de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

public class SBMLHelper
extends Object

Field Summary

Fields
Modifier and Type	Field	Description
`static PositionGridGenerator`	`_pgg`
`static SBML_SBase_Reader`	`attReader`
`static SBML_SBase_Writer`	`attWriter`	Provides necessary methods
`static String`	`SBML_LAYOUT_EXTENSION_NAMESPACE`

Constructor Summary

Constructors

Constructor Description

SBMLHelper()

Method Summary

Modifier and Type	Method	Description
`static void`	`addAlgebraicRule(Graph g, String function)`
`static void`	`addAssignmentRuleFunction(Graph g, String variable, String function)`
`static void`	`addAssignmentRuleVariable(Graph g, String variable)`
`static void`	`addCompartmentConstant(Graph g, String id, boolean constant)`
`static void`	`addCompartmentName(Graph g, String id, String name)`
`static void`	`addCompartmentSize(Graph g, String id, Double value)`
`static void`	`addCompartmentSpatialDimensions(Graph g, String id, Double value)`
`static void`	`addCompartmentUnits(Graph g, String id, String units)`
`static void`	`addConstraintConstraint(Graph g, String formula)`
`static void`	`addConstraintMessage(Graph g, String formula, String message)`
`static void`	`addDelayToEvent(Graph g, String id, String function)`
`static void`	`addDelayToEvent(Graph g, String id, org.sbml.jsbml.Delay delay)`
`static void`	`addEventAssignmentToEvent(Graph g, String id, String variable, String function)`
`static void`	`addEventAssignmentToEvent(Graph g, String id, org.sbml.jsbml.EventAssignment eventAssignment)`
`static void`	`addEventName(Graph g, String id, String name)`
`static void`	`addEventUseValuesFromTriggerTime(Graph g, String id, boolean useValuesFromTriggerTime)`
`static void`	`addFunctionDefinitionFunction(Graph g, String id, String function)`
`static void`	`addFunctionDefinitionName(Graph g, String id, String name)`
`static void`	`addInitialAssignmentFunction(Graph g, String symbol, String function)`
`static void`	`addKineticLaw(Node reactionNode, String function)`
`static void`	`addKineticLaw(Node reactionNode, org.sbml.jsbml.KineticLaw kineticLaw)`
`static void`	`addLocalParameter(Node node, String id)`
`static void`	`addLocalParameter(Node node, org.sbml.jsbml.LocalParameter lp)`
`static void`	`addLocalParameterName(Node node, String lpID, String name)`
`static void`	`addLocalParameterUnits(Node node, String lpID, String units)`
`static void`	`addLocalParameterValue(Node node, String lpID, Double value)`
`static Edge`	`addModifier(Node node, String speciesID)`
`static Edge`	`addModifier(Node node, org.sbml.jsbml.ModifierSpeciesReference ref)`
`static void`	`addParameterConstant(Graph g, String id, boolean constant)`
`static void`	`addParameterName(Graph g, String id, String name)`
`static void`	`addParameterUnits(Graph g, String id, String units)`
`static void`	`addParameterValue(Graph g, String id, Double value)`
`static void`	`addPriorityToEvent(Graph g, String id, String function)`
`static void`	`addPriorityToEvent(Graph g, String id, org.sbml.jsbml.Priority priority)`
`static Edge`	`addProduct(Node node, String speciesID)`
`static Edge`	`addProduct(Node node, org.sbml.jsbml.SpeciesReference ref)`
`static void`	`addRateRuleFunction(Graph g, String variable, String function)`
`static void`	`addRateRuleVariable(Graph g, String variable)`
`static Edge`	`addReactant(Node node, String speciesID)`
`static Edge`	`addReactant(Node node, org.sbml.jsbml.SpeciesReference ref)`
`static void`	`addSpeciesBoundaryConsition(Node speciesNode, Boolean boundaryCondition)`	Sets the attribute boundary condition of a species node
`static void`	`addSpeciesCompartment(Node speciesNode, String compartment)`	Sets the compartment of a node
`static void`	`addSpeciesConstant(Node speciesNode, Boolean constant)`	Sets the attribute constant of a species node
`static void`	`addSpeciesConversionFactor(Node speciesNode, String conversionFactor)`	Sets the attribute conversion factor of a species node
`static void`	`addSpeciesHasOnlySubstanceUnits(Node speciesNode, Boolean hasOnlySubstanceUnits)`	Sets the attribute hasOnlySubstanceUnits of a species node
`static void`	`addSpeciesID(Node speciesNode, String id)`	Sets the id of a species node
`static void`	`addSpeciesInitialAmount(Node speciesNode, Double initialAmount)`	Sets the initial amount of a node
`static void`	`addSpeciesInitialConcentration(Node speciesNode, Double initialConcentration)`	Sets the initial concentration of a node
`static void`	`addSpeciesName(Node speciesNode, String name)`
`static void`	`addSpeciesSubstanceUnits(Node speciesNode, String substanceUnits)`	Sets the substance units of a species node
`static void`	`addTriggerFunction(Graph g, String eventID, String function)`
`static void`	`addTriggerInitialValue(Graph g, String eventID, boolean initialValue)`
`static void`	`addTriggerPersistent(Graph g, String eventID, boolean persistent)`
`static void`	`addTriggerToEvent(Graph g, String id, boolean initialValue, boolean persistent, String formula)`
`static void`	`addTriggerToEvent(Graph g, String id, org.sbml.jsbml.Trigger trigger)`
`static void`	`addUnitDefinitionID(Graph g, String oldID, String newID)`
`static void`	`addUnitDefinitionName(Graph g, String id, String name)`
`static void`	`addUnitToUnitDefinition(Graph g, String id, org.sbml.jsbml.Unit unit)`
`static void`	`addUnitToUnitDefinition(Graph g, String id, org.sbml.jsbml.Unit.Kind kind, double exponent, double multiplier, int scale)`
`static int`	`countFunctionDefinitions(Graph g)`	Returns the number of function definitions in the graph
`static org.sbml.jsbml.AlgebraicRule`	`createAlgebraicRule(Graph g, String formula)`
`static void`	`createAlgebraicRule(Graph g, org.sbml.jsbml.AlgebraicRule ar)`
`static org.sbml.jsbml.AssignmentRule`	`createAssignmentRule(Graph g, String variable)`
`static org.sbml.jsbml.AssignmentRule`	`createAssignmentRule(Graph g, String variable, String formula)`
`static void`	`createAssignmentRule(Graph g, org.sbml.jsbml.AssignmentRule ar)`
`static org.sbml.jsbml.Compartment`	`createCompartment(Graph g, String id)`	Creates an compartment in the graph tab with an specific id
`static void`	`createCompartment(Graph g, org.sbml.jsbml.Compartment compartment)`
`static org.sbml.jsbml.Constraint`	`createConstraint(Graph g, String math)`
`static void`	`createConstraint(Graph g, org.sbml.jsbml.Constraint constraint)`
`static org.sbml.jsbml.Event`	`createEvent(Graph g, String id)`
`static void`	`createEvent(Graph g, org.sbml.jsbml.Event event)`
`static org.sbml.jsbml.FunctionDefinition`	`createFunctionDefinition(Graph g, String id)`
`static void`	`createFunctionDefinition(Graph g, org.sbml.jsbml.FunctionDefinition fd)`
`static org.sbml.jsbml.InitialAssignment`	`createInitialAssignment(Graph g, String symbol)`
`static void`	`createInitialAssignment(Graph g, org.sbml.jsbml.InitialAssignment ia)`
`static org.sbml.jsbml.Parameter`	`createParameter(Graph g, String id)`
`static void`	`createParameter(Graph g, org.sbml.jsbml.Parameter parameter)`
`static org.sbml.jsbml.RateRule`	`createRateRule(Graph g, String variable)`
`static org.sbml.jsbml.RateRule`	`createRateRule(Graph g, String variable, String formula)`
`static void`	`createRateRule(Graph g, org.sbml.jsbml.RateRule rr)`
`static Node`	`createReaction(Graph g, String id, String name)`
`static Node`	`createReaction(Graph g, org.sbml.jsbml.Reaction reaction)`
`static Node`	`createSpecies(Graph g, String id, String name)`	Creates a new species node and sets its id
`static Node`	`createSpecies(Graph g, org.sbml.jsbml.Species species)`
`static org.sbml.jsbml.UnitDefinition`	`createUnitDefinition(Graph g, String id)`
`static void`	`createUnitDefinition(Graph g, org.sbml.jsbml.UnitDefinition ud)`
