Package psidev.psi.mi.jami.xml.io.writer.elements.impl

Class XmlInteractorWriter

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.XmlInteractorWriter

All Implemented Interfaces:

PsiXmlElementWriter<Interactor>

Direct Known Subclasses:

XmlInteractorWriter

public class XmlInteractorWriter
extends Object
implements PsiXmlElementWriter<Interactor>

Xml interactor writer

Since:

12/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
XmlInteractorWriter(PsiXmlVersion version, XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for XmlInteractorWriter.

Method Summary

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Annotation>	getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Checksum>	getChecksumWriter()	Getter for the field checksumWriter.
PsiXmlVariableNameWriter<CvTerm>	getInteractorTypeWriter()	Getter for the field interactorTypeWriter.
protected PsiXmlObjectCache	getObjectIndex()	Getter for the field objectIndex.
PsiXmlElementWriter<Organism>	getOrganismWriter()	Getter for the field organismWriter.
protected XMLStreamWriter	getStreamWriter()	Getter for the field streamWriter.
PsiXmlXrefWriter	getXrefWriter()	Getter for the field xrefWriter.
protected void	initialiseInteractorTypeWriter()	initialiseInteractorTypeWriter.
protected void	initialiseOrganismWriter()	initialiseOrganismWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
protected void	processSequence(Interactor object)	processSequence.
void	setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	setChecksumWriter(PsiXmlElementWriter<Checksum> checksumWriter)	Setter for the field checksumWriter.
void	setInteractorTypeWriter(PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter)	Setter for the field interactorTypeWriter.
void	setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)	Setter for the field organismWriter.
void	setXrefWriter(PsiXmlXrefWriter xrefWriter)	Setter for the field xrefWriter.
void	write(Interactor object)	write.
protected void	writeAttributes(Interactor object)	writeAttributes.
protected void	writeInteractorType(Interactor object)	writeInteractorType.
protected void	writeNames(Interactor object)	writeNames.
protected void	writeNewXref(Xref preferredIdentifier, String nodeName)
protected void	writeOrganism(Interactor object)	writeOrganism.
protected void	writeOtherSetMembers(Interactor object, boolean needToWriteXref, boolean needToWritePrimaryRef)	writeOtherSetMembers.
protected void	writePolymerSequence(Polymer object)	writePolymerSequence.
protected void	writeXref(Interactor object)	writeXref.
protected void	writeXrefFromInteractorIdentifiers(Interactor object)	writeXrefFromInteractorIdentifiers.
protected void	writeXrefFromInteractorXrefs(Interactor object)	writeXrefFromInteractorXrefs.

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlInteractorWriter

public XmlInteractorWriter(PsiXmlVersion version,
                           XMLStreamWriter writer,
                           PsiXmlObjectCache objectIndex)

Constructor for XmlInteractorWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getAliasWriter

public PsiXmlElementWriter<Alias> getAliasWriter()

Getter for the field aliasWriter.

Returns:

a PsiXmlElementWriter object.

setAliasWriter

public void setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)

Setter for the field aliasWriter.

Parameters:

aliasWriter - a PsiXmlElementWriter object.

getXrefWriter

public PsiXmlXrefWriter getXrefWriter()

Getter for the field xrefWriter.

Returns:

a PsiXmlXrefWriter object.

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

setXrefWriter

public void setXrefWriter(PsiXmlXrefWriter xrefWriter)

Setter for the field xrefWriter.

Parameters:

xrefWriter - a PsiXmlXrefWriter object.

getInteractorTypeWriter

public PsiXmlVariableNameWriter<CvTerm> getInteractorTypeWriter()

Getter for the field interactorTypeWriter.

Returns:

a PsiXmlVariableNameWriter object.

initialiseInteractorTypeWriter

protected void initialiseInteractorTypeWriter()

initialiseInteractorTypeWriter.

setInteractorTypeWriter

public void setInteractorTypeWriter(PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter)

Setter for the field interactorTypeWriter.

