PluginModel

java.lang.Object
- jp.sbi.celldesigner.plugin.PluginSBase
- - jp.sbi.celldesigner.plugin.PluginModel

```
public class PluginModel
extends PluginSBase
```
This class wraps org.sbml.libsbml.Model for the plug-in.

Author:

The Systems Biology Institute

Field Summary

Fields
Modifier and Type Field and Description

protected org.sbml.libsbml.Model modelBase
- Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase
  sbase

Fields
Modifier and Type	Field and Description
`protected org.sbml.libsbml.Model`	`modelBase`

Constructor Summary

Constructors
Constructor and Description

PluginModel(org.sbml.libsbml.Model model)
Constructor

Constructors
Constructor and Description
`PluginModel(org.sbml.libsbml.Model model)` Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCompartment(PluginCompartment compartment)` Adds a PluginCompartment to the list.
`void`	`addCompartmentType(PluginCompartmentType compartmentType)`
`void`	`addConstraint(PluginConstraint constraint)`
`void`	`addEvent(PluginEvent event)` Adds the PluginEvent to the list.
`void`	`addFunctionDefinition(PluginFunctionDefinition function)` Adds a PluginFunctionDefinition to the list.
`void`	`addInitialAssignment(PluginInitialAssignment initialAssignment)`
`void`	`addParameter(PluginParameter parameter)` Adds the PluginParameter to the list.
`void`	`addReaction(PluginReaction reaction)` Adds a PluginReaction to the list.
`void`	`addRule(PluginRule rule)` Adds a PluginRule to the list.
`void`	`addSpecies(PluginSpecies species)` Adds a PluginSpecies to the list in this PluginModel.
`void`	`addSpeciesType(PluginSpeciesType speciesType)`
`void`	`addUnitDefinition(PluginUnitDefinition unit)` Adds a PluginUnitDefinition to the list.
`void`	`appendProtein(PluginProtein protein)` Adds the PluginProtein to the list.
`PluginAntiSenseRNA`	`getAntiSenseRNA(java.lang.String id)` Gets the PluginAntiSenseRNA with the given id.
`PluginCompartment`	`getCompartment(int index)` Gets the PluginCompartment with the given index.
`PluginCompartment`	`getCompartment(java.lang.String id)` Gets the PluginCompartment with the given id.
`PluginCompartmentType`	`getCompartmentType(int index)`
`PluginCompartmentType`	`getCompartmentType(java.lang.String id)`
`PluginConstraint`	`getConstraint(int index)`
`PluginConstraint`	`getConstraint(java.lang.String strMath)`
`PluginEvent`	`getEvent(int index)` Gets the PluginEvent with the given index.
`PluginEvent`	`getEvent(java.lang.String id)` Gets the PluginEvent with the given id.
`PluginFunctionDefinition`	`getFunctionDefinition(int index)` Gets the PluginFunctionDefinition with the given index.
`PluginFunctionDefinition`	`getFunctionDefinition(java.lang.String id)` Gets the PluginFunctionDefinition with the given id.
`PluginGene`	`getGene(java.lang.String id)` Gets the PluginGene with the given id.
`java.lang.String`	`getId()`
`PluginInitialAssignment`	`getInitialAssignment(int index)`
`PluginInitialAssignment`	`getInitialAssignment(java.lang.String symbol)`
`PluginListOf`	`getListOfAllSpeciesAlias()`
`PluginListOf`	`getListOfAllSpeciesAlias(java.lang.String speciesid)`
`PluginListOf`	`getListOfAntiSenseRNAs()`
`PluginListOf`	`getListOfCompartments()`
`PluginListOf`	`getListOfCompartmentTypes()`
`PluginListOf`	`getListOfConstraints()`
`PluginListOf`	`getListOfEvents()`
`PluginListOf`	`getListOfFunctionDefinitions()`
`PluginListOf`	`getListOfGenes()`
`PluginListOf`	`getListOfInitialAssignments()`
`PluginListOf`	`getListOfParameters()`
`PluginListOf`	`getListOfProteins()`
`PluginListOf`	`getListOfReactions()`
`PluginListOf`	`getListOfRNAs()`
`PluginListOf`	`getListOfRules()`
`PluginListOf`	`getListOfSpecies()`
`PluginListOf`	`getListOfSpecies(PluginAntiSenseRNA rna)`