`static void`	`deleteAlgebraicRule(Graph g, String formula)`
`static void`	`deleteAlgebraicRuleFunction(Graph g, String function)`
`static void`	`deleteAssignmentRule(Graph g, String variable)`
`static void`	`deleteAssignmentRuleFunction(Graph g, String variable)`
`static void`	`deleteAssignmentRuleVariable(Graph g, String variable)`
`static void`	`deleteCompartment(Graph g, String id)`
`static void`	`deleteCompartmentConstant(Graph g, String id)`
`static void`	`deleteCompartmentID(Graph g, String id)`
`static void`	`deleteCompartmentName(Graph g, String id)`
`static void`	`deleteCompartmentSize(Graph g, String id)`
`static void`	`deleteCompartmentSpatialDimensions(Graph g, String id)`
`static void`	`deleteCompartmentUnits(Graph g, String id)`
`static void`	`deleteConstant(Edge edge)`
`static void`	`deleteConstraint(Graph g, String formula)`
`static void`	`deleteConstraintMessage(Graph g, String constraint)`
`static void`	`deleteDelayFunction(Graph g, String id)`
`static void`	`deleteEvent(Graph g, String id)`
`static void`	`deleteEventAssignment(Graph g, String id, String variable)`
`static void`	`deleteEventID(Graph g, String id)`
`static void`	`deleteEventName(Graph g, String id)`
`static void`	`deleteEventUseValuesFromTriggerTime(Graph g, String id)`
`static void`	`deleteFunctionDefinition(Graph g, String id)`
`static void`	`deleteFunctionDefinitionFunction(Graph g, String id)`
`static void`	`deleteFunctionDefinitionID(Graph g, String id)`
`static void`	`deleteFunctionDefinitionName(Graph g, String id)`
`static void`	`deleteInitialAssignment(Graph g, String symbol)`
`static void`	`deleteInitialAssignmentFunction(Graph g, String symbol)`
`static void`	`deleteInitialAssignmentSymbol(Graph g, String symbol)`
`static void`	`deleteKineticLawFunction(Node node)`
`static void`	`deleteLocalParameter(Node node, String lpID)`
`static void`	`deleteLocalParameterID(Node node, String lpID)`
`static void`	`deleteLocalParameterName(Node node, String lpID)`
`static void`	`deleteLocalParameterUnits(Node node, String lpID)`
`static void`	`deleteLocalParameterValue(Node node, String lpID)`
`static void`	`deleteModifier(Edge edge)`
`static void`	`deleteParameter(Graph g, String id)`
`static void`	`deleteParameterConstant(Graph g, String id)`
`static void`	`deleteParameterID(Graph g, String id)`
`static void`	`deleteParameterName(Graph g, String id)`
`static void`	`deleteParameterUnits(Graph g, String id)`
`static void`	`deleteParameterValue(Graph g, String id)`
`static void`	`deletePriority(Graph g, String id)`
`static void`	`deletePriorityFunction(Graph g, String id)`
`static void`	`deleteProduct(Edge edge)`
`static void`	`deleteRateRule(Graph g, String variable)`
`static void`	`deleteRateRuleFunction(Graph g, String variable)`
`static void`	`deleteRateRuleVariable(Graph g, String variable)`
`static void`	`deleteReactant(Edge edge)`
`static void`	`deleteReactionCompartment(Node reactionNode)`
`static void`	`deleteReactionFast(Node reactionNode)`
`static void`	`deleteReactionID(Node reactionNode)`
`static void`	`deleteReactionName(Node reactionNode)`
`static void`	`deleteReactionReversible(Node reactionNode)`
`static void`	`deleteReactionSpecies(Edge edge)`
`static void`	`deleteReactionSpeciesID(Edge edge)`
`static void`	`deleteReactionSpeciesName(Edge edge)`
`static void`	`deleteSpecies(Node node)`
`static void`	`deleteSpeciesBoundaryCondition(Node node)`
`static void`	`deleteSpeciesCompartment(Node node)`
`static void`	`deleteSpeciesConstant(Node node)`
`static void`	`deleteSpeciesConversionFactor(Node node)`
`static void`	`deleteSpeciesHasOnlySubstanceUnits(Node node)`
`static void`	`deleteSpeciesID(Node node)`
`static void`	`deleteSpeciesInitialAmount(Node node)`
`static void`	`deleteSpeciesInitialConcentration(Node node)`
`static void`	`deleteSpeciesName(Node node)`
`static void`	`deleteSpeciesSubstanceUnits(Node node)`
`static void`	`deleteStoichiometry(Edge edge)`
`static void`	`deleteTriggeInitialValue(Graph g, String id)`
`static void`	`deleteTrigger(Graph g, String id)`
`static void`	`deleteTriggerFunction(Graph g, String id)`
`static void`	`deleteTriggerPersistent(Graph g, String id)`
`static void`	`deleteUnitDefinitionID(Graph g, String id)`
`static void`	`deleteUnitDefinitionName(Graph g, String id)`
`static List<org.sbml.jsbml.AssignmentRule>`	`getAllAssignmentRules(Graph g)`	Returns a list of assignment rules with distinct headlines
`static List<org.sbml.jsbml.Compartment>`	`getAllCompartments(Graph g)`	Returns a list of compartments with distinct headlines
`static List<org.sbml.jsbml.Constraint>`	`getAllConstraints(Graph g)`	Returns a list of constraint with distinct headlines
`static List<org.sbml.jsbml.Event>`	`getAllEvent(Graph g)`	Returns a list of event with distinct headlines
`static List<org.sbml.jsbml.FunctionDefinition>`	`getAllFunctionDefinitions(Graph g)`	Returns a list of filled JSBML FunctionDefinition objects
`static List<org.sbml.jsbml.InitialAssignment>`	`getAllInitialAssignment(Graph g)`	Returns a list of initial assignment with distinct headlines
`static List<org.sbml.jsbml.Parameter>`	`getAllParameters(Graph g)`	Returns a list of parameter with distinct headlines
`static List<org.sbml.jsbml.UnitDefinition>`	`getAllUnitDefinitions(Graph g)`	Returns a filled list of UnitDefinition objects
`static ArrayList<String>`	`getAssignmentRuleHeadlines(Graph g)`	Returns a list of all assignment rule headlines in the graph
`static String`	`getKineticLawFunction(Node reactionNode)`	Returns the function of a kinetic law
`static String`	`getLocalParameterID(Node reactionNode, int localParameterCount)`	Returns the value of the attribute id
`static String`	`getLocalParameterName(Node reactionNode, int localParameterCount)`	Returns the value of the attribute name
`static String`	`getLocalParameterUnits(Node reactionNode, int localParameterCount)`	Returns the value of the attribute units
`static Double`	`getLocalParameterValue(Node reactionNode, int localParameterCount)`	Returns the value of the attribute value
`static List<Edge>`	`getModifier(Node node)`	Returns the modifier edges
`static List<Edge>`	`getProducts(Node node)`	The edges with the simple species references will be returned
`static List<Edge>`	`getReactants(Node node)`	The edges with the simple species references will be returned
`static org.sbml.jsbml.Reaction`	`getReaction(Node node)`	Returns a JSBML Reaction object belonging to a reaction node
`static String`	`getReactionCompartment(Node reactionNode)`	Returns the compartment of a reaction
`static Boolean`	`getReactionConstant(Edge reactionEdge)`	Returns the value of the attribute constant
`static Boolean`	`getReactionFast(Node reactionNode)`	Returns the attribute fast of a reaction
`static String`	`getReactionID(Node reactionNode)`	Returns the id of a reaction
`static String`	`getReactionName(Node reactionNode)`	Returns the name of a reaction
`static Node`	`getReactionNode(Graph g, String id)`	Returns the reaction node with a distinct id
`static List<Node>`	`getReactionNodes(Graph g)`	Returns all reaction nodes of the graph
`static Boolean`	`getReactionReversible(Node reactionNode)`	Returns the attribute reversible of a reaction
`static String`	`getReactionSpecies(Edge reactionEdge)`	Returns the species
`static String`	`getReactionSpeciesID(Edge reactionEdge)`	Return the species id
`static String`	`getReactionSpeciesName(Edge reactionEdge)`	Returns the species name
`static org.sbml.jsbml.Species`	`getSpecies(Node node)`	Returns a JSBML Species object belonging to a species node
`static Boolean`	`getSpeciesBoundaryCondition(Node speciesNode)`	Returns the boolean value boundaryCondition of the species
`static String`	`getSpeciesCompartment(Node speciesNode)`	Returns the compartment id of a species
