Uses of Interface
psidev.psi.mi.jami.model.Polymer

Packages that use Polymer

Package	Description
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher.impl
psidev.psi.mi.jami.enricher.impl.full
psidev.psi.mi.jami.enricher.listener
psidev.psi.mi.jami.enricher.listener.impl
psidev.psi.mi.jami.enricher.listener.impl.log
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.factory
psidev.psi.mi.jami.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.interactor
psidev.psi.mi.jami.xml.io.writer.elements.impl
psidev.psi.mi.jami.xml.model.extension.factory
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300

Uses of Polymer in psidev.psi.mi.jami.crosslink.extension

Classes in psidev.psi.mi.jami.crosslink.extension that implement Polymer

Modifier and Type	Class	Description
class	CsvProtein	Crosslink CSV extension of Protein.

Uses of Polymer in psidev.psi.mi.jami.enricher.impl

Methods in psidev.psi.mi.jami.enricher.impl that return types with arguments of type Polymer

Modifier and Type	Method	Description
InteractorEnricher<Polymer>	CompositeInteractorEnricher.getPolymerBaseEnricher()	Getter for the field polymerBaseEnricher.

Method parameters in psidev.psi.mi.jami.enricher.impl with type arguments of type Polymer

Modifier and Type	Method	Description
void	CompositeInteractorEnricher.setPolymerBaseEnricher(InteractorEnricher<Polymer> polymerBaseEnricher)	Setter for the field polymerBaseEnricher.

Uses of Polymer in psidev.psi.mi.jami.enricher.impl.full

Classes in psidev.psi.mi.jami.enricher.impl.full with type parameters of type Polymer

Modifier and Type	Class	Description
class	FullPolymerEnricher<T extends Polymer>	Full polymer enricher.
class	FullPolymerUpdater<T extends Polymer>	Full updater of polymer - update all properties of interactor as described in FullInteractorBaseUpdater - update sequence of polymer.

Uses of Polymer in psidev.psi.mi.jami.enricher.listener

Classes in psidev.psi.mi.jami.enricher.listener with type parameters of type Polymer

Modifier and Type	Interface	Description
interface	PolymerEnricherListener<T extends Polymer>	Interface for polymer enricher listener

Uses of Polymer in psidev.psi.mi.jami.enricher.listener.impl

Classes in psidev.psi.mi.jami.enricher.listener.impl with type parameters of type Polymer

Modifier and Type	Class	Description
class	PolymerEnricherListenerManager<P extends Polymer>	A manager for listeners which holds a list of listeners.

Uses of Polymer in psidev.psi.mi.jami.enricher.listener.impl.log

Classes in psidev.psi.mi.jami.enricher.listener.impl.log with type parameters of type Polymer

Modifier and Type	Class	Description
class	PolymerEnricherLogger<P extends Polymer>	A logging listener.

Uses of Polymer in psidev.psi.mi.jami.enricher.listener.impl.writer

Classes in psidev.psi.mi.jami.enricher.listener.impl.writer with type parameters of type Polymer

Modifier and Type	Class	Description
class	PolymerEnricherStatisticsWriter<P extends Polymer>	A statistics logger which records changes made by the enricher.

Uses of Polymer in psidev.psi.mi.jami.factory

Methods in psidev.psi.mi.jami.factory that return Polymer

Modifier and Type	Method	Description
Polymer	DefaultInteractorFactory.createPolymer(String name, CvTerm type)	Creates a new Polymer with the name and interactor type
Polymer	InteractorFactory.createPolymer(String name, CvTerm type)	Creates a new Polymer with the name and interactor type

Uses of Polymer in psidev.psi.mi.jami.listener

Classes in psidev.psi.mi.jami.listener with type parameters of type Polymer

Modifier and Type	Interface	Description
interface	PolymerChangeListener<P extends Polymer>	Listener for changes in polymer

Uses of Polymer in psidev.psi.mi.jami.listener.impl

Classes in psidev.psi.mi.jami.listener.impl with type parameters of type Polymer

Modifier and Type	Class	Description
class	PolymerChangeLogger<P extends Polymer>	This listener will just protein change events

Uses of Polymer in psidev.psi.mi.jami.model

Subinterfaces of Polymer in psidev.psi.mi.jami.model

Modifier and Type	Interface	Description
interface	NucleicAcid	Polymers of nucleotides which can interact with other molecules
interface	Protein	Polymer of amino acids which can interact with other molecules.

