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

Class SBMLModel

java.lang.Object

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

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

de.unirostock.sems.bives.sbml.parser.SBMLModel

public class SBMLModel
extends SBMLSBase

The Class SBMLModel representing a model encoded in SBML.

Author:

Martin Scharm

Field Summary

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

documentNode, sbmlModel

Constructor Summary

Constructors

Constructor	Description
SBMLModel(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLDocument sbmlDocument)	Instantiates a new SBML model.

Method Summary

Modifier and Type	Method	Description
SBMLCompartment	getCompartment(String id)	Gets the compartment.
HashMap<String,SBMLCompartment>	getCompartments()	Gets the compartments.
SBMLCompartmentType	getCompartmentType(String id)	Gets the compartment type.
HashMap<String,SBMLCompartmentType>	getCompartmentTypes()	Gets the compartment types.
List<SBMLConstraint>	getConstraints()	Gets the constraints.
SBMLDocument	getDocument()	Gets the SBML document.
List<SBMLEvent>	getEvents()	Gets the events.
SBMLSBase	getFromMetaId(String metaId)	Gets an entity given its meta id.
SBMLSBase	getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)	Gets an entity given its tree node.
HashMap<String,SBMLFunctionDefinition>	getFunctionDefinitions()	Gets the function definitions.
String	getID()	Gets the id of the model.
List<SBMLInitialAssignment>	getInitialAssignments()	Gets the initial assignments.
String	getName()	Gets the name of the model.
HashMap<String,List<SBMLSBase>>	getOntologyMappings()	Gets the ontology mappings which group entities by there pointers into ontologies.
SBMLParameter	getParameter(String id)	Gets a specific parameter.
HashMap<String,SBMLParameter>	getParameters()	Gets the parameters.
SBMLReaction	getReaction(String id)	Gets a specific reaction.
HashMap<String,SBMLReaction>	getReactions()	Gets the reactions.
List<SBMLRule>	getRules()	Gets the rules.
static String	getSidName(SBMLSBase ref)	Gets the SId.
HashMap<String,SBMLSpecies>	getSpecies()	Gets the species.
SBMLSpecies	getSpecies(String id)	Gets the species.
SBMLSimpleSpeciesReference	getSpeciesReference(String id)	Gets the species reference.
SBMLSpeciesType	getSpeciesType(String id)	Gets the species type.
HashMap<String,SBMLSpeciesType>	getSpeciesTypes()	Gets the species types.
SBMLUnitDefinition	getUnitDefinition(String kind)	Gets the unit definition.
HashMap<String,SBMLUnitDefinition>	getUnitDefinitions()	Gets the unit definitions.
void	mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node, SBMLSBase sbase)	Map node model node to its entity.
void	registerSpeciesReference(String id, SBMLSimpleSpeciesReference ref)	Registers a species reference.
SBMLSBase	resolveSymbol(String symbol)	Resolve certain symbol.
SBMLSBase	resolveSymbole(String symbol)	Deprecated. as of version 1.3.6, replaced by resolveSymbol(String)

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

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

addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm

Constructor Detail

SBMLModel

public SBMLModel(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                 SBMLDocument sbmlDocument)
          throws BivesSBMLParseException,
                 de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

Instantiates a new SBML model.

Parameters:

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

sbmlDocument - the SBML document

Throws:

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

Method Detail

getOntologyMappings

public HashMap<String,List<SBMLSBase>> getOntologyMappings()

Gets the ontology mappings which group entities by there pointers into ontologies.

Returns:

the ontology mappings

getFunctionDefinitions

public HashMap<String,SBMLFunctionDefinition> getFunctionDefinitions()

Gets the function definitions.

Returns:

the function definitions

getUnitDefinitions

public HashMap<String,SBMLUnitDefinition> getUnitDefinitions()

Gets the unit definitions.

Returns:

the unit definitions

getUnitDefinition

public SBMLUnitDefinition getUnitDefinition(String kind)

Gets the unit definition.