`static Boolean`	`getSpeciesConstant(Node speciesNode)`	Returns the boolean value constant of the species
`static String`	`getSpeciesConversionFactor(Node speciesNode)`	Returns the conversion factor units of a species
`static Boolean`	`getSpeciesHasOnlySubstanceUnits(Node speciesNode)`	Returns the boolean value hasOnlySubstanceUnits of the species
`static String`	`getSpeciesID(Node speciesNode)`	Returns the id of the species
`static Double`	`getSpeciesInitialAmount(Node speciesNode)`	Returns the initial amount of a species
`static Double`	`getSpeciesInitialConcentration(Node speciesNode)`	Returns the initial concentration of a species
`static String`	`getSpeciesName(Node speciesNode)`	Returns the name of the species
`static Node`	`getSpeciesNode(Graph g, String id)`	Returns the species node with a distinct id
`static List<Node>`	`getSpeciesNodes(Graph g)`	Returns all species nodes of the graph
`static String`	`getSpeciesSubstanceUnits(Node speciesNode)`	Returns the substance units of a species
`static String`	`getStoichiometry(Edge reactionEdge)`	Returns the value of the attribute stoichiometry
`static Edge`	`initProductEdge(Edge e)`
`static Edge`	`initReactantEdge(Edge e)`
`static Node`	`initReactionNode(Node n)`
`static Node`	`initSpeciesNode(Node n)`	This method converts a node into a species node
`static Boolean`	`isKineticLawFunction(Node reactionNode)`	Indicates if the function of a kinetic law is set
`static Boolean`	`isLocalParameterID(Node reactionNode, int localParameterCount)`	Indicates if the attribute id is set
`static Boolean`	`isLocalParameterName(Node reactionNode, int localParameterCount)`	Indicates if the attribute name is set
`static Boolean`	`isLocalParameterUnits(Node reactionNode, int localParameterCount)`	Indicates if the attribute units is set
`static Boolean`	`isLocalParameterValue(Node reactionNode, int localParameterCount)`	Indicates if the attribute value is set
`static Boolean`	`isReactionCompartment(Node reactionNode)`	Indicates if compartment of a reaction is set
`static Boolean`	`isReactionConstant(Edge reactionEdge)`	Indicates if there is set a value for constant
`static Boolean`	`isReactionFast(Node reactionNode)`	Indicates if fast of a reaction is set
`static Boolean`	`isReactionID(Node reactionNode)`	Indicates if id of a reaction is set
`static Boolean`	`isReactionName(Node reactionNode)`	Indicates if name of a reaction is set
`static Boolean`	`isReactionReversible(Node reactionNode)`	Indicates if reversible of a reaction is set
`static Boolean`	`isReactionSpecies(Edge reactionEdge)`	Indicates if the species attribute is set
`static Boolean`	`isReactionSpeciesID(Edge reactionEdge)`	Indicates if the species id attribute is set
`static Boolean`	`isReactionSpeciesName(Edge reactionEdge)`	Indicates if the species name attribute is set
`static Boolean`	`isReactionStoichiometry(Edge reactionEdge)`	Indicates if there is set a value for stoichiometry
`static boolean`	`isSetAssignmentRuleFunction(Graph g, String variable)`
`static boolean`	`isSetAssignmentRuleVariable(Graph g, String variable)`
`static boolean`	`isSetCompartmentConstants(Graph g, String id)`
`static boolean`	`isSetCompartmentID(Graph g, String id)`
`static boolean`	`isSetCompartmentName(Graph g, String id)`
`static boolean`	`isSetCompartmentSize(Graph g, String id)`
`static boolean`	`isSetCompartmentSpatialDimensions(Graph g, String id)`
`static boolean`	`isSetCompartmentUnits(Graph g, String id)`
`static boolean`	`isSetConstant(Edge edge)`
`static boolean`	`isSetConstraintMessage(Graph g, String constraint)`
`static boolean`	`isSetDelay(Graph g, String id)`
`static boolean`	`isSetDelayFunction(Graph g, String id)`
`static boolean`	`isSetEventName(Graph g, String id)`
`static boolean`	`isSetEventUseValuesFromTriggerTime(Graph g, String id)`
`static boolean`	`isSetFunctionDefinitionFunction(Graph g, String id)`
`static boolean`	`isSetFunctionDefinitionID(Graph g, String id)`
`static boolean`	`isSetFunctionDefinitionName(Graph g, String id)`
`static boolean`	`isSetInitialAssignmentFunction(Graph g, String symbol)`
`static boolean`	`isSetInitialAssignmentSymbol(Graph g, String symbol)`
`static boolean`	`isSetLayoutID(Graph g, Node node)`
`static boolean`	`isSetLocalParameterName(Node node, String lpID)`
`static boolean`	`isSetLocalParameterUnits(Node node, String lpID)`
`static boolean`	`isSetLocalParameterValue(Node node, String lpID)`
`static boolean`	`isSetParameterConstant(Graph g, String id)`
`static boolean`	`isSetParameterName(Graph g, String id)`
`static boolean`	`isSetParameterUnits(Graph g, String id)`
`static boolean`	`isSetParameterValue(Graph g, String id)`
`static boolean`	`isSetPriority(Graph g, String id)`
`static boolean`	`isSetRateRuleFunction(Graph g, String variable)`
`static boolean`	`isSetRateRuleVariable(Graph g, String variable)`
`static boolean`	`isSetReactionSpecies(Edge edge)`
`static boolean`	`isSetReactionSpeciesID(Edge edge)`
`static boolean`	`isSetReactionSpeciesName(Edge edge)`
`static boolean`	`isSetStoichiometry(Edge edge)`
`static boolean`	`isSetTriggerFunction(Graph g, String id)`
`static boolean`	`isSetTriggerInitialValue(Graph g, String id)`
`static boolean`	`isSetTriggerPersistent(Graph g, String id)`
`static boolean`	`isSetUnitDefinitionID(Graph g, String id)`
`static boolean`	`isSetUnitDefinitionName(Graph g, String id)`
`static Boolean`	`isSpeciesBoundaryCondition(Node speciesNode)`	Indicates if boundary condition of a species is set
`static Boolean`	`isSpeciesCompartment(Node speciesNode)`	Indicates if the compartment id of a species is set
`static Boolean`	`isSpeciesConstant(Node speciesNode)`	Indicates if constant of a species is set
`static Boolean`	`isSpeciesConversionFactor(Node speciesNode)`	Indicates if conversion factor of a species is set
`static Boolean`	`isSpeciesHasOnlySubstanceUnits(Node speciesNode)`	Indicates if hasOnlySubstanceUnits of a species is set
`static Boolean`	`isSpeciesID(Node speciesNode)`	Indicates if the id of a species is set
`static Boolean`	`isSpeciesInitialAmount(Node speciesNode)`	Indicates if the initial amount of a species is set
`static Boolean`	`isSpeciesInitialConcentration(Node speciesNode)`	Indicates if the initial concentration of a species is set
`static Boolean`	`isSpeciesName(Node speciesNode)`	Indicates if the name of a species is set
`static Boolean`	`isSpeciesSubstanceUnits(Node speciesNode)`	Indicates if substance units of a species is set
`static int`	`localParameterCount(Node node)`	Returns the number of local parameter
`static void`	`setReactionCompartment(Node reactionNode, String compartment)`	Sets the compartment of a node
`static void`	`setReactionConstant(Edge reactionEdge, Boolean constant)`	Sets a value for the attribute constant
`static void`	`setReactionFast(Node reactionNode, Boolean fast)`	Sets the attribute fast of a node
`static void`	`setReactionID(Node reactionNode, String ID)`	Sets the attribute id of a node
`static void`	`setReactionLabel(Node reactionNode, String name, String id, PositionGridGenerator pgg)`	Sets the attribute name of a node
`static void`	`setReactionName(Node reactionNode, String name)`
`static void`	`setReactionReversible(Node reactionNode, Boolean reversible)`	Sets the attribute reversible of a node
`static void`	`setReactionSpecies(Edge reactionEdge, String species)`	Sets the species of a reaction
`static void`	`setReactionSpeciesID(Edge reactionEdge, String ID)`	The id of the species of an reaction
`static void`	`setReactionSpeciesName(Edge reactionEdge, String name)`	The name of the species of a reaction
`static void`	`setSpeciesAttributes(Node sbmlNode, String niceID, Object value)`
`static void`	`setStoichiometry(Edge reactionEdge, Double stoichiometry)`	Sets a value for the attribute stoichiometry