Parameters:

interactorTypeWriter - a PsiXmlVariableNameWriter object.

getOrganismWriter

public PsiXmlElementWriter<Organism> getOrganismWriter()

Getter for the field organismWriter.

Returns:

a PsiXmlElementWriter object.

initialiseOrganismWriter

protected void initialiseOrganismWriter()

initialiseOrganismWriter.

setOrganismWriter

public void setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)

Setter for the field organismWriter.

Parameters:

organismWriter - a PsiXmlElementWriter object.

getAttributeWriter

public PsiXmlElementWriter<Annotation> getAttributeWriter()

Getter for the field attributeWriter.

Returns:

a PsiXmlElementWriter object.

setAttributeWriter

public void setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)

Setter for the field attributeWriter.

Parameters:

attributeWriter - a PsiXmlElementWriter object.

getChecksumWriter

public PsiXmlElementWriter<Checksum> getChecksumWriter()

Getter for the field checksumWriter.

Returns:

a PsiXmlElementWriter object.

setChecksumWriter

public void setChecksumWriter(PsiXmlElementWriter<Checksum> checksumWriter)

Setter for the field checksumWriter.

Parameters:

checksumWriter - a PsiXmlElementWriter object.

write

public void write(Interactor object)
           throws MIIOException

write.

Specified by:

write in interface PsiXmlElementWriter<Interactor>

Parameters:

object - a T object.

Throws:

MIIOException - if any.

writeAttributes

protected void writeAttributes(Interactor object)
                        throws XMLStreamException

writeAttributes.

Parameters:

object - a Interactor object.

Throws:

XMLStreamException - if any.

writeOrganism

protected void writeOrganism(Interactor object)

writeOrganism.

Parameters:

object - a Interactor object.

writeInteractorType

protected void writeInteractorType(Interactor object)

writeInteractorType.

Parameters:

object - a Interactor object.

writeXref

protected void writeXref(Interactor object)
                  throws XMLStreamException

writeXref.

Parameters:

object - a Interactor object.

Throws:

XMLStreamException - if any.

writeNames

protected void writeNames(Interactor object)
                   throws XMLStreamException

writeNames.

Parameters:

object - a Interactor object.

Throws:

XMLStreamException - if any.

processSequence

protected void processSequence(Interactor object)
                        throws XMLStreamException

processSequence.

Parameters:

object - a Interactor object.

Throws:

XMLStreamException - if any.

writePolymerSequence

protected void writePolymerSequence(Polymer object)
                             throws XMLStreamException

writePolymerSequence.

Parameters:

object - a Polymer object.

Throws:

XMLStreamException - if any.

writeXrefFromInteractorXrefs

protected void writeXrefFromInteractorXrefs(Interactor object)
                                     throws XMLStreamException

writeXrefFromInteractorXrefs.

Parameters:

object - a Interactor object.

Throws:

XMLStreamException - if any.

writeXrefFromInteractorIdentifiers

protected void writeXrefFromInteractorIdentifiers(Interactor object)
                                           throws XMLStreamException

writeXrefFromInteractorIdentifiers.

Parameters:

object - a Interactor object.

Throws:

XMLStreamException - if any.

writeOtherSetMembers

protected void writeOtherSetMembers(Interactor object,
                                    boolean needToWriteXref,
                                    boolean needToWritePrimaryRef)
                             throws XMLStreamException

writeOtherSetMembers.

Parameters:

object - a Interactor object.

needToWriteXref - a boolean.

needToWritePrimaryRef - a boolean.

Throws:

XMLStreamException - if any.

getStreamWriter

protected XMLStreamWriter getStreamWriter()

Getter for the field streamWriter.

Returns:

a XMLStreamWriter object.

getObjectIndex

protected PsiXmlObjectCache getObjectIndex()

Getter for the field objectIndex.

Returns:

a PsiXmlObjectCache object.

writeNewXref

protected void writeNewXref(Xref preferredIdentifier,
                            String nodeName)