Uses of Polymer in psidev.psi.mi.jami.model.impl

Classes in psidev.psi.mi.jami.model.impl that implement Polymer

Modifier and Type	Class	Description
class	DefaultNucleicAcid	Default implementation for NucleicAcid.
class	DefaultPolymer	Default implementation for Polymer Notes: The equals and hashcode methods have NOT been overridden because the Polymer object is a complex object.
class	DefaultProtein	Default implementation for proteins and peptides Notes: The equals and hashcode methods have NOT been overridden because the Protein object is a complex object.

Uses of Polymer in psidev.psi.mi.jami.tab.extension

Classes in psidev.psi.mi.jami.tab.extension that implement Polymer

Modifier and Type	Class	Description
class	MitabNucleicAcid	Mitab extension for NucleicAcid It will contain a FileSourceLocator
class	MitabPolymer	Mitab extension of Polymer.
class	MitabProtein	Mitab extension of Protein.

Uses of Polymer in psidev.psi.mi.jami.utils

Methods in psidev.psi.mi.jami.utils that return Polymer

Modifier and Type	Method	Description
static Polymer	InteractorUtils.createPolymer(String name, String sequence)	createPolymer

Uses of Polymer in psidev.psi.mi.jami.utils.clone

Methods in psidev.psi.mi.jami.utils.clone with parameters of type Polymer

Modifier and Type	Method	Description
static void	InteractorCloner.copyAndOverrideBasicPolymerProperties(Polymer source, Polymer target)	copyAndOverrideBasicPolymerProperties

Uses of Polymer in psidev.psi.mi.jami.utils.comparator.interactor

Methods in psidev.psi.mi.jami.utils.comparator.interactor that return types with arguments of type Polymer

Modifier and Type	Method	Description
Comparator<Polymer>	InteractorComparator.getPolymerComparator()	Getter for the field polymerComparator.

Methods in psidev.psi.mi.jami.utils.comparator.interactor with parameters of type Polymer

Modifier and Type	Method	Description
static boolean	DefaultExactPolymerComparator.areEquals(Polymer polymer1, Polymer polymer2)	Use DefaultExactPolymerComparator to know if two polymers are equals.
static boolean	DefaultPolymerComparator.areEquals(Polymer polymer1, Polymer polymer2)	Use DefaultPolymerComparator to know if two proteins are equals.
static boolean	UnambiguousExactPolymerComparator.areEquals(Polymer polymer1, Polymer polymer2)	Use UnambiguousPolymerComparator to know if two polymers are equals.
static boolean	UnambiguousPolymerComparator.areEquals(Polymer polymer1, Polymer polymer2)	Use UnambiguousPolymerComparator to know if two polymers are equals.
int	PolymerComparator.compare(Polymer polymer1, Polymer polymer2)	It will first use DefaultExactInteractorBaseComparator to compare the basic interactor properties If the basic interactor properties are the same, it will look at sequence/organism.
int	UnambiguousExactPolymerComparator.compare(Polymer polymer1, Polymer polymer2)

Uses of Polymer in psidev.psi.mi.jami.xml.io.writer.elements.impl

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl with parameters of type Polymer

Modifier and Type	Method	Description
protected void	XmlInteractorWriter.writePolymerSequence(Polymer object)	writePolymerSequence.

Uses of Polymer in psidev.psi.mi.jami.xml.model.extension.factory

Methods in psidev.psi.mi.jami.xml.model.extension.factory that return Polymer

Modifier and Type	Method	Description
Polymer	XmlInteractorFactory.createPolymer(String name, CvTerm type)	Creates a new Polymer with the name and interactor type

Uses of Polymer in psidev.psi.mi.jami.xml.model.extension.xml253

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Polymer

Modifier and Type	Class	Description
class	XmlNucleicAcid	Xml implementation of Nucleic acid
class	XmlPolymer	Xml implementation of Polymer
class	XmlProtein	Xml implementation of protein

Uses of Polymer in psidev.psi.mi.jami.xml.model.extension.xml254

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Polymer

Modifier and Type	Class	Description
class	XmlNucleicAcid	Xml implementation of Nucleic acid
class	XmlPolymer	Xml implementation of Polymer
class	XmlProtein	Xml implementation of protein

Uses of Polymer in psidev.psi.mi.jami.xml.model.extension.xml300

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Polymer

Modifier and Type	Class	Description
class	XmlNucleicAcid	Xml implementation of Nucleic acid
class	XmlPolymer	Xml implementation of Polymer
class	XmlProtein	Xml implementation of protein