org.biojava3.protmod.structure
public class ModifiedCompoundImpl extends java.lang.Object implements ModifiedCompound, java.io.Serializable, java.lang.Comparable<ModifiedCompound>
Modifier and Type | Field and Description |
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static java.lang.String |
newline |
Constructor and Description |
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ModifiedCompoundImpl() |
ModifiedCompoundImpl(ProteinModification modification,
java.util.Collection<StructureAtomLinkage> linkages) |
ModifiedCompoundImpl(ProteinModification modification,
StructureGroup modifiedResidue)
Create a ModifiedCompoundImpl that has only one involved component.
|
Modifier and Type | Method and Description |
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boolean |
addAtomLinkage(StructureAtomLinkage linkage)
Add a linkage.
|
void |
addAtomLinkages(java.util.Collection<StructureAtomLinkage> linkages)
Add a collections of linkages.
|
int |
compareTo(ModifiedCompound compound) |
boolean |
crossChains() |
boolean |
equals(java.lang.Object obj) |
java.util.Set<StructureAtomLinkage> |
getAtomLinkages() |
java.lang.String |
getDescription()
return a description of this compound
|
java.util.Set<StructureGroup> |
getGroups() |
java.util.Set<StructureGroup> |
getGroups(boolean isAminoAcid) |
ProteinModification |
getModification() |
java.lang.String |
getOriginalModificationId()
Deprecated.
use getModification().getId()
|
int |
hashCode() |
void |
setAtomLinkages(java.util.Set<StructureAtomLinkage> linkages)
Set atom linkages
|
void |
setDescription(java.lang.String desc) |
void |
setGroups(java.util.Set<StructureGroup> groups) |
void |
setModification(ProteinModification protmod) |
java.lang.String |
toString() |
public ModifiedCompoundImpl()
public ModifiedCompoundImpl(ProteinModification modification, StructureGroup modifiedResidue)
modification
- ProteinModification
.modifiedResidue
- modified group.java.lang.IllegalArgumentException
- if either argument is null.public ModifiedCompoundImpl(ProteinModification modification, java.util.Collection<StructureAtomLinkage> linkages)
modification
- ProteinModification.linkages
- a collection of atom linkages.ProteinModification
,
StructureAtomLinkage
public void setModification(ProteinModification protmod)
setModification
in interface ModifiedCompound
public ProteinModification getModification()
getModification
in interface ModifiedCompound
ProteinModificationBean
occurred on the residue.public java.lang.String getOriginalModificationId()
public java.util.Set<StructureGroup> getGroups()
getGroups
in interface ModifiedCompound
public java.util.Set<StructureGroup> getGroups(boolean isAminoAcid)
getGroups
in interface ModifiedCompound
isAminoAcid
- true if amino acids.public void setGroups(java.util.Set<StructureGroup> groups)
setGroups
in interface ModifiedCompound
public java.util.Set<StructureAtomLinkage> getAtomLinkages()
getAtomLinkages
in interface ModifiedCompound
#getLinkedGroupPairs
,
StructureAtomLinkage
public void setAtomLinkages(java.util.Set<StructureAtomLinkage> linkages)
ModifiedCompound
setAtomLinkages
in interface ModifiedCompound
public boolean addAtomLinkage(StructureAtomLinkage linkage)
ModifiedCompound
addGroup
.addAtomLinkage
in interface ModifiedCompound
linkage
- an atom linkage.StructureAtomLinkage
public void addAtomLinkages(java.util.Collection<StructureAtomLinkage> linkages)
ModifiedCompound
addAtomLinkages
in interface ModifiedCompound
linkages
- an atom linkage.public boolean crossChains()
crossChains
in interface ModifiedCompound
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String getDescription()
ModifiedCompound
getDescription
in interface ModifiedCompound
public void setDescription(java.lang.String desc)
setDescription
in interface ModifiedCompound
public int compareTo(ModifiedCompound compound)
compareTo
in interface java.lang.Comparable<ModifiedCompound>
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object