`PluginListOf`	`getListOfSpecies(PluginGene rna)`
`PluginListOf`	`getListOfSpecies(PluginProtein rna)` Gets the list of PluginProtein added the given PluginProtein to.
`PluginListOf`	`getListOfSpecies(PluginRNA rna)`
`PluginListOf`	`getListOfSpeciesTypes()`
`PluginListOf`	`getListOfUnitDefinitions()`
`java.lang.String`	`getName()`
`int`	`getNumCompartments()`
`int`	`getNumCompartmentTypes()`
`int`	`getNumConstraints()`
`int`	`getNumEvents()`
`int`	`getNumFunctionDefinitions()`
`int`	`getNumInitialAssignments()`
`int`	`getNumParameters()`
`int`	`getNumReactions()`
`int`	`getNumRules()`
`int`	`getNumSpecies()`
`int`	`getNumSpeciesTypes()`
`int`	`getNumUnitDefinitions()`
`PluginParameter`	`getParameter(int index)` Gets the PluginParameter with the given index.
`PluginParameter`	`getParameter(java.lang.String id)` Gets the PluginParameter with the given id.
`PluginSpeciesAlias`	`getPluginSpeciesAlias(java.lang.String aliasID)` Gets PluginSpeciesAlias with the given id.
`PluginProtein`	`getProtein(java.lang.String id)` Gets the PluginProtein with the given id.
`java.lang.String`	`getPureSBMLString()`
`PluginReaction`	`getReaction(int index)` Gets the PluginReaction with the given index.
`PluginReaction`	`getReaction(java.lang.String id)` Gets the PluginReaction with the given id.
`PluginRNA`	`getRNA(java.lang.String id)` Gets the PluginRNA with the given id.
`PluginRule`	`getRule(int index)` Gets the PluginRule with the given index from the list.
`PluginSpecies`	`getSpecies(int index)` Gets the PluginSpecies with the given index.
`PluginSpecies`	`getSpecies(java.lang.String id)` Gets the PluginSpecies with the given id.
`PluginSpeciesType`	`getSpeciesType(int index)`
`PluginSpeciesType`	`getSpeciesType(java.lang.String id)`
`PluginUnitDefinition`	`getUnitDefinition(int index)` Gets the PluginUnitDefinition with the given index.
`PluginUnitDefinition`	`getUnitDefinition(java.lang.String id)` Gets the PluginUnitDefinition with the given id.
`boolean`	`isReferenceSameModel(PluginSBase any)`
`boolean`	`isSameModel(org.sbml.libsbml.Model any)`
`void`	`removeAntiSenseRNA(int index)` Removes the PluginAntiSenseRNA with the given index from the list.
`void`	`removeAntiSenseRNA(PluginAntiSenseRNA rna)` Removes the given PluginAntiSenseRNA from the list.
`void`	`removeCompartment(int index)` Removes the PluginCompartment with the given index from the list.
`void`	`removeCompartment(PluginCompartment compartment)` Removes the given PluginCompartment from the list.
`void`	`removeCompartment(java.lang.String id)` Removes the PluginCompartment with the given id from the list.
`void`	`removeCompartmentType(int index)`
`void`	`removeCompartmentType(PluginCompartmentType compartmentType)`
`void`	`removeCompartmentType(java.lang.String id)`
`void`	`removeConstraint(int index)`
`void`	`removeConstraint(PluginConstraint constraint)`
`void`	`removeConstraint(java.lang.String strMath)`
`void`	`removeEvent(int index)` Removes the PluginEvent with the given index.
`void`	`removeEvent(PluginEvent event)` Removes the given PluginEvent from the list.
`void`	`removeEvent(java.lang.String id)` Remove the PluginEvent with the given id.
`void`	`removeFunctionDefinition(int index)` Removes the PluginFunctionDefinition with the given index from the list.
`void`	`removeFunctionDefinition(PluginFunctionDefinition function)` Removes the given PluginFunctionDefinition from the list.
`void`	`removeFunctionDefinition(java.lang.String id)` Removes the PluginFunctionDefinition with the given id from the list.
`void`	`removeGene(int index)` Removes the PluginGene with the given index from the list.
`void`	`removeGene(PluginGene rna)` Removes the given PluginGene from the list.
`void`	`removeInitialAssignment(int index)`