Methods inherited from class java.lang.Object

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

Field Details
- attWriter
  
  public static SBML_SBase_Writer attWriter
  
  Provides necessary methods
- _pgg
  
  public static PositionGridGenerator _pgg
- attReader
  
  public static SBML_SBase_Reader attReader
- SBML_LAYOUT_EXTENSION_NAMESPACE
  
  public static final String SBML_LAYOUT_EXTENSION_NAMESPACE
  
  See Also:
  
  Constant Field Values
Constructor Details
- SBMLHelper
  
  public SBMLHelper()
Method Details
- createFunctionDefinition
  
  public static org.sbml.jsbml.FunctionDefinition createFunctionDefinition(Graph g, String id)
- createFunctionDefinition
  
  public static void createFunctionDefinition(Graph g, org.sbml.jsbml.FunctionDefinition fd)
- addFunctionDefinitionName
  
  public static void addFunctionDefinitionName(Graph g, String id, String name)
- addFunctionDefinitionFunction
  
  public static void addFunctionDefinitionFunction(Graph g, String id, String function)
- deleteFunctionDefinitionID
  
  public static void deleteFunctionDefinitionID(Graph g, String id)
- deleteFunctionDefinitionName
  
  public static void deleteFunctionDefinitionName(Graph g, String id)
- deleteFunctionDefinitionFunction
  
  public static void deleteFunctionDefinitionFunction(Graph g, String id)
- deleteFunctionDefinition
  
  public static void deleteFunctionDefinition(Graph g, String id)
- isSetFunctionDefinitionName
  
  public static boolean isSetFunctionDefinitionName(Graph g, String id)
- isSetFunctionDefinitionID
  
  public static boolean isSetFunctionDefinitionID(Graph g, String id)
- isSetFunctionDefinitionFunction
  
  public static boolean isSetFunctionDefinitionFunction(Graph g, String id)
- countFunctionDefinitions
  
  public static int countFunctionDefinitions(Graph g)
  
  Returns the number of function definitions in the graph
  
  Parameters:
  
  g - where the information is read from
  
  Returns:
  
  number of function definitios
- getAllFunctionDefinitions
  
  public static List<org.sbml.jsbml.FunctionDefinition> getAllFunctionDefinitions(Graph g)
  
  Returns a list of filled JSBML FunctionDefinition objects
  
  Parameters:
  
  g - contains the information
  
  Returns:
  
  a filled list of function definitions
- createUnitDefinition
  
  public static org.sbml.jsbml.UnitDefinition createUnitDefinition(Graph g, String id)
- createUnitDefinition
  
  public static void createUnitDefinition(Graph g, org.sbml.jsbml.UnitDefinition ud)
- addUnitToUnitDefinition
  
  public static void addUnitToUnitDefinition(Graph g, String id, org.sbml.jsbml.Unit unit)
- addUnitToUnitDefinition
  
  public static void addUnitToUnitDefinition(Graph g, String id, org.sbml.jsbml.Unit.Kind kind, double exponent, double multiplier, int scale)
- addUnitDefinitionName
  
  public static void addUnitDefinitionName(Graph g, String id, String name)
- addUnitDefinitionID
  
  public static void addUnitDefinitionID(Graph g, String oldID, String newID)
- deleteUnitDefinitionID
  
  public static void deleteUnitDefinitionID(Graph g, String id)
- deleteUnitDefinitionName
  
  public static void deleteUnitDefinitionName(Graph g, String id)
- isSetUnitDefinitionName
  
  public static boolean isSetUnitDefinitionName(Graph g, String id)
- isSetUnitDefinitionID
  
  public static boolean isSetUnitDefinitionID(Graph g, String id)
- getAllUnitDefinitions
  
  public static List<org.sbml.jsbml.UnitDefinition> getAllUnitDefinitions(Graph g)
  
  Returns a filled list of UnitDefinition objects
  
  Parameters:
  
  g - the graph where the information can be found
  
  Returns:
  
  a filled UnitDefinition list
- createCompartment
  
  public static org.sbml.jsbml.Compartment createCompartment(Graph g, String id)
  
  Creates an compartment in the graph tab with an specific id
  
  Returns:
  
  the Compartment object will be returned
- createCompartment
  
  public static void createCompartment(Graph g, org.sbml.jsbml.Compartment compartment)
  
  Parameters:
  
  compartment -
- isSetCompartmentName
  
  public static boolean isSetCompartmentName(Graph g, String id)
- isSetCompartmentID
  
  public static boolean isSetCompartmentID(Graph g, String id)
- isSetCompartmentSpatialDimensions
  
  public static boolean isSetCompartmentSpatialDimensions(Graph g, String id)
- isSetCompartmentSize
  
  public static boolean isSetCompartmentSize(Graph g, String id)
- isSetCompartmentUnits
  
  public static boolean isSetCompartmentUnits(Graph g, String id)
- isSetCompartmentConstants
  
  public static boolean isSetCompartmentConstants(Graph g, String id)
- addCompartmentName
  
  public static void addCompartmentName(Graph g, String id, String name)
- addCompartmentSpatialDimensions
  
  public static void addCompartmentSpatialDimensions(Graph g, String id, Double value)
- addCompartmentSize
  
  public static void addCompartmentSize(Graph g, String id, Double value)
- addCompartmentUnits
  
  public static void addCompartmentUnits(Graph g, String id, String units)
- addCompartmentConstant
  
  public static void addCompartmentConstant(Graph g, String id, boolean constant)
- deleteCompartmentID
  
  public static void deleteCompartmentID(Graph g, String id)
- deleteCompartmentName
  
  public static void deleteCompartmentName(Graph g, String id)
- deleteCompartmentSpatialDimensions
  
  public static void deleteCompartmentSpatialDimensions(Graph g, String id)
- deleteCompartmentSize
  
  public static void deleteCompartmentSize(Graph g, String id)
- deleteCompartmentUnits
  
  public static void deleteCompartmentUnits(Graph g, String id)
- deleteCompartmentConstant
  
  public static void deleteCompartmentConstant(Graph g, String id)
- deleteCompartment
  
  public static void deleteCompartment(Graph g, String id)
- getAllCompartments
  
  public static List<org.sbml.jsbml.Compartment> getAllCompartments(Graph g)
  
  Returns a list of compartments with distinct headlines
  
  Parameters:
  
  g - contains the information
  
  Returns:
  
  a filled list of compartments
- isSpeciesID
  
  public static Boolean isSpeciesID(Node speciesNode)
  
  Indicates if the id of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if the id is set else false
- isSpeciesName
  
  public static Boolean isSpeciesName(Node speciesNode)
  
  Indicates if the name of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if the name is set else false
- isSpeciesCompartment
  
  public static Boolean isSpeciesCompartment(Node speciesNode)
  
  Indicates if the compartment id of a species is set
  
  Parameters:
  
  node - the node where the information is read from
  
  Returns:
  
  true if the compartment id is set else false
- isSpeciesInitialAmount
  
  public static Boolean isSpeciesInitialAmount(Node speciesNode)
  
  Indicates if the initial amount of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if the initial amount is set else false
- isSpeciesInitialConcentration
  
  public static Boolean isSpeciesInitialConcentration(Node speciesNode)
  
  Indicates if the initial concentration of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if the initial concentration is set else false
- isSpeciesSubstanceUnits
  
  public static Boolean isSpeciesSubstanceUnits(Node speciesNode)
  
  Indicates if substance units of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if substance units is set else false
- isSpeciesHasOnlySubstanceUnits
  
  public static Boolean isSpeciesHasOnlySubstanceUnits(Node speciesNode)
  
  Indicates if hasOnlySubstanceUnits of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if hasOnlySubstanceUnits is set else false
- isSpeciesBoundaryCondition
  
  public static Boolean isSpeciesBoundaryCondition(Node speciesNode)
  
  Indicates if boundary condition of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if boundary condition is set else false
- isSpeciesConstant
  
  public static Boolean isSpeciesConstant(Node speciesNode)
  
  Indicates if constant of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if constant is set else false
- isSpeciesConversionFactor
  
  public static Boolean isSpeciesConversionFactor(Node speciesNode)
  
  Indicates if conversion factor of a species is set
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  true if conversion factor is set else false
- getSpeciesID
  
  public static String getSpeciesID(Node speciesNode)
  
  Returns the id of the species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  the species id if it is set else the empty string
- getSpeciesName
  
  public static String getSpeciesName(Node speciesNode)
  
