Package psidev.psi.mi.jami.model.impl

Class DefaultPolymer

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultInteractor

psidev.psi.mi.jami.model.impl.DefaultMolecule

psidev.psi.mi.jami.model.impl.DefaultPolymer

All Implemented Interfaces:

Interactor, Molecule, Polymer

Direct Known Subclasses:

DefaultNucleicAcid, DefaultProtein, MitabPolymer

public class DefaultPolymer
extends DefaultMolecule
implements Polymer

Default implementation for Polymer Notes: The equals and hashcode methods have NOT been overridden because the Polymer object is a complex object. To compare Polymer objects, you can use some comparators provided by default: - DefaultPolymerComparator - UnambiguousPolymerComparator - DefaultExactPolymerComparator - UnambiguousExactPolymerComparator - AbstractPolymerComparator

Since:

21/05/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.Interactor

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Fields inherited from interface psidev.psi.mi.jami.model.Polymer

POLYMER, POLYMER_MI

Constructor Summary

Constructors

Constructor	Description
DefaultPolymer(String name)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, CvTerm type)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, CvTerm type, Organism organism)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, Organism organism)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, CvTerm type)	Constructor for DefaultPolymer.
DefaultPolymer(String name, CvTerm type, Organism organism)	Constructor for DefaultPolymer.
DefaultPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, Organism organism)	Constructor for DefaultPolymer.
DefaultPolymer(String name, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, Xref uniqueId)	Constructor for DefaultPolymer.

Method Summary

Modifier and Type	Method	Description
String	getSequence()	Getter for the field sequence.
void	setInteractorType(CvTerm interactorType)	Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)
void	setSequence(String sequence)	Sets the sequence of the polymer.

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultInteractor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumsWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseXrefs, initialiseXrefsWith, setFullName, setOrganism, setShortName, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface psidev.psi.mi.jami.model.Interactor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

Constructor Detail

DefaultPolymer

public DefaultPolymer(String name,
                      CvTerm type)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      CvTerm type)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultPolymer

public DefaultPolymer(String name,
                      CvTerm type,
                      Organism organism)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      CvTerm type,
                      Organism organism)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultPolymer

public DefaultPolymer(String name,
                      CvTerm type,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      CvTerm type,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name,
                      CvTerm type,
                      Organism organism,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      CvTerm type,
                      Organism organism,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

DefaultPolymer

public DefaultPolymer(String name,
                      Organism organism)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

organism - a Organism object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      Organism organism)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

DefaultPolymer

public DefaultPolymer(String name,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name,
                      Organism organism,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultPolymer

public DefaultPolymer(String name,
                      String fullName,
                      Organism organism,
                      Xref uniqueId)

Constructor for DefaultPolymer.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

getSequence

public String getSequence()

Getter for the field sequence.

Specified by:

getSequence in interface Polymer

Returns:

a String object.

setSequence

public void setSequence(String sequence)

Sets the sequence of the polymer.

Setter for the field sequence.

Specified by:

setSequence in interface Polymer

Parameters:

sequence - : sequence to set

setInteractorType

public void setInteractorType(CvTerm interactorType)

Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329) Sets the interactor type of this polymer. If the given interactorType is null, it sets the interactorType to 'biopolymer'(MI:0383)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultInteractor

Parameters:

interactorType - : molecule type