`void`	`removeInitialAssignment(PluginInitialAssignment initialAssignment)`
`void`	`removeInitialAssignment(java.lang.String symbol)`
`void`	`removeParameter(int index)` Removes the PluginParameter with the given index to the list.
`void`	`removeParameter(PluginParameter parameter)` Remove the given PluginParameter from the list.
`void`	`removeParameter(java.lang.String id)` Remove the PluginParameter with the given id.
`void`	`removeProtein(int index)` Removes the PluginProtein with the given index.
`void`	`removeProtein(PluginProtein rna)` Removes the given PluginProtein from the list.
`void`	`removeReaction(int index)` Removes the PluginReaction with the given index from the list.
`void`	`removeReaction(PluginReaction reaction)` Removes the given PluginReaction from the list.
`void`	`removeReaction(java.lang.String id)` Removes the PluginReaction with the given id from the list.
`void`	`removeRNA(int index)` Removes the PluginRNA with the given index from the list.
`void`	`removeRNA(PluginRNA rna)` Adds a PluginRNA to the list
`void`	`removeRule(int index)` Removes the PluginRule with the given index from the list.
`void`	`removeRule(PluginRule rule)` Removes the given PluginRule from the list.
`void`	`removeSpecies(int index)` Removes the PluginSpecies with the given index from the list.
`void`	`removeSpecies(java.lang.String id)` Removes the PluginSpecies with the given id from the list
`void`	`removeSpeciesType(int index)`
`void`	`removeSpeciesType(PluginSpeciesType speciesType)`
`void`	`removeSpeciesType(java.lang.String id)`
`void`	`removeUnitDefinition(int index)` Remove the PluginUnitDefinition with the given index from the list.
`void`	`removeUnitDefinition(PluginUnitDefinition unit)` Remove the given PluginUnitDefinition from the list.
`void`	`removeUnitDefinition(java.lang.String id)` Removes the PluginUnitDefinition with the given id from the list.
`void`	`setListOfAntiSenseRNAs(PluginListOf listOfAntiSenseRNAs)` Sets the list of PluginAntiSenseRNA of this PluginModel.
`void`	`setListOfCompartments(PluginListOf listOfCompartments)` Sets the list of PluginCompartment of this PluginModel
`void`	`setListOfCompartmentTypes(PluginListOf listOfCompartmentTypes)`
`void`	`setListOfConstraints(PluginListOf listOfConstraints)`
`void`	`setListOfEvents(PluginListOf listOfEvents)` Sets the list of PluginEvent of this PluginModel.
`void`	`setListOfFunctionDefinitions(PluginListOf listOfFunctionDefinitions)` Sets the list of PluginFunctionDefinition of this PluginModel.
`void`	`setListOfGenes(PluginListOf listOfGenes)` Sets the list of PluginGene of this PluginModel.
`void`	`setListOfInitialAssignments(PluginListOf listOfInitialAssignments)`
`void`	`setListOfParameters(PluginListOf listOfParameters)` Sets the list of PluginParameter of this PluginModel.
`void`	`setListOfProteins(PluginListOf listOfProteins)` Sets the list of PluginProtein of this PluginModel.
`void`	`setListOfReactions(PluginListOf listOfReactions)` Sets the PluginReaction of this PluginModel.
`void`	`setListOfRNAs(PluginListOf listOfRNAs)` Sets the list of PluginRNA of this PluginModel.
`void`	`setListOfRules(PluginListOf listOfRules)` Sets the list of PluginRule of this PluginModel.
`void`	`setListOfSpecies(PluginListOf listOfSpecies)` Sets the list of PluginSpecies of this PluginModel.
`void`	`setListOfSpeciesTypes(PluginListOf listOfSpeciesTypes)`
`void`	`setListOfUnitDefinitions(PluginListOf listOfUnitDefinitions)` Sets the list of PluginUnitDefinition of this PluginModel
`void`	`setName(java.lang.String name)` Sets the name of this PluginModel.
`void`	`toSBMLString()`
`void`	`update(PluginModel model)` Update all properties of this PluginModel to the same as the given PluginModel

