MultiSpeciesType (jsbml-multi 1.3 API)

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase
  - - org.sbml.jsbml.AbstractNamedSBase
    - - org.sbml.jsbml.SpeciesType
      - org.sbml.jsbml.ext.multi.MultiSpeciesType

All Implemented Interfaces:: Serializable, Cloneable, TreeNode, CompartmentalizedSBase, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

Direct Known Subclasses:: BindingSiteSpeciesType

public class MultiSpeciesType
extends SpeciesType
implements CompartmentalizedSBase, UniqueNamedSBase

The element MultiSpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 Core any more. Instead, it will be defined in the multi package. The MultiSpeciesType element carries not only the basic attributes which it had in SBML Level 2 Version 4 (metaid, id, name), but is also extended for the needs of describing multi-component entities with the attribute bindingSite and for the needs of multistate entities by linking it to a list of StateFeatures

A species type can be used to describe a component of a supra-macromolecular assembly, but also a domain of a macromolecule. Such a domain can be a portion of the macromolecule, a non-connex set of atoms forming a functional domain, or just a conceptual construct suiting the needs of the modeler. The type of component can be specified by referring terms from the subbranch functional entity of the Systems Biology Ontology through the optional sboTerm attribute. The following table provides typical examples of component or domains (the list is absolutely not complete).

Typical examples of components or domains
SBO identifier	Definition
SBO:0000242	channel
SBO:0000244	receptor
SBO:0000284	transporter
SBO:0000280	ligand
SBO:0000493	functional domain
SBO:0000494	binding site
SBO:0000495	catalytic site
SBO:0000496	transmembrane domain

Author:: Nicolas Rodriguez
See Also:: Serialized Form

Field Summary
- Fields inherited from class org.sbml.jsbml.AbstractSBase
  ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName
- Fields inherited from class org.sbml.jsbml.AbstractTreeNode
  listOfListeners, parent, resourceBundle