  Returns the name of the species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  the species name if it is set else the empty string
- getSpeciesCompartment
  
  public static String getSpeciesCompartment(Node speciesNode)
  
  Returns the compartment id of a species
  
  Parameters:
  
  Node - the node where the information is read from
  
  Returns:
  
  the compartment id if it is set else the empty string
- getSpeciesInitialAmount
  
  public static Double getSpeciesInitialAmount(Node speciesNode)
  
  Returns the initial amount of a species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  initial amount if it is set else null
- getSpeciesInitialConcentration
  
  public static Double getSpeciesInitialConcentration(Node speciesNode)
  
  Returns the initial concentration of a species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  initial concentration if it is set else null
- getSpeciesSubstanceUnits
  
  public static String getSpeciesSubstanceUnits(Node speciesNode)
  
  Returns the substance units of a species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  substance Units if it is set else the empty string
- getSpeciesHasOnlySubstanceUnits
  
  public static Boolean getSpeciesHasOnlySubstanceUnits(Node speciesNode)
  
  Returns the boolean value hasOnlySubstanceUnits of the species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  a boolean value if the attribute hasOnlySubstanceUnits is set else null
- getSpeciesBoundaryCondition
  
  public static Boolean getSpeciesBoundaryCondition(Node speciesNode)
  
  Returns the boolean value boundaryCondition of the species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  a boolean value if the attribute boundaryCondition is set else null
- getSpeciesConstant
  
  public static Boolean getSpeciesConstant(Node speciesNode)
  
  Returns the boolean value constant of the species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  a boolean value if the attribute constant is set else null
- getSpeciesConversionFactor
  
  public static String getSpeciesConversionFactor(Node speciesNode)
  
  Returns the conversion factor units of a species
  
  Parameters:
  
  speciesNode - the node where the information is read from
  
  Returns:
  
  conversion factor if it is set else null
- addSpeciesID
  
  public static void addSpeciesID(Node speciesNode, String id)
  
  Sets the id of a species node
  
  Parameters:
  
  speciesNode - where the information should be read in
  
  id - the id to set
- addSpeciesName
  
  public static void addSpeciesName(Node speciesNode, String name)
- setSpeciesAttributes
  
  public static void setSpeciesAttributes(Node sbmlNode, String niceID, Object value)
- addSpeciesCompartment
  
  public static void addSpeciesCompartment(Node speciesNode, String compartment)
  
  Sets the compartment of a node
  
  Parameters:
  
  speciesNode - the compartment belongs to this node
  
  compartment - the id of the compartment that will be set
- addSpeciesInitialAmount
  
  public static void addSpeciesInitialAmount(Node speciesNode, Double initialAmount)
  
  Sets the initial amount of a node
  
  Parameters:
  
  speciesNode - the initial amount belongs to this node
  
  initialAmount - the value that will be set
- addSpeciesInitialConcentration
  
  public static void addSpeciesInitialConcentration(Node speciesNode, Double initialConcentration)
  
  Sets the initial concentration of a node
  
  Parameters:
  
  speciesNode - the initial concentration belongs to this node
  
  initialConcentration - the value that will be set
- addSpeciesSubstanceUnits
  
  public static void addSpeciesSubstanceUnits(Node speciesNode, String substanceUnits)
  
  Sets the substance units of a species node
  
  Parameters:
  
  speciesNode - the substance units belong to this node
  
  substanceUnits - the substance units to set
- addSpeciesHasOnlySubstanceUnits
  
  public static void addSpeciesHasOnlySubstanceUnits(Node speciesNode, Boolean hasOnlySubstanceUnits)
  
  Sets the attribute hasOnlySubstanceUnits of a species node
  
  Parameters:
  
  speciesNode - where the attribute is going to be added
  
  hasOnlySubstanceUnits - the value that will be set
- addSpeciesBoundaryConsition
  
  public static void addSpeciesBoundaryConsition(Node speciesNode, Boolean boundaryCondition)
  
  Sets the attribute boundary condition of a species node
  
  Parameters:
  
  speciesNode - where the attribute is going to be added
  
  boundaryCondition - the value that will be set
- addSpeciesConstant
  
  public static void addSpeciesConstant(Node speciesNode, Boolean constant)
  
  Sets the attribute constant of a species node
  
  Parameters:
  
  speciesNode - where the attribute is going to be added
  
  constant - the value that will be set
- addSpeciesConversionFactor
  
  public static void addSpeciesConversionFactor(Node speciesNode, String conversionFactor)
  
  Sets the attribute conversion factor of a species node
  
  Parameters:
  
  speciesNode - where the attribute is going to be added
  
  conversionFactor - the value that will be set
- deleteSpeciesID
  
  public static void deleteSpeciesID(Node node)
- deleteSpeciesName
  
  public static void deleteSpeciesName(Node node)
- deleteSpeciesCompartment
  
  public static void deleteSpeciesCompartment(Node node)
- deleteSpeciesInitialAmount
  
  public static void deleteSpeciesInitialAmount(Node node)
- deleteSpeciesInitialConcentration
  
  public static void deleteSpeciesInitialConcentration(Node node)
- deleteSpeciesSubstanceUnits
  
  public static void deleteSpeciesSubstanceUnits(Node node)
- deleteSpeciesHasOnlySubstanceUnits
  
  public static void deleteSpeciesHasOnlySubstanceUnits(Node node)
- deleteSpeciesBoundaryCondition
  
  public static void deleteSpeciesBoundaryCondition(Node node)
- deleteSpeciesConstant
  
  public static void deleteSpeciesConstant(Node node)
- deleteSpeciesConversionFactor
  
  public static void deleteSpeciesConversionFactor(Node node)
- deleteSpecies
  
  public static void deleteSpecies(Node node)
- getSpeciesNodes
  
  public static List<Node> getSpeciesNodes(Graph g)
  
  Returns all species nodes of the graph
  
  Returns:
  
  a list of all species nodes of the graph
- getSpeciesNode
  
  public static Node getSpeciesNode(Graph g, String id)
  
  Returns the species node with a distinct id
  
  Parameters:
  
  id - the id of the asked node
  
  Returns:
  
  the node with a certain id or null if no node has this id
- getSpecies
  
  public static org.sbml.jsbml.Species getSpecies(Node node)
  
  Returns a JSBML Species object belonging to a species node
  
  Parameters:
  
  node - the species node
  
  Returns:
  
  a JSBML Species object
- createSpecies
  
  public static Node createSpecies(Graph g, String id, String name)
  
  Creates a new species node and sets its id
  
  Parameters:
  
  g - the node is added to this graph
  
  id - the value of the id that will be set
  
  Returns:
  
  a node or null if the id is the empty string
- initSpeciesNode
  
  public static Node initSpeciesNode(Node n)
  
  This method converts a node into a species node
  
  Parameters:
  
  n - the node that will be transformed
  
  Returns:
  
  the species node that will be returned
- createSpecies
  
  public static Node createSpecies(Graph g, org.sbml.jsbml.Species species)
- createParameter
  
  public static org.sbml.jsbml.Parameter createParameter(Graph g, String id)
- createParameter
  
  public static void createParameter(Graph g, org.sbml.jsbml.Parameter parameter)
- addParameterName
  
  public static void addParameterName(Graph g, String id, String name)
- addParameterValue
  
  public static void addParameterValue(Graph g, String id, Double value)
- addParameterUnits
  
  public static void addParameterUnits(Graph g, String id, String units)
- addParameterConstant
  
  public static void addParameterConstant(Graph g, String id, boolean constant)
- deleteParameterName
  
  public static void deleteParameterName(Graph g, String id)
- deleteParameterID
  
  public static void deleteParameterID(Graph g, String id)
- deleteParameterValue
  
  public static void deleteParameterValue(Graph g, String id)
- deleteParameterUnits
  
  public static void deleteParameterUnits(Graph g, String id)
- deleteParameterConstant
  
  public static void deleteParameterConstant(Graph g, String id)
- deleteParameter
  
  public static void deleteParameter(Graph g, String id)
- isSetParameterName
  
  public static boolean isSetParameterName(Graph g, String id)
- isSetParameterValue
  
  public static boolean isSetParameterValue(Graph g, String id)
- isSetParameterUnits
  
  public static boolean isSetParameterUnits(Graph g, String id)
- isSetParameterConstant
  
  public static boolean isSetParameterConstant(Graph g, String id)
- getAllParameters
  
  public static List<org.sbml.jsbml.Parameter> getAllParameters(Graph g)
  