Methods inherited from class jp.sbi.celldesigner.plugin.PluginSBase
addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, getNotes, getNotesString, getNumCVTerms, getParentSBase, getRelationFromCVTerm, setAnnotation, setAnnotationString, setCVTerm, setNotes, setNotes, setParentSBase, toSBML

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - modelBase
```
protected org.sbml.libsbml.Model modelBase
```
- Constructor Detail
  - PluginModel
```
public PluginModel(org.sbml.libsbml.Model model)
```
    Constructor
    
    Parameters:
    
    model - Model
- Method Detail
  - update
```
public void update(PluginModel model)
```
    Update all properties of this PluginModel to the same as the given PluginModel
    
    Parameters:
    
    model - PluginModel
  - toSBMLString
```
public void toSBMLString()
```
  - getId
```
public java.lang.String getId()
```
    Returns:
    
    the id of this PluginModel.
  - getPureSBMLString
```
public java.lang.String getPureSBMLString()
```
    Returns:
    
    SBML Document in string.
  - getName
```
public java.lang.String getName()
```
    Returns:
    
    the name of this PluginModel.
  - setName
```
public void setName(java.lang.String name)
```
    Sets the name of this PluginModel.
    
    Parameters:
    
    name - String
  - getListOfCompartments
```
public PluginListOf getListOfCompartments()
```
    Returns:
    
    the list of PluginCompartment of this PluginModel
  - setListOfCompartments
```
public void setListOfCompartments(PluginListOf listOfCompartments)
```
    Sets the list of PluginCompartment of this PluginModel
    
    Parameters:
    
    listOfCompartments - the list of PluginCompartment
  - getListOfEvents
```
public PluginListOf getListOfEvents()
```
    Returns:
    
    the list of PluginEvent
  - setListOfEvents
```
public void setListOfEvents(PluginListOf listOfEvents)
```
    Sets the list of PluginEvent of this PluginModel.
    
    Parameters:
    
    listOfEvents - the list of PluginEvent
  - getListOfFunctionDefinitions
```
public PluginListOf getListOfFunctionDefinitions()
```
    Returns:
    
    the list of PluginFunctionDefinition
  - setListOfFunctionDefinitions
```
public void setListOfFunctionDefinitions(PluginListOf listOfFunctionDefinitions)
```
    Sets the list of PluginFunctionDefinition of this PluginModel.
    
    Parameters:
    
    listOfFunctionDefinitions - the list of PluginFunctionDefinition
  - getListOfParameters
```
public PluginListOf getListOfParameters()
```
    Returns:
    
    the list of PluginParameter of this PluginModel.
  - setListOfParameters
```
public void setListOfParameters(PluginListOf listOfParameters)
```
    Sets the list of PluginParameter of this PluginModel.
    
    Parameters:
    
    listOfParameters - the list of PluginParameter
  - getListOfReactions
```
public PluginListOf getListOfReactions()
```
    Returns:
    
    the list of PluginReaction
  - setListOfReactions
```
public void setListOfReactions(PluginListOf listOfReactions)
```
    Sets the PluginReaction of this PluginModel.
    
    Parameters:
    
    listOfReactions - the list of PluginReaction.
  - getListOfRules
```
public PluginListOf getListOfRules()
```
    Returns:
    
    the list of PluginRule of this PluginModel.
  - setListOfRules
```
public void setListOfRules(PluginListOf listOfRules)
```
    Sets the list of PluginRule of this PluginModel.
    
    Parameters:
    
    listOfRules - the list of PluginRule
  - getListOfSpecies
```
public PluginListOf getListOfSpecies()
```
    Returns:
    
    the list of PluginSpecies
  - setListOfSpecies
```
public void setListOfSpecies(PluginListOf listOfSpecies)
```
    Sets the list of PluginSpecies of this PluginModel.
    
    Parameters:
    
    listOfSpecies - the listOfPluginSpecies
  - getListOfUnitDefinitions
```
public PluginListOf getListOfUnitDefinitions()
```
    Returns:
    
    the list of PluginUnitDefinition of this PluginModel.
  - setListOfUnitDefinitions
```
public void setListOfUnitDefinitions(PluginListOf listOfUnitDefinitions)
```
    Sets the list of PluginUnitDefinition of this PluginModel
    
    Parameters:
    
    listOfUnitDefinitions - the list of PluginUnitDefinition
  - getListOfSpeciesTypes
```
public PluginListOf getListOfSpeciesTypes()
```
  - setListOfSpeciesTypes
```
public void setListOfSpeciesTypes(PluginListOf listOfSpeciesTypes)
```
  - getListOfCompartmentTypes
```
public PluginListOf getListOfCompartmentTypes()
```
  - setListOfCompartmentTypes
```
public void setListOfCompartmentTypes(PluginListOf listOfCompartmentTypes)
```
  - getListOfInitialAssignments
```
public PluginListOf getListOfInitialAssignments()
```
  - setListOfInitialAssignments
```
public void setListOfInitialAssignments(PluginListOf listOfInitialAssignments)
```
  - getListOfConstraints
```
public PluginListOf getListOfConstraints()
```
  - setListOfConstraints
```
public void setListOfConstraints(PluginListOf listOfConstraints)
```
  - addSpecies
```
public void addSpecies(PluginSpecies species)
```
    Adds a PluginSpecies to the list in this PluginModel.
    