Constructor Summary

Constructors
Constructor and Description
`MultiSpeciesType()` Creates an MultiSpeciesType instance
`MultiSpeciesType(int level, int version)` Creates a MultiSpeciesType instance with a level and version.
`MultiSpeciesType(MultiSpeciesType obj)` Creates a new `MultiSpeciesType` instance cloned from the given `MultiSpeciesType`.
`MultiSpeciesType(String id)` Creates a MultiSpeciesType instance with an id.
`MultiSpeciesType(String id, int level, int version)` Creates a MultiSpeciesType instance with an id, level, and version.
`MultiSpeciesType(String id, String name, int level, int version)` Creates a MultiSpeciesType instance with an id, name, level, and version.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond)` Adds a new `InSpeciesTypeBond` to the `listOfInSpeciesTypeBonds`.
`boolean`	`addSpeciesFeatureType(SpeciesFeatureType speciesFeatureType)` Adds a new `SpeciesFeatureType` to the `listOfSpeciesFeatureTypes`.
`boolean`	`addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex)` Adds a new `SpeciesTypeComponentIndex` to the `listOfSpeciesTypeComponentIndexes`.
`boolean`	`addSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)` Adds a new `SpeciesTypeInstance` to the `listOfSpeciesTypeInstances`.
`MultiSpeciesType`	`clone()` clones this class
`InSpeciesTypeBond`	`createInSpeciesTypeBond()` Creates a new InSpeciesTypeBond element and adds it to the `listOfInSpeciesTypeBonds` list.
`InSpeciesTypeBond`	`createInSpeciesTypeBond(String id)` Creates a new `InSpeciesTypeBond` element and adds it to the `listOfInSpeciesTypeBonds` list.
`SpeciesFeatureType`	`createSpeciesFeatureType()` Creates a new SpeciesFeatureType element and adds it to the `listOfSpeciesFeatureTypes` list.
`SpeciesFeatureType`	`createSpeciesFeatureType(String id)` Creates a new `SpeciesFeatureType` element and adds it to the `listOfSpeciesFeatureTypes` list.
`SpeciesTypeComponentIndex`	`createSpeciesTypeComponentIndex()` Creates a new SpeciesTypeComponentIndex element and adds it to the `listOfSpeciesTypeComponentIndexes` list.
`SpeciesTypeComponentIndex`	`createSpeciesTypeComponentIndex(String id)` Creates a new `SpeciesTypeComponentIndex` element and adds it to the `listOfSpeciesTypeComponentIndexes` list.
`SpeciesTypeInstance`	`createSpeciesTypeInstance()` Creates a new SpeciesTypeInstance element and adds it to the `listOfSpeciesTypeInstances` list.
`SpeciesTypeInstance`	`createSpeciesTypeInstance(String id)` Creates a new `SpeciesTypeInstance` element and adds it to the `listOfSpeciesTypeInstances` list.
`boolean`	`equals(Object obj)`
`TreeNode`	`getChildAt(int index)`
`int`	`getChildCount()`
`String`	`getCompartment()`
`Compartment`	`getCompartmentInstance()`
`String`	`getElementName()`
`InSpeciesTypeBond`	`getInSpeciesTypeBond(int i)` Gets an element from the `listOfInSpeciesTypeBonds` at the given index.
`InSpeciesTypeBond`	`getInSpeciesTypeBond(String inSpeciesTypeBondId)` Gets an element from the listOfInSpeciesTypeBonds, with the given id.
`int`	`getInSpeciesTypeBondCount()` Returns the number of `InSpeciesTypeBond`s in this `MultiSpeciesType`.
`ListOf<InSpeciesTypeBond>`	`getListOfInSpeciesTypeBonds()` Returns the `listOfInSpeciesTypeBonds`.
`ListOf<SpeciesFeatureType>`	`getListOfSpeciesFeatureTypes()` Returns the `listOfSpeciesFeatureTypes`.
`ListOf<SpeciesTypeComponentIndex>`	`getListOfSpeciesTypeComponentIndexes()` Returns the `listOfSpeciesTypeComponentIndexes`.
`ListOf<SpeciesTypeInstance>`	`getListOfSpeciesTypeInstances()` Returns the `listOfSpeciesTypeInstances`.
`int`	`getNumInSpeciesTypeBonds()` Returns the number of `InSpeciesTypeBond`s in this `MultiSpeciesType`.
`int`	`getNumSpeciesFeatureTypes()` Returns the number of `SpeciesFeatureType`s in this `MultiSpeciesType`.
`int`	`getNumSpeciesTypeComponentIndexes()` Returns the number of `SpeciesTypeComponentIndex`s in this `MultiSpeciesType`.
`int`	`getNumSpeciesTypeInstances()` Returns the number of `SpeciesTypeInstance`s in this `MultiSpeciesType`.
`SpeciesFeatureType`	`getSpeciesFeatureType(int i)` Gets an element from the `listOfSpeciesFeatureTypes` at the given index.
`SpeciesFeatureType`	`getSpeciesFeatureType(String speciesFeatureTypeId)` Gets an element from the listOfSpeciesFeatureTypes, with the given id.
`int`	`getSpeciesFeatureTypeCount()` Returns the number of `SpeciesFeatureType`s in this `MultiSpeciesType`.
`SpeciesTypeComponentIndex`	`getSpeciesTypeComponentIndex(int i)` Gets an element from the `listOfSpeciesTypeComponentIndexes` at the given index.