Parameters:

kind - the kind

Returns:

the unit definition

getCompartmentType

public SBMLCompartmentType getCompartmentType(String id)

Gets the compartment type.

Parameters:

id - the id

Returns:

the compartment type

getCompartmentTypes

public HashMap<String,SBMLCompartmentType> getCompartmentTypes()

Gets the compartment types.

Returns:

the compartment types

getCompartments

public HashMap<String,SBMLCompartment> getCompartments()

Gets the compartments.

Returns:

the compartments

getCompartment

public SBMLCompartment getCompartment(String id)

Gets the compartment.

Parameters:

id - the id

Returns:

the compartment

getSpecies

public SBMLSpecies getSpecies(String id)

Gets the species.

Parameters:

id - the id

Returns:

the species

getSpecies

public HashMap<String,SBMLSpecies> getSpecies()

Gets the species.

Returns:

the species

getSpeciesType

public SBMLSpeciesType getSpeciesType(String id)

Gets the species type.

Parameters:

id - the id

Returns:

the species type

getSpeciesTypes

public HashMap<String,SBMLSpeciesType> getSpeciesTypes()

Gets the species types.

Returns:

the species types

getParameters

public HashMap<String,SBMLParameter> getParameters()

Gets the parameters.

Returns:

the parameters

getParameter

public SBMLParameter getParameter(String id)

Gets a specific parameter.

Parameters:

id - the id of the parameter

Returns:

the parameter

registerSpeciesReference

public void registerSpeciesReference(String id,
                                     SBMLSimpleSpeciesReference ref)

Registers a species reference.

Parameters:

id - the id of the species reference

ref - the reference

getSpeciesReference

public SBMLSimpleSpeciesReference getSpeciesReference(String id)

Gets the species reference.

Parameters:

id - the id of the species reference

Returns:

the species reference

getReaction

public SBMLReaction getReaction(String id)

Gets a specific reaction.

Parameters:

id - the id of the reaction

Returns:

the reaction

getReactions

public HashMap<String,SBMLReaction> getReactions()

Gets the reactions.

Returns:

the reactions

getConstraints

public List<SBMLConstraint> getConstraints()

Gets the constraints.

Returns:

the constraints

getInitialAssignments

public List<SBMLInitialAssignment> getInitialAssignments()

Gets the initial assignments.

Returns:

the initial assignments

getEvents

public List<SBMLEvent> getEvents()

Gets the events.

Returns:

the events

getRules

public List<SBMLRule> getRules()

Gets the rules.

Returns:

the rules

getID

public String getID()

Gets the id of the model.

Returns:

the id

getName

public String getName()

Gets the name of the model.

Returns:

the name

mapNode

public void mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node,
                    SBMLSBase sbase)

Map node model node to its entity.

Parameters:

node - the document node in the corresponding XML tree

sbase - the entity to get mapped

getFromNode

public SBMLSBase getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)

Gets an entity given its tree node.

Parameters:

node - the node in the XML tree

Returns:

the entity registered for this node

getFromMetaId

public SBMLSBase getFromMetaId(String metaId)

Gets an entity given its meta id.

Parameters:

metaId - the meta id

Returns:

the entity registered for this meta id

getDocument

public SBMLDocument getDocument()

Gets the SBML document.

Returns:

the document

resolveSymbole

public SBMLSBase resolveSymbole(String symbol)

Deprecated.

as of version 1.3.6, replaced by resolveSymbol(String)

Resolve certain symbol.

Parameters:

symbol - the symbol

Returns:

the SBMLS base

resolveSymbol

public SBMLSBase resolveSymbol(String symbol)

Resolve certain symbol.

Parameters:

symbol - the symbol

Returns:

the SBMLS base

getSidName

public static String getSidName(SBMLSBase ref)

Gets the SId.

Parameters:

ref - the ref

Returns:

the sid name