    Parameters:
    
    species - PluginSpecies
  - removeSpecies
```
public void removeSpecies(java.lang.String id)
```
    Removes the PluginSpecies with the given id from the list
    
    Parameters:
    
    id - String
  - removeSpecies
```
public void removeSpecies(int index)
```
    Removes the PluginSpecies with the given index from the list.
    
    Parameters:
    
    index - int
  - getSpecies
```
public PluginSpecies getSpecies(int index)
```
    Gets the PluginSpecies with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginSpecies
  - getSpecies
```
public PluginSpecies getSpecies(java.lang.String id)
```
    Gets the PluginSpecies with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginSpecies
  - addCompartment
```
public void addCompartment(PluginCompartment compartment)
```
    Adds a PluginCompartment to the list.
    
    Parameters:
    
    compartment - PluginCompartment
  - removeCompartment
```
public void removeCompartment(PluginCompartment compartment)
```
    Removes the given PluginCompartment from the list.
    
    Parameters:
    
    compartment - PluginCompartment
  - removeCompartment
```
public void removeCompartment(java.lang.String id)
```
    Removes the PluginCompartment with the given id from the list.
    
    Parameters:
    
    id - String
  - removeCompartment
```
public void removeCompartment(int index)
```
    Removes the PluginCompartment with the given index from the list.
    
    Parameters:
    
    index - int
  - getCompartment
```
public PluginCompartment getCompartment(int index)
```
    Gets the PluginCompartment with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginCompartment
  - getCompartment
```
public PluginCompartment getCompartment(java.lang.String id)
```
    Gets the PluginCompartment with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginCompartment
  - addReaction
```
public void addReaction(PluginReaction reaction)
```
    Adds a PluginReaction to the list.
    
    Parameters:
    
    reaction - PluginReaction
  - removeReaction
```
public void removeReaction(PluginReaction reaction)
```
    Removes the given PluginReaction from the list.
    
    Parameters:
    
    reaction - PluginReaction
  - removeReaction
```
public void removeReaction(java.lang.String id)
```
    Removes the PluginReaction with the given id from the list.
    
    Parameters:
    
    id - String
  - removeReaction
```
public void removeReaction(int index)
```
    Removes the PluginReaction with the given index from the list.
    
    Parameters:
    
    index - int
  - getReaction
```
public PluginReaction getReaction(int index)
```
    Gets the PluginReaction with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginReaction
  - getReaction
```
public PluginReaction getReaction(java.lang.String id)
```
    Gets the PluginReaction with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginReaction
  - addEvent
```
public void addEvent(PluginEvent event)
```
    Adds the PluginEvent to the list.
    
    Parameters:
    
    event - PluginEvent
  - removeEvent
```
public void removeEvent(PluginEvent event)
```
    Removes the given PluginEvent from the list.
    
    Parameters:
    
    event - PluginEvent
  - removeEvent
```
public void removeEvent(java.lang.String id)
```
    Remove the PluginEvent with the given id.
    
    Parameters:
    
    id - String
  - removeEvent
```
public void removeEvent(int index)
```
    Removes the PluginEvent with the given index.
    
    Parameters:
    
    index - int
  - getEvent
```
public PluginEvent getEvent(int index)
```
    Gets the PluginEvent with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginEvent
  - getEvent
```
public PluginEvent getEvent(java.lang.String id)
```
    Gets the PluginEvent with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginEvent
  - addParameter
```
public void addParameter(PluginParameter parameter)
```
    Adds the PluginParameter to the list.
    
    Parameters:
    
    parameter - PluginParameter
  - removeParameter
```
public void removeParameter(PluginParameter parameter)
```
    Remove the given PluginParameter from the list.
    
    Parameters:
    
    parameter - PluginParameter
  - removeParameter
```
public void removeParameter(java.lang.String id)
```
    Remove the PluginParameter with the given id.
    
    Parameters:
    
    id - String
  - removeParameter
```
public void removeParameter(int index)
```
    Removes the PluginParameter with the given index to the list.
    
    Parameters:
    
    index - int
  - getParameter
```
public PluginParameter getParameter(int index)
```
    Gets the PluginParameter with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginParameter
  - getParameter
```
public PluginParameter getParameter(java.lang.String id)
```
    Gets the PluginParameter with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginParameter
  - addFunctionDefinition
```
public void addFunctionDefinition(PluginFunctionDefinition function)
```
    Adds a PluginFunctionDefinition to the list.
    