`SpeciesTypeComponentIndex`	`getSpeciesTypeComponentIndex(String speciesTypeComponentIndexId)` Gets an element from the listOfSpeciesTypeComponentIndexes, with the given id.
`int`	`getSpeciesTypeComponentIndexCount()` Returns the number of `SpeciesTypeComponentIndex`s in this `MultiSpeciesType`.
`SpeciesTypeInstance`	`getSpeciesTypeInstance(int i)` Gets an element from the `listOfSpeciesTypeInstances` at the given index.
`SpeciesTypeInstance`	`getSpeciesTypeInstance(String speciesTypeInstanceId)` Gets an element from the listOfSpeciesTypeInstances, with the given id.
`int`	`getSpeciesTypeInstanceCount()` Returns the number of `SpeciesTypeInstance`s in this `MultiSpeciesType`.
`int`	`hashCode()`
`void`	`initDefaults()` Initializes the default values.
`boolean`	`isCompartmentMandatory()`
`boolean`	`isIdMandatory()`
`boolean`	`isSetCompartment()`
`boolean`	`isSetCompartmentInstance()`
`boolean`	`isSetListOfInSpeciesTypeBonds()` Returns `true` if `listOfInSpeciesTypeBonds` contains at least one element.
`boolean`	`isSetListOfSpeciesFeatureTypes()` Returns `true` if `listOfSpeciesFeatureTypes` contains at least one element.
`boolean`	`isSetListOfSpeciesTypeComponentIndexes()` Returns `true` if `listOfSpeciesTypeComponentIndexes` contains at least one element.
`boolean`	`isSetListOfSpeciesTypeInstances()` Returns `true` if `listOfSpeciesTypeInstances` contains at least one element.
`boolean`	`readAttribute(String attributeName, String prefix, String value)`
`boolean`	`removeInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond)` Removes an element from the `listOfInSpeciesTypeBonds`.
`InSpeciesTypeBond`	`removeInSpeciesTypeBond(int i)` Removes an element from the `listOfInSpeciesTypeBonds` at the given index.
`InSpeciesTypeBond`	`removeInSpeciesTypeBond(String inSpeciesTypeBondId)` Removes an element from the `listOfInSpeciesTypeBonds`.
`SpeciesFeatureType`	`removeSpeciesFeatureType(int i)` Removes an element from the `listOfSpeciesFeatureTypes` at the given index.
`boolean`	`removeSpeciesFeatureType(SpeciesFeatureType speciesFeatureType)` Removes an element from the `listOfSpeciesFeatureTypes`.
`SpeciesFeatureType`	`removeSpeciesFeatureType(String speciesFeatureTypeId)` Removes an element from the `listOfSpeciesFeatureTypes`.
`SpeciesTypeComponentIndex`	`removeSpeciesTypeComponentIndex(int i)` Removes an element from the `listOfSpeciesTypeComponentIndexes` at the given index.
`boolean`	`removeSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex)` Removes an element from the `listOfSpeciesTypeComponentIndexes`.
`SpeciesTypeComponentIndex`	`removeSpeciesTypeComponentIndex(String speciesTypeComponentIndexId)` Removes an element from the `listOfSpeciesTypeComponentIndexes`.
`SpeciesTypeInstance`	`removeSpeciesTypeInstance(int i)` Removes an element from the `listOfSpeciesTypeInstances` at the given index.
`boolean`	`removeSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)` Removes an element from the `listOfSpeciesTypeInstances`.
`SpeciesTypeInstance`	`removeSpeciesTypeInstance(String speciesTypeInstanceId)` Removes an element from the `listOfSpeciesTypeInstances`.
`boolean`	`setCompartment(Compartment compartment)`
`boolean`	`setCompartment(String compartment)`
`void`	`setListOfInSpeciesTypeBonds(ListOf<InSpeciesTypeBond> listOfInSpeciesTypeBonds)` Sets the given `ListOf<InSpeciesTypeBond>`.
`void`	`setListOfSpeciesFeatureTypes(ListOf<SpeciesFeatureType> listOfSpeciesFeatureTypes)` Sets the given `ListOf<SpeciesFeatureType>`.
`void`	`setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex> listOfSpeciesTypeComponentIndexes)` Sets the given `ListOf<SpeciesTypeComponentIndex>`.
`void`	`setListOfSpeciesTypeInstances(ListOf<SpeciesTypeInstance> listOfSpeciesTypeInstances)` Sets the given `ListOf<SpeciesTypeInstance>`.
`boolean`	`unsetCompartment()`
`boolean`	`unsetListOfInSpeciesTypeBonds()` Returns `true` if `listOfInSpeciesTypeBonds` contains at least one element, otherwise `false`.
`boolean`	`unsetListOfSpeciesFeatureTypes()` Returns `true` if `listOfSpeciesFeatureTypes` contains at least one element, otherwise `false`.
`boolean`	`unsetListOfSpeciesTypeComponentIndexes()` Returns `true` if `listOfSpeciesTypeComponentIndexes` contains at least one element, otherwise `false`.
`boolean`	`unsetListOfSpeciesTypeInstances()` Returns `true` if `listOfSpeciesTypeInstances` contains at least one element, otherwise `false`.
`Map<String,String>`	`writeXMLAttributes()`

