pid
Class Molecule

java.lang.Object
  extended by pid.Molecule
All Implemented Interfaces:
java.io.Serializable
Direct Known Subclasses:
Complex, Compound, Protein, RNA

public class Molecule
extends java.lang.Object
implements java.io.Serializable

Generic type of molecule, this class represent a structured sequence of atoms.

Author:
Samuel Croset
See Also:
Serialized Form

Field Summary
private  java.util.ArrayList<ComplexComponent> complexComponents
           
private  java.util.ArrayList<FamilyMember> familyMembers
           
private  int id
           
private  java.util.ArrayList<Name> names
           
private  java.util.ArrayList<MoleculePart> parts
           
 
Constructor Summary
Molecule()
          Only constructor, initialise the array.
 
Method Summary
 java.util.ArrayList<ComplexComponent> getComplexComponents()
           
 int getId()
           
 java.util.ArrayList<FamilyMember> getMembers()
           
 java.util.ArrayList<Name> getNames()
           
 java.util.ArrayList<MoleculePart> getParts()
           
 PreferredSymbolName getPreferredSymbolName()
           
 UniprotName getUniprotName()
           
 void setComplexComponents(java.util.ArrayList<ComplexComponent> complexComponents)
           
 void setId(int id)
           
 void setMembers(java.util.ArrayList<FamilyMember> familyMembers)
           
 void setNames(java.util.ArrayList<Name> names)
           
 void setParts(java.util.ArrayList<MoleculePart> parts)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

id

private int id

names

private java.util.ArrayList<Name> names

complexComponents

private java.util.ArrayList<ComplexComponent> complexComponents

familyMembers

private java.util.ArrayList<FamilyMember> familyMembers

parts

private java.util.ArrayList<MoleculePart> parts
Constructor Detail

Molecule

public Molecule()
Only constructor, initialise the array.

Method Detail

setParts

public void setParts(java.util.ArrayList<MoleculePart> parts)

getParts

public java.util.ArrayList<MoleculePart> getParts()
Returns:
the molecules in which the current molecule is part of.

setMembers

public void setMembers(java.util.ArrayList<FamilyMember> familyMembers)

getMembers

public java.util.ArrayList<FamilyMember> getMembers()
Returns:
the family members of the current molecule.

setComplexComponents

public void setComplexComponents(java.util.ArrayList<ComplexComponent> complexComponents)

getComplexComponents

public java.util.ArrayList<ComplexComponent> getComplexComponents()
Returns:
the component of a complex molecule.

setId

public void setId(int id)

getId

public int getId()
Returns:
the id of the current molecule.

setNames

public void setNames(java.util.ArrayList<Name> names)

getNames

public java.util.ArrayList<Name> getNames()
Returns:
the names associated with the current molecule. Names are ways to describe proteins by the community.

getUniprotName

public UniprotName getUniprotName()
Returns:
the uniprot name for the current molecule. Uniprot name is a cross-reference to a uniprot identifier.

getPreferredSymbolName

public PreferredSymbolName getPreferredSymbolName()
Returns:
the preferred symbol of the current molecule. Useful to display the protein name to users.