    Parameters:
    
    function - PluginFunctionDefinition.
  - removeFunctionDefinition
```
public void removeFunctionDefinition(PluginFunctionDefinition function)
```
    Removes the given PluginFunctionDefinition from the list.
    
    Parameters:
    
    function - PluginFunctionDefinition
  - removeFunctionDefinition
```
public void removeFunctionDefinition(java.lang.String id)
```
    Removes the PluginFunctionDefinition with the given id from the list.
    
    Parameters:
    
    id - String
  - removeFunctionDefinition
```
public void removeFunctionDefinition(int index)
```
    Removes the PluginFunctionDefinition with the given index from the list.
    
    Parameters:
    
    index - PluginFunctionDefinition
  - getFunctionDefinition
```
public PluginFunctionDefinition getFunctionDefinition(int index)
```
    Gets the PluginFunctionDefinition with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginFunctionDefinition
  - getFunctionDefinition
```
public PluginFunctionDefinition getFunctionDefinition(java.lang.String id)
```
    Gets the PluginFunctionDefinition with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginFunctionDefinition
  - addRule
```
public void addRule(PluginRule rule)
```
    Adds a PluginRule to the list.
    
    Parameters:
    
    rule - PluginRule
  - removeRule
```
public void removeRule(PluginRule rule)
```
    Removes the given PluginRule from the list.
    
    Parameters:
    
    rule - PluginRule
  - removeRule
```
public void removeRule(int index)
```
    Removes the PluginRule with the given index from the list.
    
    Parameters:
    
    index - int
  - getRule
```
public PluginRule getRule(int index)
```
    Gets the PluginRule with the given index from the list.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginRule
  - addUnitDefinition
```
public void addUnitDefinition(PluginUnitDefinition unit)
```
    Adds a PluginUnitDefinition to the list.
    
    Parameters:
    
    unit - PluginUnitDefinition
  - removeUnitDefinition
```
public void removeUnitDefinition(PluginUnitDefinition unit)
```
    Remove the given PluginUnitDefinition from the list.
    
    Parameters:
    
    unit - PluginUnitDefinition
  - removeUnitDefinition
```
public void removeUnitDefinition(java.lang.String id)
```
    Removes the PluginUnitDefinition with the given id from the list.
    
    Parameters:
    
    id - String
  - removeUnitDefinition
```
public void removeUnitDefinition(int index)
```
    Remove the PluginUnitDefinition with the given index from the list.
    
    Parameters:
    
    index - int
  - getUnitDefinition
```
public PluginUnitDefinition getUnitDefinition(int index)
```
    Gets the PluginUnitDefinition with the given index.
    
    Parameters:
    
    index - int
    
    Returns:
    
    PluginUnitDefinition
  - getUnitDefinition
```
public PluginUnitDefinition getUnitDefinition(java.lang.String id)
```
    Gets the PluginUnitDefinition with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginUnitDefinition
  - addSpeciesType
```
public void addSpeciesType(PluginSpeciesType speciesType)
```
  - removeSpeciesType
```
public void removeSpeciesType(PluginSpeciesType speciesType)
```
  - removeSpeciesType
```
public void removeSpeciesType(java.lang.String id)
```
  - removeSpeciesType
```
public void removeSpeciesType(int index)
```
  - getSpeciesType
```
public PluginSpeciesType getSpeciesType(int index)
```
  - getSpeciesType
```
public PluginSpeciesType getSpeciesType(java.lang.String id)
```
  - addCompartmentType
```
public void addCompartmentType(PluginCompartmentType compartmentType)
```
  - removeCompartmentType
```
public void removeCompartmentType(PluginCompartmentType compartmentType)
```
  - removeCompartmentType
```
public void removeCompartmentType(java.lang.String id)
```
  - removeCompartmentType
```
public void removeCompartmentType(int index)
```
  - getCompartmentType
```
public PluginCompartmentType getCompartmentType(int index)
```
  - getCompartmentType
```
public PluginCompartmentType getCompartmentType(java.lang.String id)
```
  - addInitialAssignment
```
public void addInitialAssignment(PluginInitialAssignment initialAssignment)
```
  - removeInitialAssignment
```
public void removeInitialAssignment(PluginInitialAssignment initialAssignment)
```
  - removeInitialAssignment
```
public void removeInitialAssignment(java.lang.String symbol)
```
  - removeInitialAssignment
```
public void removeInitialAssignment(int index)
```
  - getInitialAssignment
```
public PluginInitialAssignment getInitialAssignment(int index)
```
  - getInitialAssignment
```
public PluginInitialAssignment getInitialAssignment(java.lang.String symbol)
```
  - addConstraint
```
public void addConstraint(PluginConstraint constraint)
```
  - removeConstraint
```
public void removeConstraint(PluginConstraint constraint)
```
  - removeConstraint
```
public void removeConstraint(java.lang.String strMath)
```
  - removeConstraint
```
public void removeConstraint(int index)
```
  - getConstraint
```
public PluginConstraint getConstraint(int index)
```
  - getConstraint
```
public PluginConstraint getConstraint(java.lang.String strMath)
```
  - getNumSpecies
```
public int getNumSpecies()
```
    Returns:
    