  Returns a list of parameter with distinct headlines
  
  Parameters:
  
  g - contains the information
  
  Returns:
  
  a filled list of parameters
- createInitialAssignment
  
  public static org.sbml.jsbml.InitialAssignment createInitialAssignment(Graph g, String symbol)
- createInitialAssignment
  
  public static void createInitialAssignment(Graph g, org.sbml.jsbml.InitialAssignment ia)
- addInitialAssignmentFunction
  
  public static void addInitialAssignmentFunction(Graph g, String symbol, String function)
- deleteInitialAssignmentSymbol
  
  public static void deleteInitialAssignmentSymbol(Graph g, String symbol)
- deleteInitialAssignmentFunction
  
  public static void deleteInitialAssignmentFunction(Graph g, String symbol)
- deleteInitialAssignment
  
  public static void deleteInitialAssignment(Graph g, String symbol)
- isSetInitialAssignmentFunction
  
  public static boolean isSetInitialAssignmentFunction(Graph g, String symbol)
- isSetInitialAssignmentSymbol
  
  public static boolean isSetInitialAssignmentSymbol(Graph g, String symbol)
- getAllInitialAssignment
  
  public static List<org.sbml.jsbml.InitialAssignment> getAllInitialAssignment(Graph g)
  
  Returns a list of initial assignment with distinct headlines
  
  Parameters:
  
  g - contains the information
  
  Returns:
  
  a filled list of initial assignment
- deleteAssignmentRule
  
  public static void deleteAssignmentRule(Graph g, String variable)
- deleteRateRule
  
  public static void deleteRateRule(Graph g, String variable)
- deleteAlgebraicRule
  
  public static void deleteAlgebraicRule(Graph g, String formula)
- createAssignmentRule
  
  public static org.sbml.jsbml.AssignmentRule createAssignmentRule(Graph g, String variable)
- createRateRule
  
  public static org.sbml.jsbml.RateRule createRateRule(Graph g, String variable)
- createAlgebraicRule
  
  public static org.sbml.jsbml.AlgebraicRule createAlgebraicRule(Graph g, String formula)
- createAssignmentRule
  
  public static org.sbml.jsbml.AssignmentRule createAssignmentRule(Graph g, String variable, String formula)
- createRateRule
  
  public static org.sbml.jsbml.RateRule createRateRule(Graph g, String variable, String formula)
- createAssignmentRule
  
  public static void createAssignmentRule(Graph g, org.sbml.jsbml.AssignmentRule ar)
- createRateRule
  
  public static void createRateRule(Graph g, org.sbml.jsbml.RateRule rr)
- createAlgebraicRule
  
  public static void createAlgebraicRule(Graph g, org.sbml.jsbml.AlgebraicRule ar)
- isSetAssignmentRuleFunction
  
  public static boolean isSetAssignmentRuleFunction(Graph g, String variable)
- isSetAssignmentRuleVariable
  
  public static boolean isSetAssignmentRuleVariable(Graph g, String variable)
- isSetRateRuleFunction
  
  public static boolean isSetRateRuleFunction(Graph g, String variable)
- isSetRateRuleVariable
  
  public static boolean isSetRateRuleVariable(Graph g, String variable)
- deleteAssignmentRuleVariable
  
  public static void deleteAssignmentRuleVariable(Graph g, String variable)
- deleteAssignmentRuleFunction
  
  public static void deleteAssignmentRuleFunction(Graph g, String variable)
- deleteRateRuleVariable
  
  public static void deleteRateRuleVariable(Graph g, String variable)
- deleteRateRuleFunction
  
  public static void deleteRateRuleFunction(Graph g, String variable)
- deleteAlgebraicRuleFunction
  
  public static void deleteAlgebraicRuleFunction(Graph g, String function)
- addAssignmentRuleFunction
  
  public static void addAssignmentRuleFunction(Graph g, String variable, String function)
- addAssignmentRuleVariable
  
  public static void addAssignmentRuleVariable(Graph g, String variable)
- addRateRuleFunction
  
  public static void addRateRuleFunction(Graph g, String variable, String function)
- addRateRuleVariable
  
  public static void addRateRuleVariable(Graph g, String variable)
- addAlgebraicRule
  
  public static void addAlgebraicRule(Graph g, String function)
- getAssignmentRuleHeadlines
  
  public static ArrayList<String> getAssignmentRuleHeadlines(Graph g)
  
  Returns a list of all assignment rule headlines in the graph
  
  Parameters:
  
  g - the graph where the information can be found
  
  Returns:
  
  list of headlines
- getAllAssignmentRules
  
  public static List<org.sbml.jsbml.AssignmentRule> getAllAssignmentRules(Graph g)
  
  Returns a list of assignment rules with distinct headlines
  
  Parameters:
  
  g - contains the information
  
  internHeadlines - a list which contains the number of the current assignment rule
  
  Returns:
  
  a filled list of assignment rules
- createConstraint
  
  public static org.sbml.jsbml.Constraint createConstraint(Graph g, String math)
- createConstraint
  
  public static void createConstraint(Graph g, org.sbml.jsbml.Constraint constraint)
- deleteConstraint
  
  public static void deleteConstraint(Graph g, String formula)
- addConstraintMessage
  
  public static void addConstraintMessage(Graph g, String formula, String message)
- addConstraintConstraint
  
  public static void addConstraintConstraint(Graph g, String formula)
- deleteConstraintMessage
  
  public static void deleteConstraintMessage(Graph g, String constraint)
- isSetConstraintMessage
  
  public static boolean isSetConstraintMessage(Graph g, String constraint)
- getAllConstraints
  
  public static List<org.sbml.jsbml.Constraint> getAllConstraints(Graph g)
  
  Returns a list of constraint with distinct headlines
  
  Parameters:
  
  g - contains the information
  
  Returns:
  
  a filled list of constraint
- isReactionCompartment
  
  public static Boolean isReactionCompartment(Node reactionNode)
  
  Indicates if compartment of a reaction is set
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  true if compartment is set else false
- isReactionFast
  
  public static Boolean isReactionFast(Node reactionNode)
  
  Indicates if fast of a reaction is set
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  true if fast is set else false
- isReactionReversible
  
  public static Boolean isReactionReversible(Node reactionNode)
  
  Indicates if reversible of a reaction is set
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  true if reversible is set else false
- isReactionName
  
  public static Boolean isReactionName(Node reactionNode)
  
  Indicates if name of a reaction is set
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  true if name is set else false
- isReactionID
  
  public static Boolean isReactionID(Node reactionNode)
  
  Indicates if id of a reaction is set
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  true if id is set else false
- getReactionID
  
  public static String getReactionID(Node reactionNode)
  
  Returns the id of a reaction
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  id if it is set else the empty string
- getReactionName
  
  public static String getReactionName(Node reactionNode)
  
  Returns the name of a reaction
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  name if it is set else the empty string
- getReactionReversible
  
  public static Boolean getReactionReversible(Node reactionNode)
  
  Returns the attribute reversible of a reaction
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  reversible if it is set else null
- getReactionFast
  
  public static Boolean getReactionFast(Node reactionNode)
  
  Returns the attribute fast of a reaction
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  fast if it is set else the empty string
- getReactionCompartment
  
  public static String getReactionCompartment(Node reactionNode)
  
  Returns the compartment of a reaction
  
  Parameters:
  
  reactionNode - the node where the information is read from
  
  Returns:
  
  compartment if it is set else the empty string
- setReactionID
  
  public static void setReactionID(Node reactionNode, String ID)
  
  Sets the attribute id of a node
  
  Parameters:
  
  reactionNode - the attribute belongs to this node
  
  id - the value that will be set
- deleteReactionID
  
  public static void deleteReactionID(Node reactionNode)
- setReactionName
  
  public static void setReactionName(Node reactionNode, String name)
- deleteReactionName
  
  public static void deleteReactionName(Node reactionNode)
- setReactionLabel
  
  public static void setReactionLabel(Node reactionNode, String name, String id, PositionGridGenerator pgg)
  
  Sets the attribute name of a node
  
  Parameters:
  
  reactionNode - the attribute belongs to this node
  
  name - the value that will be set
- setReactionReversible
  
  public static void setReactionReversible(Node reactionNode, Boolean reversible)
  
  Sets the attribute reversible of a node
  
  Parameters:
  
  reactionNode - the attribute belongs to this node
  
  reversible - the value that will be set
- deleteReactionReversible
  
  public static void deleteReactionReversible(Node reactionNode)
- setReactionFast
  
  public static void setReactionFast(Node reactionNode, Boolean fast)
  
