Package de.unirostock.sems.bives.sbml.parser

Class SBMLSBase

java.lang.Object

de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

de.unirostock.sems.bives.sbml.parser.SBMLSBase

Direct Known Subclasses:

SBMLConstraint, SBMLEvent, SBMLEventAssignment, SBMLEventDelay, SBMLEventPriority, SBMLEventTrigger, SBMLGenericIdNameObject, SBMLInitialAssignment, SBMLKineticLaw, SBMLListOf, SBMLModel, SBMLRule, SBMLSimpleSpeciesReference, SBMLUnit

public abstract class SBMLSBase
extends SBMLGenericObject

The Class SBMLSBase. This base type is designed to allow a modeler or a software package to attach arbitrary information to each major element or list in an SBML model.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

documentNode, sbmlModel

Constructor Summary

Constructors

Constructor	Description
SBMLSBase(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)	Instantiates a new SBMLS base.

Method Summary

Modifier and Type	Method	Description
void	addOntologyLink(String qualifier, String link)	Adds an link into an ontology.
boolean	flagMetaModifcations(de.unirostock.sems.bives.markup.MarkupElement me)	Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.
de.unirostock.sems.xmlutils.ds.DocumentNode	getAnnotation()	Gets the annotation.
String	getMetaId()	Gets the meta id.
de.unirostock.sems.bives.ds.Xhtml	getNotes()	Gets the notes.
HashMap<String,List<String>>	getOntologyLinks()	Gets the links that point to an ontology.
de.unirostock.sems.bives.ds.ontology.SBOTerm	getSBOTerm()	Gets the SBO term.

Methods inherited from class java.lang.Object

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

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

getDocumentNode, getModel

Constructor Detail

SBMLSBase

public SBMLSBase(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                 SBMLModel sbmlModel)
          throws BivesSBMLParseException

Instantiates a new SBMLS base.

Parameters:

documentNode - the document node encoding this entity in the corresponding XML tree

sbmlModel - the SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

Method Detail

flagMetaModifcations

public boolean flagMetaModifcations(de.unirostock.sems.bives.markup.MarkupElement me)

Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.

Parameters:

me - the MarkupElement that should be flagged

Returns:

true, if flagged

getOntologyLinks

public HashMap<String,List<String>> getOntologyLinks()

Gets the links that point to an ontology.

Returns:

the ontology links

addOntologyLink

public void addOntologyLink(String qualifier,
                            String link)

Adds an link into an ontology.

Parameters:

qualifier - the qualifier

link - the link

getSBOTerm

public de.unirostock.sems.bives.ds.ontology.SBOTerm getSBOTerm()

Gets the SBO term.

Returns:

the SBO term

getMetaId

public String getMetaId()

Gets the meta id.

Returns:

the meta id

getNotes

public de.unirostock.sems.bives.ds.Xhtml getNotes()

Gets the notes.

Returns:

the notes

getAnnotation

public de.unirostock.sems.xmlutils.ds.DocumentNode getAnnotation()

Gets the annotation.

Returns:

the annotation