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E

export(Collection<EnzymeEntry>, OutputStream) - Method in interface uk.ac.ebi.intenz.tools.export.IntenzExporter

Exports a collection of enzymes.

export(EnzymeEntry, OutputStream) - Method in interface uk.ac.ebi.intenz.tools.export.IntenzExporter

Exports just one enzyme.

export(Collection<EnzymeEntry>, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

export(EnzymeEntry, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

export(EnzymeSubSubclass, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

Exports an EC sub-subclass as JSON, including only its active EC numbers (not deleted, not transferred).

export(EnzymeSubSubclass, OutputStream, boolean) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

Exports an EC sub-subclass as JSON.

export(EnzymeSubclass, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

Exports an EC subclass as JSON.

export(EnzymeClass, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

Exports an EC class as JSON.

export(List<EnzymeClass>, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.JsonExporter

Turns a list of EC classes into a JSON array.

export(Collection<EnzymeEntry>, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.KeggExporter

export(EnzymeEntry, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.KeggExporter

export(Collection<String>, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.SitemapExporter

Dumps a list of URLs as sitemap (see http://www.sitemaps.org)

export(Collection<EnzymeEntry>, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

export(EnzymeEntry, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

export(EnzymeEntry, String, String, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

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.

export(List<EnzymeEntry>, String, String, OutputStream) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

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.

exportBiopax(Collection<EnzymeEntry>, String) - Method in class uk.ac.ebi.intenz.tools.export.ExporterApp

ExporterApp - Class in uk.ac.ebi.intenz.tools.export

ExporterApp(String) - Constructor for class uk.ac.ebi.intenz.tools.export.ExporterApp

exportKegg(Collection<EnzymeEntry>, String) - Method in class uk.ac.ebi.intenz.tools.export.ExporterApp

exportSitemap(Collection<EnzymeEntry>, Map<String, Object>, String) - Method in class uk.ac.ebi.intenz.tools.export.ExporterApp

exportXML(Collection<EnzymeEntry>, Map<String, Object>, String) - Method in class uk.ac.ebi.intenz.tools.export.ExporterApp

Exports data in XML format.

F

finalize() - Method in class uk.ac.ebi.intenz.tools.export.ExporterApp

G

getDescriptions(Connection) - Static method in class uk.ac.ebi.intenz.tools.export.ExporterApp

Builds a map of EC numbers (as String) to EnzymeClass, EnzymeSubClass or EnzymeSubSubClass objects from which to retrieve names and descriptions.

getEnzymeList(String) - Method in class uk.ac.ebi.intenz.tools.export.ExporterApp

Gets the list of enzymes to be exported.

I

IntenzExporter - Interface in uk.ac.ebi.intenz.tools.export

Interface to export IntEnz objects.

IntEnzMessenger - Class in uk.ac.ebi.intenz.tools.export

This class ...

IntEnzMessenger() - Constructor for class uk.ac.ebi.intenz.tools.export.IntEnzMessenger

J

JsonExporter - Class in uk.ac.ebi.intenz.tools.export

Utility class to export enzyme entries - but also classes, subclasses and subsubclasses - as JSON.

JsonExporter() - Constructor for class uk.ac.ebi.intenz.tools.export.JsonExporter

K

KeggExporter - Class in uk.ac.ebi.intenz.tools.export

KeggExporter() - Constructor for class uk.ac.ebi.intenz.tools.export.KeggExporter

L

LOGGER - Static variable in class uk.ac.ebi.intenz.tools.export.ExporterApp

M

main(String[]) - Static method in class uk.ac.ebi.intenz.tools.export.ExporterApp

Exports IntEnz data in the following formats: XML (both flavours ASCII and XCHARS), using the XmlExporter class. Site map XML file (sitemap.xml) to be used in Google sitemaps to make every IntEnz entry available to Google indexing.

S

sendError(String, String, String) - Static method in class uk.ac.ebi.intenz.tools.export.IntEnzMessenger

sendNotificationWithAttachment(String, String, String, String, File) - Static method in class uk.ac.ebi.intenz.tools.export.IntEnzMessenger

setDescriptions(Map<String, Object>) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

setFlavour(XmlExporter.Flavour) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

setReleaseDate(String) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

setReleaseNumber(int) - Method in class uk.ac.ebi.intenz.tools.export.XmlExporter

SitemapExporter - Class in uk.ac.ebi.intenz.tools.export

Exports IntEnz as a sitemap XML file

SitemapExporter() - Constructor for class uk.ac.ebi.intenz.tools.export.SitemapExporter

U

uk.ac.ebi.intenz.tools.export - package uk.ac.ebi.intenz.tools.export

V

valueOf(String) - Static method in enum uk.ac.ebi.intenz.tools.export.XmlExporter.Flavour

Returns the enum constant of this type with the specified name.

values() - Static method in enum uk.ac.ebi.intenz.tools.export.XmlExporter.Flavour

Returns an array containing the constants of this enum type, in the order they are declared.

X

XmlExporter - Class in uk.ac.ebi.intenz.tools.export

Exporter of IntEnz data in XML format.

XmlExporter() - Constructor for class uk.ac.ebi.intenz.tools.export.XmlExporter

XmlExporter.Flavour - Enum in uk.ac.ebi.intenz.tools.export

E F G I J K L M S U V X