Methods inherited from class org.sbml.jsbml.SpeciesType
getParent

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase
isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface javax.swing.tree.TreeNode
children, getAllowsChildren, getIndex, getParent, isLeaf

- Constructor Detail
  - MultiSpeciesType
```
public MultiSpeciesType()
```
    Creates an MultiSpeciesType instance
  - MultiSpeciesType
```
public MultiSpeciesType(int level,
                        int version)
```
    Creates a MultiSpeciesType instance with a level and version.
    
    Parameters:
    
    level - SBML Level
    
    version - SBML Version
  - MultiSpeciesType
```
public MultiSpeciesType(MultiSpeciesType obj)
```
    Creates a new MultiSpeciesType instance cloned from the given MultiSpeciesType.
    
    Parameters:
    
    obj - the MultiSpeciesType to clone
  - MultiSpeciesType
```
public MultiSpeciesType(String id)
```
    Creates a MultiSpeciesType instance with an id.
    
    Parameters:
    
    id - the identifier for the new element.
  - MultiSpeciesType
```
public MultiSpeciesType(String id,
                        int level,
                        int version)
```
    Creates a MultiSpeciesType instance with an id, level, and version.
    
    Parameters:
    
    id - the identifier for this element.
    
    level - the SBML Level
    
    version - the SBML Version
  - MultiSpeciesType
```
public MultiSpeciesType(String id,
                        String name,
                        int level,
                        int version)
```
    Creates a MultiSpeciesType instance with an id, name, level, and version.
    
    Parameters:
    
    id - the identifier for this element.
    
    name - a human-readable name for this element that can be used for display purposes.
    
    level - the SBML Level
    
    version - the SBML Version
- Method Detail
  - addInSpeciesTypeBond
```
public boolean addInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond)
```
    Adds a new InSpeciesTypeBond to the listOfInSpeciesTypeBonds.
    The listOfInSpeciesTypeBonds is initialized if necessary.
    
    Parameters:
    
    inSpeciesTypeBond - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
    
    See Also:
    
    Collection.add(Object)
  - addSpeciesFeatureType
```
public boolean addSpeciesFeatureType(SpeciesFeatureType speciesFeatureType)
```
    Adds a new SpeciesFeatureType to the listOfSpeciesFeatureTypes.
    The listOfSpeciesFeatureTypes is initialized if necessary.
    
    Parameters:
    
    speciesFeatureType - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
    
    See Also:
    
    Collection.add(Object)
  - addSpeciesTypeComponentIndex
```
public boolean addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex)
```
    Adds a new SpeciesTypeComponentIndex to the listOfSpeciesTypeComponentIndexes.
    The listOfSpeciesTypeComponentIndexes is initialized if necessary.
    
    Parameters:
    
    speciesTypeComponentIndex - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
    
    See Also:
    
    Collection.add(Object)
  - addSpeciesTypeInstance
```
public boolean addSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)
```
    Adds a new SpeciesTypeInstance to the listOfSpeciesTypeInstances.
    The listOfSpeciesTypeInstances is initialized if necessary.
    
    Parameters:
    
    speciesTypeInstance - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
    
    See Also:
    
    Collection.add(Object)
  - clone
```
public MultiSpeciesType clone()
```
    clones this class
    
    Specified by:
    
    clone in interface SBase
    
    Overrides:
    
    clone in class SpeciesType
  - createInSpeciesTypeBond
```
public InSpeciesTypeBond createInSpeciesTypeBond()
```
    Creates a new InSpeciesTypeBond element and adds it to the listOfInSpeciesTypeBonds list.
    
    Returns:
    
    the newly created element, i.e., the last item in the listOfInSpeciesTypeBonds
  - createInSpeciesTypeBond
```
public InSpeciesTypeBond createInSpeciesTypeBond(String id)
```
    Creates a new InSpeciesTypeBond element and adds it to the listOfInSpeciesTypeBonds list.
    
    Parameters:
    
    id - the identifier that is to be applied to the new element.
    
