fr.curie.cd2sbgnml

Class CD2SBGNML

java.lang.Object

org.sbfc.converter.GeneralConverter

fr.curie.cd2sbgnml.CD2SBGNML

public class CD2SBGNML
extends org.sbfc.converter.GeneralConverter

Field Summary

Fields inherited from class org.sbfc.converter.GeneralConverter

inputModel, options

Constructor Summary

Constructors

Constructor and Description
CD2SBGNML()

Method Summary

Modifier and Type	Method and Description
org.sbfc.converter.models.GeneralModel	convert(org.sbfc.converter.models.GeneralModel generalModel)
Element	getAllStyles(List<StyleInfo> styleInfoList, Sbml sbmldoc)
org.sbgn.bindings.Arc	getArc(LinkModel linkM)
String	getDescription()
org.sbgn.bindings.Glyph	getGlyph(AliasWrapper aliasW, boolean isClone)
String	getHtmlDescription()
String	getName()
String	getResultExtension()
org.sbgn.bindings.SBGNBase.Extension	getSBGNAnnotation(Element rdf, String refId) Convert a rdf element to an SBGN extension, with an annotation element inside wrapping the rdf.
org.sbgn.bindings.SBGNBase.Notes	getSBGNNotes(Element notes) Convert html Element into an SBGN notes object
org.sbgn.bindings.Glyph	getStateVariable(String prefix, String value, Rectangle2D.Float parentBbox, float angle)
org.sbgn.bindings.Glyph	getStateVariableFromResidueWrapper(ResidueWrapper residueW, Rectangle2D.Float parentBbox)
org.sbgn.bindings.Glyph	getUnitOfInfo(String text, Rectangle2D.Float parentBbox, float angle)
void	processCompartment(Compartment compartment, ModelWrapper modelW, org.sbgn.bindings.Map map)
void	processSpecies(SpeciesWrapper species, ModelWrapper modelW, org.sbgn.bindings.Map map)
org.sbgn.bindings.Glyph	processSpeciesAlias(SpeciesWrapper species, AliasWrapper alias, ModelWrapper modelW, boolean isClone)
org.sbgn.bindings.Sbgn	toSbgn(Sbml sbml)

Methods inherited from class org.sbfc.converter.GeneralConverter

getInputModel, setOptions

Methods inherited from class java.lang.Object

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

Constructor Detail

CD2SBGNML

public CD2SBGNML()

Method Detail

toSbgn

public org.sbgn.bindings.Sbgn toSbgn(Sbml sbml)

processCompartment

public void processCompartment(Compartment compartment,
                               ModelWrapper modelW,
                               org.sbgn.bindings.Map map)

processSpeciesAlias

public org.sbgn.bindings.Glyph processSpeciesAlias(SpeciesWrapper species,
                                                   AliasWrapper alias,
                                                   ModelWrapper modelW,
                                                   boolean isClone)

processSpecies

public void processSpecies(SpeciesWrapper species,
                           ModelWrapper modelW,
                           org.sbgn.bindings.Map map)

getGlyph

public org.sbgn.bindings.Glyph getGlyph(AliasWrapper aliasW,
                                        boolean isClone)

getStateVariable

public org.sbgn.bindings.Glyph getStateVariable(String prefix,
                                                String value,
                                                Rectangle2D.Float parentBbox,
                                                float angle)

getStateVariableFromResidueWrapper

public org.sbgn.bindings.Glyph getStateVariableFromResidueWrapper(ResidueWrapper residueW,
                                                                  Rectangle2D.Float parentBbox)

getUnitOfInfo

public org.sbgn.bindings.Glyph getUnitOfInfo(String text,
                                             Rectangle2D.Float parentBbox,
                                             float angle)

getArc

public org.sbgn.bindings.Arc getArc(LinkModel linkM)

getAllStyles

public Element getAllStyles(List<StyleInfo> styleInfoList,
                            Sbml sbmldoc)

getSBGNNotes

public org.sbgn.bindings.SBGNBase.Notes getSBGNNotes(Element notes)

Convert html Element into an SBGN notes object

Parameters:

notes -

Returns:

getSBGNAnnotation

public org.sbgn.bindings.SBGNBase.Extension getSBGNAnnotation(Element rdf,
                                                              String refId)

Convert a rdf element to an SBGN extension, with an annotation element inside wrapping the rdf.

Parameters:

rdf -

Returns:

convert

public org.sbfc.converter.models.GeneralModel convert(org.sbfc.converter.models.GeneralModel generalModel)
                                               throws org.sbfc.converter.exceptions.ConversionException,
                                                      org.sbfc.converter.exceptions.ReadModelException

Specified by:

convert in class org.sbfc.converter.GeneralConverter

Throws:

org.sbfc.converter.exceptions.ConversionException

org.sbfc.converter.exceptions.ReadModelException

getResultExtension

public String getResultExtension()

Specified by:

getResultExtension in class org.sbfc.converter.GeneralConverter

getName

public String getName()

Specified by:

getName in class org.sbfc.converter.GeneralConverter

getDescription

public String getDescription()

Specified by:

getDescription in class org.sbfc.converter.GeneralConverter

getHtmlDescription

public String getHtmlDescription()

Specified by:

getHtmlDescription in class org.sbfc.converter.GeneralConverter