java.lang.Object
- org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<ModifiedCompound>, ModifiedCompound
```
public class ModifiedCompoundImpl
extends java.lang.Object
implements ModifiedCompound, java.io.Serializable, java.lang.Comparable<ModifiedCompound>
```
Since:

3.0

Author:

Jianjiong Gao

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field Description

static java.lang.String newline

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`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()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - newline
```
public static final java.lang.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:
    
    java.lang.IllegalArgumentException - if either argument is null.
  - ModifiedCompoundImpl
```
public ModifiedCompoundImpl(ProteinModification modification,
                            java.util.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 java.lang.String getOriginalModificationId()
```
    Deprecated.
    use getModification().getId()
    
    Returns:
    
    the original modification ID.
  - getGroups
```
public java.util.Set<StructureGroup> getGroups()
```
    Specified by:
    
    getGroups in interface ModifiedCompound
    
    Returns:
    
    a set of involved group.
  - getGroups
```
public java.util.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(java.util.Set<StructureGroup> groups)
```
    Specified by:
    
    setGroups in interface ModifiedCompound
  - getAtomLinkages
```
public java.util.Set<StructureAtomLinkage> getAtomLinkages()
```
    Specified by:
    
    getAtomLinkages in interface ModifiedCompound
    
    Returns:
    
    a set of atom linkages.
    
    See Also:
    
    #getLinkedGroupPairs, StructureAtomLinkage
  - setAtomLinkages
```
public void setAtomLinkages(java.util.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(java.util.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 java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getDescription
```
public java.lang.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(java.lang.String desc)
```
    Specified by:
    
    setDescription in interface ModifiedCompound
  - compareTo
```
public int compareTo(ModifiedCompound compound)
```
    Specified by:
    
    compareTo in interface java.lang.Comparable<ModifiedCompound>
  - equals
```
public boolean equals(java.lang.Object obj)
```
    Overrides:
    
    equals in class java.lang.Object
    
    Returns:
    
    true if same modification and same components; false, otherwise.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object

Class ModifiedCompoundImpl

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

newline

Constructor Detail

ModifiedCompoundImpl

ModifiedCompoundImpl

ModifiedCompoundImpl

Method Detail

setModification

getModification

getOriginalModificationId

getGroups

getGroups

setGroups

getAtomLinkages

setAtomLinkages

addAtomLinkage

addAtomLinkages

crossChains

toString

getDescription

setDescription

compareTo

equals

hashCode