    the number of PluginSpecies of this PluginModel.
  - getNumReactions
```
public int getNumReactions()
```
    Returns:
    
    the number of PluginReaction of this PluginModel.
  - getNumCompartments
```
public int getNumCompartments()
```
    Returns:
    
    the number of PluginCompartment of this PluginModel.
  - getNumEvents
```
public int getNumEvents()
```
    Returns:
    
    the number of PluginEvent of this PluginModel.
  - getNumParameters
```
public int getNumParameters()
```
    Returns:
    
    the number of PluginParameter of this PluginModel.
  - getNumFunctionDefinitions
```
public int getNumFunctionDefinitions()
```
    Returns:
    
    the number of PluginFunctionDefinition of this PluginModel
  - getNumRules
```
public int getNumRules()
```
    Returns:
    
    the number of PluginRule of this PluginModel.
  - getNumUnitDefinitions
```
public int getNumUnitDefinitions()
```
    Returns:
    
    the number of PluginUnitDefinition of this PluginModel.
  - getNumSpeciesTypes
```
public int getNumSpeciesTypes()
```
  - getNumCompartmentTypes
```
public int getNumCompartmentTypes()
```
  - getNumInitialAssignments
```
public int getNumInitialAssignments()
```
  - getNumConstraints
```
public int getNumConstraints()
```
  - getAntiSenseRNA
```
public PluginAntiSenseRNA getAntiSenseRNA(java.lang.String id)
```
    Gets the PluginAntiSenseRNA with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginAntiSenseRNA
  - getListOfAntiSenseRNAs
```
public PluginListOf getListOfAntiSenseRNAs()
```
    Returns:
    
    the list of PluginAntiSenseRNA
  - getListOfSpecies
```
public PluginListOf getListOfSpecies(PluginAntiSenseRNA rna)
```
    Parameters:
    
    rna - PluginAntiSenseRNA
    
    Returns:
    
    the list of PluginAntiSenseRNA
  - setListOfAntiSenseRNAs
```
public void setListOfAntiSenseRNAs(PluginListOf listOfAntiSenseRNAs)
```
    Sets the list of PluginAntiSenseRNA of this PluginModel.
    
    Parameters:
    
    listOfAntiSenseRNAs - the list of PluginAntiSenseRNA
  - removeAntiSenseRNA
```
public void removeAntiSenseRNA(PluginAntiSenseRNA rna)
```
    Removes the given PluginAntiSenseRNA from the list.
    
    Parameters:
    
    rna - PluginAntiSenseRNA
  - removeAntiSenseRNA
```
public void removeAntiSenseRNA(int index)
```
    Removes the PluginAntiSenseRNA with the given index from the list.
    
    Parameters:
    
    index - int
  - getGene
```
public PluginGene getGene(java.lang.String id)
```
    Gets the PluginGene with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginGene if found, otherwise null
  - getListOfGenes
```
public PluginListOf getListOfGenes()
```
    Returns:
    
    the list of PluginGene.
  - getListOfSpecies
```
public PluginListOf getListOfSpecies(PluginGene rna)
```
    Parameters:
    
    rna - PluginGene
    
    Returns:
    
    the list of PluginGene
  - setListOfGenes
```
public void setListOfGenes(PluginListOf listOfGenes)
```
    Sets the list of PluginGene of this PluginModel.
    
    Parameters:
    
    listOfGenes - a list of PluginGene
  - removeGene
```
public void removeGene(PluginGene rna)
```
    Removes the given PluginGene from the list.
    
    Parameters:
    
    rna - PluginGene
  - removeGene
```
public void removeGene(int index)
```
    Removes the PluginGene with the given index from the list.
    
    Parameters:
    
    index - int
  - appendProtein
```
public void appendProtein(PluginProtein protein)
```
    Adds the PluginProtein to the list.
    
