public class SBMLModel extends SBMLSBase
documentNode, sbmlModel
Constructor and Description |
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SBMLModel(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
SBMLDocument sbmlDocument)
Instantiates a new SBML model.
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Modifier and Type | Method and Description |
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SBMLCompartment |
getCompartment(String id)
Gets the compartment.
|
HashMap<String,SBMLCompartment> |
getCompartments()
Gets the compartments.
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SBMLCompartmentType |
getCompartmentType(String id)
Gets the compartment type.
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HashMap<String,SBMLCompartmentType> |
getCompartmentTypes()
Gets the compartment types.
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List<SBMLConstraint> |
getConstraints()
Gets the constraints.
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SBMLDocument |
getDocument()
Gets the SBML document.
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List<SBMLEvent> |
getEvents()
Gets the events.
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SBMLSBase |
getFromMetaId(String metaId)
Gets an entity given its meta id.
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SBMLSBase |
getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets an entity given its tree node.
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HashMap<String,SBMLFunctionDefinition> |
getFunctionDefinitions()
Gets the function definitions.
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String |
getID()
Gets the id of the model.
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List<SBMLInitialAssignment> |
getInitialAssignments()
Gets the initial assignments.
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String |
getName()
Gets the name of the model.
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HashMap<String,List<SBMLSBase>> |
getOntologyMappings()
Gets the ontology mappings which group entities by there pointers into ontologies.
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SBMLParameter |
getParameter(String id)
Gets a specific parameter.
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HashMap<String,SBMLParameter> |
getParameters()
Gets the parameters.
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SBMLReaction |
getReaction(String id)
Gets a specific reaction.
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HashMap<String,SBMLReaction> |
getReactions()
Gets the reactions.
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List<SBMLRule> |
getRules()
Gets the rules.
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static String |
getSidName(SBMLSBase ref)
Gets the SId.
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HashMap<String,SBMLSpecies> |
getSpecies()
Gets the species.
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SBMLSpecies |
getSpecies(String id)
Gets the species.
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SBMLSimpleSpeciesReference |
getSpeciesReference(String id)
Gets the species reference.
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SBMLSpeciesType |
getSpeciesType(String id)
Gets the species type.
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HashMap<String,SBMLSpeciesType> |
getSpeciesTypes()
Gets the species types.
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SBMLUnitDefinition |
getUnitDefinition(String kind)
Gets the unit definition.
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HashMap<String,SBMLUnitDefinition> |
getUnitDefinitions()
Gets the unit definitions.
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void |
mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node,
SBMLSBase sbase)
Map node model node to its entity.
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void |
registerSpeciesReference(String id,
SBMLSimpleSpeciesReference ref)
Registers a species reference.
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SBMLSBase |
resolveSymbol(String symbol)
Resolve certain symbol.
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SBMLSBase |
resolveSymbole(String symbol)
Deprecated.
as of version 1.3.6, replaced by
resolveSymbol(String) |
addOntologyLink, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm
getDocumentNode, getModel
public SBMLModel(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLDocument sbmlDocument) throws BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
documentNode
- the document node encoding this entity in the corresponding XML treesbmlDocument
- the SBML documentBivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionpublic HashMap<String,List<SBMLSBase>> getOntologyMappings()
public HashMap<String,SBMLFunctionDefinition> getFunctionDefinitions()
public HashMap<String,SBMLUnitDefinition> getUnitDefinitions()
public SBMLUnitDefinition getUnitDefinition(String kind)
kind
- the kindpublic SBMLCompartmentType getCompartmentType(String id)
id
- the idpublic HashMap<String,SBMLCompartmentType> getCompartmentTypes()
public HashMap<String,SBMLCompartment> getCompartments()
public SBMLCompartment getCompartment(String id)
id
- the idpublic SBMLSpecies getSpecies(String id)
id
- the idpublic HashMap<String,SBMLSpecies> getSpecies()
public SBMLSpeciesType getSpeciesType(String id)
id
- the idpublic HashMap<String,SBMLSpeciesType> getSpeciesTypes()
public HashMap<String,SBMLParameter> getParameters()
public SBMLParameter getParameter(String id)
id
- the id of the parameterpublic void registerSpeciesReference(String id, SBMLSimpleSpeciesReference ref)
id
- the id of the species referenceref
- the referencepublic SBMLSimpleSpeciesReference getSpeciesReference(String id)
id
- the id of the species referencepublic SBMLReaction getReaction(String id)
id
- the id of the reactionpublic HashMap<String,SBMLReaction> getReactions()
public List<SBMLConstraint> getConstraints()
public List<SBMLInitialAssignment> getInitialAssignments()
public String getID()
public String getName()
public void mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node, SBMLSBase sbase)
node
- the document node in the corresponding XML treesbase
- the entity to get mappedpublic SBMLSBase getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)
node
- the node in the XML treepublic SBMLSBase getFromMetaId(String metaId)
metaId
- the meta idpublic SBMLDocument getDocument()
public SBMLSBase resolveSymbole(String symbol)
resolveSymbol(String)
symbol
- the symbolpublic SBMLSBase resolveSymbol(String symbol)
symbol
- the symbolCopyright © 2017 SEMS project @ University of Rostock. All rights reserved.