org.ginsim.service.format.sbml

Class SBMLqualService

java.lang.Object

org.ginsim.core.service.FormatSupportService<org.colomoto.biolqm.io.sbml.SBMLFormat>

org.ginsim.service.format.sbml.SBMLqualService

All Implemented Interfaces:

Service

@MetaInfServices(value=Service.class)
 @Alias(value="SBML")
 @ServiceStatus(value=DEVELOPMENT)
public class SBMLqualService
extends FormatSupportService<org.colomoto.biolqm.io.sbml.SBMLFormat>

Field Summary

Fields inherited from class org.ginsim.core.service.FormatSupportService

format

Constructor Summary

Constructors

Constructor and Description
SBMLqualService()

Method Summary

Modifier and Type	Method and Description
String	export(RegulatoryGraph graph, String filename) Convenience method to export without having to configure anything.
String	export(SBMLQualConfig config, String filename) Perform the SBML export, using the JSBML-based encoder from LogicalModel.
void	exportAnnotation(org.sbml.jsbml.SBase elt, Annotation gsnote)
void	importAnnotation(RegulatoryGraph lrg, org.sbml.jsbml.SBase elt, Annotation gsnote)
RegulatoryGraph	importLRG(String filename) Return the graph built from the SBML file at the given path

Methods inherited from class org.ginsim.core.service.FormatSupportService

addMissingFormats, blacklistFormat, canExport, canExportModel, canImport, export, export, importFile, importFile

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLqualService

public SBMLqualService()

Method Detail

importLRG

public RegulatoryGraph importLRG(String filename)

Return the graph built from the SBML file at the given path

Overrides:

importLRG in class FormatSupportService<org.colomoto.biolqm.io.sbml.SBMLFormat>

Parameters:

filename - the path of the SBML file describing the graph

Returns:

the graph built from the SBML file at the given path

export

public String export(RegulatoryGraph graph,
                     String filename)
              throws IOException

Convenience method to export without having to configure anything.

Overrides:

export in class FormatSupportService<org.colomoto.biolqm.io.sbml.SBMLFormat>

Parameters:

graph -

filename -

Throws:

IOException

export

public String export(SBMLQualConfig config,
                     String filename)
              throws IOException

Perform the SBML export, using the JSBML-based encoder from LogicalModel.

Parameters:

config - the configuration structure

filename - the path to the target file

Throws:

IOException

exportAnnotation

public void exportAnnotation(org.sbml.jsbml.SBase elt,
                             Annotation gsnote)
                      throws XMLStreamException

Throws:

XMLStreamException

importAnnotation

public void importAnnotation(RegulatoryGraph lrg,
                             org.sbml.jsbml.SBase elt,
                             Annotation gsnote)
                      throws XMLStreamException

Throws:

XMLStreamException