Class SBMLModel
- java.lang.Object
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- de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
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- de.unirostock.sems.bives.sbml.parser.SBMLSBase
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- de.unirostock.sems.bives.sbml.parser.SBMLModel
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public class SBMLModel extends SBMLSBase
The Class SBMLModel representing a model encoded in SBML.- Author:
- Martin Scharm
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Field Summary
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Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
documentNode, sbmlModel
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Constructor Summary
Constructors Constructor Description SBMLModel(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLDocument sbmlDocument)
Instantiates a new SBML model.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods 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 byresolveSymbol(String)
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Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSBase
addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm
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Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
getDocumentNode, getModel
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Constructor Detail
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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 treesbmlDocument
- the SBML document- Throws:
BivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exception
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Method Detail
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getOntologyMappings
public HashMap<String,List<SBMLSBase>> getOntologyMappings()
Gets the ontology mappings which group entities by there pointers into ontologies.- Returns:
- the ontology mappings
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getFunctionDefinitions
public HashMap<String,SBMLFunctionDefinition> getFunctionDefinitions()
Gets the function definitions.- Returns:
- the function definitions
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getUnitDefinitions
public HashMap<String,SBMLUnitDefinition> getUnitDefinitions()
Gets the unit definitions.- Returns:
- the unit definitions
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getUnitDefinition
public SBMLUnitDefinition getUnitDefinition(String kind)
Gets the unit definition.- Parameters:
kind
- the kind- Returns:
- the unit definition
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getCompartmentType
public SBMLCompartmentType getCompartmentType(String id)
Gets the compartment type.- Parameters:
id
- the id- Returns:
- the compartment type
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getCompartmentTypes
public HashMap<String,SBMLCompartmentType> getCompartmentTypes()
Gets the compartment types.- Returns:
- the compartment types
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getCompartments
public HashMap<String,SBMLCompartment> getCompartments()
Gets the compartments.- Returns:
- the compartments
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getCompartment
public SBMLCompartment getCompartment(String id)
Gets the compartment.- Parameters:
id
- the id- Returns:
- the compartment
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getSpecies
public SBMLSpecies getSpecies(String id)
Gets the species.- Parameters:
id
- the id- Returns:
- the species
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getSpecies
public HashMap<String,SBMLSpecies> getSpecies()
Gets the species.- Returns:
- the species
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getSpeciesType
public SBMLSpeciesType getSpeciesType(String id)
Gets the species type.- Parameters:
id
- the id- Returns:
- the species type
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getSpeciesTypes
public HashMap<String,SBMLSpeciesType> getSpeciesTypes()
Gets the species types.- Returns:
- the species types
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getParameters
public HashMap<String,SBMLParameter> getParameters()
Gets the parameters.- Returns:
- the parameters
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getParameter
public SBMLParameter getParameter(String id)
Gets a specific parameter.- Parameters:
id
- the id of the parameter- Returns:
- the parameter
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registerSpeciesReference
public void registerSpeciesReference(String id, SBMLSimpleSpeciesReference ref)
Registers a species reference.- Parameters:
id
- the id of the species referenceref
- the reference
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getSpeciesReference
public SBMLSimpleSpeciesReference getSpeciesReference(String id)
Gets the species reference.- Parameters:
id
- the id of the species reference- Returns:
- the species reference
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getReaction
public SBMLReaction getReaction(String id)
Gets a specific reaction.- Parameters:
id
- the id of the reaction- Returns:
- the reaction
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getReactions
public HashMap<String,SBMLReaction> getReactions()
Gets the reactions.- Returns:
- the reactions
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getConstraints
public List<SBMLConstraint> getConstraints()
Gets the constraints.- Returns:
- the constraints
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getInitialAssignments
public List<SBMLInitialAssignment> getInitialAssignments()
Gets the initial assignments.- Returns:
- the initial assignments
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getID
public String getID()
Gets the id of the model.- Returns:
- the id
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getName
public String getName()
Gets the name of the model.- Returns:
- the name
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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 treesbase
- the entity to get mapped
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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
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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
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getDocument
public SBMLDocument getDocument()
Gets the SBML document.- Returns:
- the document
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resolveSymbole
public SBMLSBase resolveSymbole(String symbol)
Deprecated.as of version 1.3.6, replaced byresolveSymbol(String)
Resolve certain symbol.- Parameters:
symbol
- the symbol- Returns:
- the SBMLS base
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resolveSymbol
public SBMLSBase resolveSymbol(String symbol)
Resolve certain symbol.- Parameters:
symbol
- the symbol- Returns:
- the SBMLS base
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