uk.ac.ebi.intenz.tools.export

Class XmlExporter

java.lang.Object

uk.ac.ebi.intenz.tools.export.XmlExporter

All Implemented Interfaces:

IntenzExporter

public class XmlExporter
extends Object
implements IntenzExporter

Exporter of IntEnz data in XML format. Currently, the following flavours of XML are available:

• ASCII: the IntEnz fields with XML markup are translated into ASCII.
• XCHARS: those fields are left as are, but within CDATA sections.

The flavour can be changed using the setFlavour method.
Note that the export methods are synchronized in order to avoid changing the flavour in the middle of a dump.

Author:

rafalcan

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	XmlExporter.Flavour

Constructor Summary

Constructors

Constructor and Description
XmlExporter()

Method Summary

Methods

Modifier and Type	Method and Description
void	export(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymes, OutputStream os) Exports a collection of enzymes.
void	export(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry enzyme, OutputStream os) Exports just one enzyme.
void	export(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry entry, String release, String relDate, OutputStream os) Deprecated. Use the method from the interface IntenzExporter.export(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry, java.io.OutputStream) instead, using the setters for release date and number beforehand.
void	export(List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> entries, String release, String relDate, OutputStream os) Deprecated. Use the method from the interface IntenzExporter.export(java.util.Collection, java.io.OutputStream) instead, using the setters for release date and number beforehand.
void	setDescriptions(Map<String,Object> descriptions)
void	setFlavour(XmlExporter.Flavour flavour)
void	setReleaseDate(String releaseDate)
void	setReleaseNumber(int releaseNumber)

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlExporter

public XmlExporter()
            throws javax.xml.bind.JAXBException,
                   SAXException

Throws:

javax.xml.bind.JAXBException

SAXException

Method Detail

setReleaseNumber

public void setReleaseNumber(int releaseNumber)

setReleaseDate

public void setReleaseDate(String releaseDate)

setDescriptions

public void setDescriptions(Map<String,Object> descriptions)

setFlavour

public void setFlavour(XmlExporter.Flavour flavour)

export

public void export(Collection<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> enzymes,
          OutputStream os)
            throws IOException

Description copied from interface: IntenzExporter

Exports a collection of enzymes.

Specified by:

export in interface IntenzExporter

Parameters:

enzymes - the enzymes to export.

os - the output stream to write the export to.

Throws:

IOException

export

public void export(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry enzyme,
          OutputStream os)
            throws IOException

Description copied from interface: IntenzExporter

Exports just one enzyme.

Specified by:

export in interface IntenzExporter

Parameters:

enzyme - the enzyme to export.

os - the output stream to write the entry to.

Throws:

IOException

export

public void export(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry entry,
          String release,
          String relDate,
          OutputStream os)
            throws Exception

Deprecated. Use the method from the interface IntenzExporter.export(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry, java.io.OutputStream) instead, using the setters for release date and number beforehand.

Exports one enzyme entry as IntEnzXML.

Parameters:

entry - the enzyme entry to export.

release - the IntEnz release number to mention in the exported XML.

relDate - the IntEnz release date to mention in the exported XML.

os - the OutputStream to write the XML to.

Throws:

Exception

export

public void export(List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> entries,
          String release,
          String relDate,
          OutputStream os)
            throws Exception

Deprecated. Use the method from the interface IntenzExporter.export(java.util.Collection, java.io.OutputStream) instead, using the setters for release date and number beforehand.

Exports a list of enzymes as IntEnzXML.

Parameters:

entries - the entries to export.

release - the IntEnz release number to mention in the exported XML.

relDate - the IntEnz release date to mention in the exported XML.

os - the OutputStream to write the XML to.

Throws:

Exception