  Sets the attribute fast of a node
  
  Parameters:
  
  reactionNode - the attribute belongs to this node
  
  fast - the value that will be set
- deleteReactionFast
  
  public static void deleteReactionFast(Node reactionNode)
- setReactionCompartment
  
  public static void setReactionCompartment(Node reactionNode, String compartment)
  
  Sets the compartment of a node
  
  Parameters:
  
  reactionNode - the compartment belongs to this node
  
  compartment - the id of the compartment that will be set
- deleteReactionCompartment
  
  public static void deleteReactionCompartment(Node reactionNode)
- setReactionSpecies
  
  public static void setReactionSpecies(Edge reactionEdge, String species)
  
  Sets the species of a reaction
  
  Parameters:
  
  reactionEdge - the edge where the information will be read in
  
  species - the value that will be read in
- setReactionSpeciesID
  
  public static void setReactionSpeciesID(Edge reactionEdge, String ID)
  
  The id of the species of an reaction
  
  Parameters:
  
  reactionEdge - the edge where the information will be read in
  
  ID - the value that will be read in
- setReactionSpeciesName
  
  public static void setReactionSpeciesName(Edge reactionEdge, String name)
  
  The name of the species of a reaction
  
  Parameters:
  
  reactionEdge - the edge where the information will be read in
  
  name - the value that will be read in
- isReactionSpecies
  
  public static Boolean isReactionSpecies(Edge reactionEdge)
  
  Indicates if the species attribute is set
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  true if the value is set
- isReactionSpeciesID
  
  public static Boolean isReactionSpeciesID(Edge reactionEdge)
  
  Indicates if the species id attribute is set
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  true if the value is set
- isReactionSpeciesName
  
  public static Boolean isReactionSpeciesName(Edge reactionEdge)
  
  Indicates if the species name attribute is set
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  true if the value is set
- getReactionSpecies
  
  public static String getReactionSpecies(Edge reactionEdge)
  
  Returns the species
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  the value of the attribute species
- getReactionSpeciesName
  
  public static String getReactionSpeciesName(Edge reactionEdge)
  
  Returns the species name
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  the value of the attribute name
- getReactionSpeciesID
  
  public static String getReactionSpeciesID(Edge reactionEdge)
  
  Return the species id
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  the value of the attribute id
- isReactionStoichiometry
  
  public static Boolean isReactionStoichiometry(Edge reactionEdge)
  
  Indicates if there is set a value for stoichiometry
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  true if the attribute stoichiometry is set
- isReactionConstant
  
  public static Boolean isReactionConstant(Edge reactionEdge)
  
  Indicates if there is set a value for constant
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  true if the attribute constant is set
- getStoichiometry
  
  public static String getStoichiometry(Edge reactionEdge)
  
  Returns the value of the attribute stoichiometry
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  the value of stoichiometry if the value is set. Else null
- getReactionConstant
  
  public static Boolean getReactionConstant(Edge reactionEdge)
  
  Returns the value of the attribute constant
  
  Parameters:
  
  reactionEdge - the edge where the information will be read from
  
  Returns:
  
  the value of constant if the value is set. Else null
- setStoichiometry
  
  public static void setStoichiometry(Edge reactionEdge, Double stoichiometry)
  
  Sets a value for the attribute stoichiometry
  
  Parameters:
  
  reactionEdge - the edge where the information will be read in
  
  stoichiometry - the value that will be set
- deleteStoichiometry
  
  public static void deleteStoichiometry(Edge edge)
- deleteConstant
  
  public static void deleteConstant(Edge edge)
- deleteReactionSpecies
  
  public static void deleteReactionSpecies(Edge edge)
- deleteReactionSpeciesID
  
  public static void deleteReactionSpeciesID(Edge edge)
- deleteReactionSpeciesName
  
  public static void deleteReactionSpeciesName(Edge edge)
- isSetStoichiometry
  
  public static boolean isSetStoichiometry(Edge edge)
- isSetConstant
  
  public static boolean isSetConstant(Edge edge)
- isSetReactionSpecies
  
  public static boolean isSetReactionSpecies(Edge edge)
- isSetReactionSpeciesID
  
  public static boolean isSetReactionSpeciesID(Edge edge)
- isSetReactionSpeciesName
  
  public static boolean isSetReactionSpeciesName(Edge edge)
- setReactionConstant
  
  public static void setReactionConstant(Edge reactionEdge, Boolean constant)
  
  Sets a value for the attribute constant
  
  Parameters:
  
  reactionEdge - the edge where the information will be read in
  
  constant - the value that will be set
- isKineticLawFunction
  
  public static Boolean isKineticLawFunction(Node reactionNode)
  
  Indicates if the function of a kinetic law is set
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  Returns:
  
  true id the value is set. Else false
- getKineticLawFunction
  
  public static String getKineticLawFunction(Node reactionNode)
  
  Returns the function of a kinetic law
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  Returns:
  
  the function string if it is set. Else the empty string
- addKineticLaw
  
  public static void addKineticLaw(Node reactionNode, String function)
- addKineticLaw
  
  public static void addKineticLaw(Node reactionNode, org.sbml.jsbml.KineticLaw kineticLaw)
- deleteKineticLawFunction
  
  public static void deleteKineticLawFunction(Node node)
- isLocalParameterID
  
  public static Boolean isLocalParameterID(Node reactionNode, int localParameterCount)
  
  Indicates if the attribute id is set
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  true if the value is set
- isLocalParameterName
  
  public static Boolean isLocalParameterName(Node reactionNode, int localParameterCount)
  
  Indicates if the attribute name is set
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  true if the value is set
- isLocalParameterValue
  
  public static Boolean isLocalParameterValue(Node reactionNode, int localParameterCount)
  
  Indicates if the attribute value is set
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  true if the value is set
- isLocalParameterUnits
  
  public static Boolean isLocalParameterUnits(Node reactionNode, int localParameterCount)
  
  Indicates if the attribute units is set
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  true if the value is set
- getLocalParameterID
  
  public static String getLocalParameterID(Node reactionNode, int localParameterCount)
  
  Returns the value of the attribute id
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  the value if it is set. Else the empty string
- getLocalParameterName
  
  public static String getLocalParameterName(Node reactionNode, int localParameterCount)
  
  Returns the value of the attribute name
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  the value if it is set. Else the empty string
- getLocalParameterValue
  
  public static Double getLocalParameterValue(Node reactionNode, int localParameterCount)
  
  Returns the value of the attribute value
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  the value if it is set. Else the empty string
- getLocalParameterUnits
  
  public static String getLocalParameterUnits(Node reactionNode, int localParameterCount)
  
  Returns the value of the attribute units
  
  Parameters:
  
  reactionNode - the node where the information will be read from
  
  localParameterCount - the number of the current local parameter
  
  Returns:
  
  the value if it is set. Else the empty string
- getReactionNodes
  
  public static List<Node> getReactionNodes(Graph g)
  
  Returns all reaction nodes of the graph
  
  Returns:
  
  a list of all reaction nodes of the graph
- getReactionNode
  
  public static Node getReactionNode(Graph g, String id)
  
  Returns the reaction node with a distinct id
  
  Parameters:
  
  id - the id of the asked node
  
  Returns:
  
  the node with a certain id or null if no node has this id
- createReaction
  
  public static Node createReaction(Graph g, String id, String name)
- initReactionNode
  
  public static Node initReactionNode(Node n)
- addReactant
  
  public static Edge addReactant(Node node, String speciesID)
- initReactantEdge
  
  public static Edge initReactantEdge(Edge e)
- initProductEdge
  
  public static Edge initProductEdge(Edge e)
- addProduct
  
  public static Edge addProduct(Node node, String speciesID)
- addModifier
  
  public static Edge addModifier(Node node, String speciesID)
- addReactant
  
  public static Edge addReactant(Node node, org.sbml.jsbml.SpeciesReference ref)
- deleteReactant
  
  public static void deleteReactant(Edge edge)
- deleteProduct
  
  public static void deleteProduct(Edge edge)
- deleteModifier
  
  public static void deleteModifier(Edge edge)
- addModifier
  
  public static Edge addModifier(Node node, org.sbml.jsbml.ModifierSpeciesReference ref)
- addProduct
  
  public static Edge addProduct(Node node, org.sbml.jsbml.SpeciesReference ref)
- createReaction
  
  public static Node createReaction(Graph g, org.sbml.jsbml.Reaction reaction)
- addLocalParameterName
  
  public static void addLocalParameterName(Node node, String lpID, String name)
- isSetLocalParameterName
  
  public static boolean isSetLocalParameterName(Node node, String lpID)
- isSetLocalParameterUnits
  
  public static boolean isSetLocalParameterUnits(Node node, String lpID)
- isSetLocalParameterValue
  
  public static boolean isSetLocalParameterValue(Node node, String lpID)
- deleteLocalParameterName
  
  public static void deleteLocalParameterName(Node node, String lpID)
- deleteLocalParameterValue
  
  public static void deleteLocalParameterValue(Node node, String lpID)
- deleteLocalParameterUnits
  
  public static void deleteLocalParameterUnits(Node node, String lpID)
- deleteLocalParameter
  
  public static void deleteLocalParameter(Node node, String lpID)
- deleteLocalParameterID
  
  public static void deleteLocalParameterID(Node node, String lpID)
- addLocalParameterValue
  
  public static void addLocalParameterValue(Node node, String lpID, Double value)
- addLocalParameterUnits
  
  public static void addLocalParameterUnits(Node node, String lpID, String units)
- getProducts
  
  public static List<Edge> getProducts(Node node)
  