    Returns:
    
    the newly created InSpeciesTypeBond element, which is the last element in the listOfInSpeciesTypeBonds.
  - createSpeciesFeatureType
```
public SpeciesFeatureType createSpeciesFeatureType()
```
    Creates a new SpeciesFeatureType element and adds it to the listOfSpeciesFeatureTypes list.
    
    Returns:
    
    the newly created element, i.e., the last item in the listOfSpeciesFeatureTypes
  - createSpeciesFeatureType
```
public SpeciesFeatureType createSpeciesFeatureType(String id)
```
    Creates a new SpeciesFeatureType element and adds it to the listOfSpeciesFeatureTypes list.
    
    Parameters:
    
    id - the identifier that is to be applied to the new element.
    
    Returns:
    
    the newly created SpeciesFeatureType element, which is the last element in the listOfSpeciesFeatureTypes.
  - createSpeciesTypeComponentIndex
```
public SpeciesTypeComponentIndex createSpeciesTypeComponentIndex()
```
    Creates a new SpeciesTypeComponentIndex element and adds it to the listOfSpeciesTypeComponentIndexes list.
    
    Returns:
    
    the newly created element, i.e., the last item in the listOfSpeciesTypeComponentIndexes
  - createSpeciesTypeComponentIndex
```
public SpeciesTypeComponentIndex createSpeciesTypeComponentIndex(String id)
```
    Creates a new SpeciesTypeComponentIndex element and adds it to the listOfSpeciesTypeComponentIndexes list.
    
    Parameters:
    
    id - the identifier that is to be applied to the new element.
    
    Returns:
    
    the newly created SpeciesTypeComponentIndex element, which is the last element in the listOfSpeciesTypeComponentIndexes.
  - createSpeciesTypeInstance
```
public SpeciesTypeInstance createSpeciesTypeInstance()
```
    Creates a new SpeciesTypeInstance element and adds it to the listOfSpeciesTypeInstances list.
    
    Returns:
    
    the newly created element, i.e., the last item in the listOfSpeciesTypeInstances
  - createSpeciesTypeInstance
```
public SpeciesTypeInstance createSpeciesTypeInstance(String id)
```
    Creates a new SpeciesTypeInstance element and adds it to the listOfSpeciesTypeInstances list.
    
    Parameters:
    
    id - the identifier that is to be applied to the new element.
    
    Returns:
    
    the newly created SpeciesTypeInstance element, which is the last element in the listOfSpeciesTypeInstances.
  - equals
```
public boolean equals(Object obj)
```
    Specified by:
    
    equals in interface SBase
    
    Overrides:
    
    equals in class AbstractSBase
  - getChildAt
```
public TreeNode getChildAt(int index)
```
    Specified by:
    
    getChildAt in interface TreeNode
    
    Overrides:
    
    getChildAt in class AbstractSBase
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface TreeNode
    
    Overrides:
    
    getChildCount in class AbstractSBase
  - getCompartment
```
public String getCompartment()
```
    Specified by:
    
    getCompartment in interface CompartmentalizedSBase
  - getCompartmentInstance
```
public Compartment getCompartmentInstance()
```
    Specified by:
    
    getCompartmentInstance in interface CompartmentalizedSBase
  - getElementName
```
public String getElementName()
```
    Specified by:
    
    getElementName in interface SBase
    
    Overrides:
    
    getElementName in class AbstractSBase
  - getInSpeciesTypeBond
```
public InSpeciesTypeBond getInSpeciesTypeBond(int i)
```
    Gets an element from the listOfInSpeciesTypeBonds at the given index.
    
    Parameters:
    
    i - the index of the InSpeciesTypeBond element to get.
    
    Returns:
    
    an element from the listOfInSpeciesTypeBonds at the given index.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getInSpeciesTypeBond
```
public InSpeciesTypeBond getInSpeciesTypeBond(String inSpeciesTypeBondId)
```
    Gets an element from the listOfInSpeciesTypeBonds, with the given id.
    
    Parameters:
    
    inSpeciesTypeBondId - the id of the InSpeciesTypeBond element to get.
    
    Returns:
    
    an element from the listOfInSpeciesTypeBonds with the given id or null.
  - getInSpeciesTypeBondCount
```
public int getInSpeciesTypeBondCount()
```
    Returns the number of InSpeciesTypeBonds in this MultiSpeciesType.
    