    Parameters:
    
    protein - PluginProtein
  - getProtein
```
public PluginProtein getProtein(java.lang.String id)
```
    Gets the PluginProtein with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginProtein
  - getListOfProteins
```
public PluginListOf getListOfProteins()
```
    Returns:
    
    the list of PluginProtein
  - getListOfSpecies
```
public PluginListOf getListOfSpecies(PluginProtein rna)
```
    Gets the list of PluginProtein added the given PluginProtein to.
    
    Parameters:
    
    rna - PluginProtein
    
    Returns:
    
    the list of PluginProtein
  - setListOfProteins
```
public void setListOfProteins(PluginListOf listOfProteins)
```
    Sets the list of PluginProtein of this PluginModel.
    
    Parameters:
    
    listOfProteins - the list of PluginProtein
  - removeProtein
```
public void removeProtein(PluginProtein rna)
```
    Removes the given PluginProtein from the list.
    
    Parameters:
    
    rna - PluginProtein
  - removeProtein
```
public void removeProtein(int index)
```
    Removes the PluginProtein with the given index.
    
    Parameters:
    
    index - int
  - getRNA
```
public PluginRNA getRNA(java.lang.String id)
```
    Gets the PluginRNA with the given id.
    
    Parameters:
    
    id - String
    
    Returns:
    
    PluginRNA
  - getListOfRNAs
```
public PluginListOf getListOfRNAs()
```
    Returns:
    
    the list of PluginRNA
  - getListOfSpecies
```
public PluginListOf getListOfSpecies(PluginRNA rna)
```
    Parameters:
    
    rna - PluginRNA
    
    Returns:
    
    the list of PluginRNA
  - setListOfRNAs
```
public void setListOfRNAs(PluginListOf listOfRNAs)
```
    Sets the list of PluginRNA of this PluginModel.
    
    Parameters:
    
    listOfRNAs - PluginListOf
  - removeRNA
```
public void removeRNA(PluginRNA rna)
```
    Adds a PluginRNA to the list
    
    Parameters:
    
    rna - PluginRNA
  - removeRNA
```
public void removeRNA(int index)
```
    Removes the PluginRNA with the given index from the list.
    
    Parameters:
    
    index - int
  - getListOfAllSpeciesAlias
```
public PluginListOf getListOfAllSpeciesAlias()
```
    Returns:
    
    the list of PluginSpeciesAlias.
  - getPluginSpeciesAlias
```
public PluginSpeciesAlias getPluginSpeciesAlias(java.lang.String aliasID)
```
    Gets PluginSpeciesAlias with the given id.
    
    Parameters:
    
    aliasID - String
    
    Returns:
    
    PluginSpeciesAlias
  - getListOfAllSpeciesAlias
```
public PluginListOf getListOfAllSpeciesAlias(java.lang.String speciesid)
```
  - isReferenceSameModel
```
public boolean isReferenceSameModel(PluginSBase any)
```
  - isSameModel
```
public boolean isSameModel(org.sbml.libsbml.Model any)
```

Class PluginModel

Field Summary

Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase

Constructor Summary

Method Summary

Methods inherited from class jp.sbi.celldesigner.plugin.PluginSBase

Methods inherited from class java.lang.Object

Field Detail

modelBase

Constructor Detail

PluginModel

Method Detail

update

toSBMLString

getId

getPureSBMLString

getName

setName

getListOfCompartments

setListOfCompartments

getListOfEvents

setListOfEvents

getListOfFunctionDefinitions

setListOfFunctionDefinitions

getListOfParameters

setListOfParameters

getListOfReactions

setListOfReactions

getListOfRules

setListOfRules

getListOfSpecies

setListOfSpecies

getListOfUnitDefinitions

setListOfUnitDefinitions

getListOfSpeciesTypes

setListOfSpeciesTypes

getListOfCompartmentTypes

setListOfCompartmentTypes

getListOfInitialAssignments

setListOfInitialAssignments

getListOfConstraints

setListOfConstraints

addSpecies

removeSpecies

removeSpecies

getSpecies

getSpecies

addCompartment

removeCompartment

removeCompartment

removeCompartment

getCompartment

getCompartment

addReaction

removeReaction

removeReaction

removeReaction

getReaction

getReaction

addEvent

removeEvent

removeEvent

removeEvent

getEvent

getEvent

addParameter

removeParameter

removeParameter

removeParameter

getParameter

getParameter

addFunctionDefinition

removeFunctionDefinition

removeFunctionDefinition

removeFunctionDefinition

getFunctionDefinition

getFunctionDefinition

addRule

removeRule

removeRule