  The edges with the simple species references will be returned
  
  Parameters:
  
  node - the reaction node
  
  Returns:
  
  all outgoing edges
- getReactants
  
  public static List<Edge> getReactants(Node node)
  
  The edges with the simple species references will be returned
  
  Parameters:
  
  node - the reaction node
  
  Returns:
  
  all ingoing edges
- getModifier
  
  public static List<Edge> getModifier(Node node)
  
  Returns the modifier edges
  
  Parameters:
  
  node - the reaction node
  
  Returns:
  
  all modifier edges
- getReaction
  
  public static org.sbml.jsbml.Reaction getReaction(Node node)
  
  Returns a JSBML Reaction object belonging to a reaction node
  
  Parameters:
  
  node - the reaction node
  
  Returns:
  
  a JSBML Reaction object
- addLocalParameter
  
  public static void addLocalParameter(Node node, org.sbml.jsbml.LocalParameter lp)
- addLocalParameter
  
  public static void addLocalParameter(Node node, String id)
- localParameterCount
  
  public static int localParameterCount(Node node)
  
  Returns the number of local parameter
  
  Parameters:
  
  node - the current node
  
  Returns:
  
  the amount of local parameter
- createEvent
  
  public static org.sbml.jsbml.Event createEvent(Graph g, String id)
- createEvent
  
  public static void createEvent(Graph g, org.sbml.jsbml.Event event)
- addEventName
  
  public static void addEventName(Graph g, String id, String name)
- addEventUseValuesFromTriggerTime
  
  public static void addEventUseValuesFromTriggerTime(Graph g, String id, boolean useValuesFromTriggerTime)
- addTriggerInitialValue
  
  public static void addTriggerInitialValue(Graph g, String eventID, boolean initialValue)
- addTriggerPersistent
  
  public static void addTriggerPersistent(Graph g, String eventID, boolean persistent)
- addTriggerFunction
  
  public static void addTriggerFunction(Graph g, String eventID, String function)
- isSetEventName
  
  public static boolean isSetEventName(Graph g, String id)
- isSetEventUseValuesFromTriggerTime
  
  public static boolean isSetEventUseValuesFromTriggerTime(Graph g, String id)
- isSetTriggerInitialValue
  
  public static boolean isSetTriggerInitialValue(Graph g, String id)
- isSetTriggerPersistent
  
  public static boolean isSetTriggerPersistent(Graph g, String id)
- isSetTriggerFunction
  
  public static boolean isSetTriggerFunction(Graph g, String id)
- isSetDelayFunction
  
  public static boolean isSetDelayFunction(Graph g, String id)
- isSetPriority
  
  public static boolean isSetPriority(Graph g, String id)
- isSetDelay
  
  public static boolean isSetDelay(Graph g, String id)
- deleteEventName
  
  public static void deleteEventName(Graph g, String id)
- deleteEventUseValuesFromTriggerTime
  
  public static void deleteEventUseValuesFromTriggerTime(Graph g, String id)
- deleteEventID
  
  public static void deleteEventID(Graph g, String id)
- deleteTriggeInitialValue
  
  public static void deleteTriggeInitialValue(Graph g, String id)
- deleteTriggerPersistent
  
  public static void deleteTriggerPersistent(Graph g, String id)
- deleteTriggerFunction
  
  public static void deleteTriggerFunction(Graph g, String id)
- deleteDelayFunction
  
  public static void deleteDelayFunction(Graph g, String id)
- deletePriorityFunction
  
  public static void deletePriorityFunction(Graph g, String id)
- deleteTrigger
  
  public static void deleteTrigger(Graph g, String id)
- deletePriority
  
  public static void deletePriority(Graph g, String id)
- addTriggerToEvent
  
  public static void addTriggerToEvent(Graph g, String id, org.sbml.jsbml.Trigger trigger)
- addTriggerToEvent
  
  public static void addTriggerToEvent(Graph g, String id, boolean initialValue, boolean persistent, String formula)
- addPriorityToEvent
  
  public static void addPriorityToEvent(Graph g, String id, org.sbml.jsbml.Priority priority)
- addDelayToEvent
  
  public static void addDelayToEvent(Graph g, String id, org.sbml.jsbml.Delay delay)
- addPriorityToEvent
  
  public static void addPriorityToEvent(Graph g, String id, String function)
- addDelayToEvent
  
  public static void addDelayToEvent(Graph g, String id, String function)
- addEventAssignmentToEvent
  
  public static void addEventAssignmentToEvent(Graph g, String id, String variable, String function)
- addEventAssignmentToEvent
  
  public static void addEventAssignmentToEvent(Graph g, String id, org.sbml.jsbml.EventAssignment eventAssignment)
- deleteEventAssignment
  
  public static void deleteEventAssignment(Graph g, String id, String variable)
- deleteEvent
  
  public static void deleteEvent(Graph g, String id)
- getAllEvent
  
  public static List<org.sbml.jsbml.Event> getAllEvent(Graph g)
  
  Returns a list of event with distinct headlines
  
  Parameters:
  
  g - contains the information
  
  internHeadlines - a list which contains the number of the current event
  
  Returns:
  
  a filled list of event
- isSetLayoutID
  
  public static boolean isSetLayoutID(Graph g, Node node)

Class SBMLHelper

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

attWriter

_pgg

attReader

SBML_LAYOUT_EXTENSION_NAMESPACE

Constructor Details

SBMLHelper

Method Details

createFunctionDefinition

createFunctionDefinition

addFunctionDefinitionName

addFunctionDefinitionFunction

deleteFunctionDefinitionID

deleteFunctionDefinitionName

deleteFunctionDefinitionFunction

deleteFunctionDefinition

isSetFunctionDefinitionName

isSetFunctionDefinitionID

isSetFunctionDefinitionFunction

countFunctionDefinitions

getAllFunctionDefinitions

createUnitDefinition

createUnitDefinition

addUnitToUnitDefinition

addUnitToUnitDefinition

addUnitDefinitionName

addUnitDefinitionID

deleteUnitDefinitionID

deleteUnitDefinitionName

isSetUnitDefinitionName

isSetUnitDefinitionID

getAllUnitDefinitions

createCompartment

createCompartment

isSetCompartmentName

isSetCompartmentID

isSetCompartmentSpatialDimensions

isSetCompartmentSize

isSetCompartmentUnits

isSetCompartmentConstants

addCompartmentName

addCompartmentSpatialDimensions

addCompartmentSize

addCompartmentUnits

addCompartmentConstant

deleteCompartmentID

deleteCompartmentName

deleteCompartmentSpatialDimensions

deleteCompartmentSize

deleteCompartmentUnits

deleteCompartmentConstant

deleteCompartment

getAllCompartments

isSpeciesID

isSpeciesName

isSpeciesCompartment

isSpeciesInitialAmount

isSpeciesInitialConcentration

isSpeciesSubstanceUnits

isSpeciesHasOnlySubstanceUnits

isSpeciesBoundaryCondition

isSpeciesConstant

isSpeciesConversionFactor

getSpeciesID

getSpeciesName

getSpeciesCompartment

getSpeciesInitialAmount

getSpeciesInitialConcentration

getSpeciesSubstanceUnits

getSpeciesHasOnlySubstanceUnits

getSpeciesBoundaryCondition

getSpeciesConstant

getSpeciesConversionFactor

addSpeciesID

addSpeciesName