages.- Specified by:
addAtomLinkages
in interfaceModifiedCompound
- Parameters:
linkages
- an atom linkage.
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crossChains
public boolean crossChains()
- Specified by:
crossChains
in interfaceModifiedCompound
- Returns:
- true if groups from multiple chains were involved
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getDescription
public String getDescription()
Description copied from interface:ModifiedCompound
return a description of this compound- Specified by:
getDescription
in interfaceModifiedCompound
- Returns:
- a description
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setDescription
public void setDescription(String desc)
- Specified by:
setDescription
in interfaceModifiedCompound
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compareTo
public int compareTo(ModifiedCompound compound)
- Specified by:
compareTo
in interfaceComparable<ModifiedCompound>
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