    Returns:
    
    the number of InSpeciesTypeBonds in this MultiSpeciesType.
  - getListOfInSpeciesTypeBonds
```
public ListOf<InSpeciesTypeBond> getListOfInSpeciesTypeBonds()
```
    Returns the listOfInSpeciesTypeBonds. Creates it if it does not already exist.
    
    Returns:
    
    the listOfInSpeciesTypeBonds.
  - getListOfSpeciesFeatureTypes
```
public ListOf<SpeciesFeatureType> getListOfSpeciesFeatureTypes()
```
    Returns the listOfSpeciesFeatureTypes. Creates it if it does not already exist.
    
    Returns:
    
    the listOfSpeciesFeatureTypes.
  - getListOfSpeciesTypeComponentIndexes
```
public ListOf<SpeciesTypeComponentIndex> getListOfSpeciesTypeComponentIndexes()
```
    Returns the listOfSpeciesTypeComponentIndexes. Creates it if it does not already exist.
    
    Returns:
    
    the listOfSpeciesTypeComponentIndexes.
  - getListOfSpeciesTypeInstances
```
public ListOf<SpeciesTypeInstance> getListOfSpeciesTypeInstances()
```
    Returns the listOfSpeciesTypeInstances. Creates it if it does not already exist.
    
    Returns:
    
    the listOfSpeciesTypeInstances.
  - getNumInSpeciesTypeBonds
```
public int getNumInSpeciesTypeBonds()
```
    Returns the number of InSpeciesTypeBonds in this MultiSpeciesType.
    
    Returns:
    
    the number of InSpeciesTypeBonds in this MultiSpeciesType.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getInSpeciesTypeBondCount()
  - getNumSpeciesFeatureTypes
```
public int getNumSpeciesFeatureTypes()
```
    Returns the number of SpeciesFeatureTypes in this MultiSpeciesType.
    
    Returns:
    
    the number of SpeciesFeatureTypes in this MultiSpeciesType.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getSpeciesFeatureTypeCount()
  - getNumSpeciesTypeComponentIndexes
```
public int getNumSpeciesTypeComponentIndexes()
```
    Returns the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.
    
    Returns:
    
    the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getSpeciesTypeComponentIndexCount()
  - getNumSpeciesTypeInstances
```
public int getNumSpeciesTypeInstances()
```
    Returns the number of SpeciesTypeInstances in this MultiSpeciesType.
    
    Returns:
    
    the number of SpeciesTypeInstances in this MultiSpeciesType.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getSpeciesTypeInstanceCount()
  - getSpeciesFeatureType
```
public SpeciesFeatureType getSpeciesFeatureType(int i)
```
    Gets an element from the listOfSpeciesFeatureTypes at the given index.
    
    Parameters:
    
    i - the index of the SpeciesFeatureType element to get.
    
    Returns:
    
    an element from the listOfSpeciesFeatureTypes at the given index.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getSpeciesFeatureType
```
public SpeciesFeatureType getSpeciesFeatureType(String speciesFeatureTypeId)
```
    Gets an element from the listOfSpeciesFeatureTypes, with the given id.
    
    Parameters:
    
    speciesFeatureTypeId - the id of the SpeciesFeatureType element to get.
    
    Returns:
    
    an element from the listOfSpeciesFeatureTypes with the given id or null.
  - getSpeciesFeatureTypeCount
```
public int getSpeciesFeatureTypeCount()
```
    Returns the number of SpeciesFeatureTypes in this MultiSpeciesType.
    
    Returns:
    
    the number of SpeciesFeatureTypes in this MultiSpeciesType.
  - getSpeciesTypeComponentIndex
```
public SpeciesTypeComponentIndex getSpeciesTypeComponentIndex(int i)
```
    Gets an element from the listOfSpeciesTypeComponentIndexes at the given index.
    
    Parameters:
    
    i - the index of the SpeciesTypeComponentIndex element to get.
    
    Returns:
    
    an element from the listOfSpeciesTypeComponentIndexes at the given index.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getSpeciesTypeComponentIndex
```
public SpeciesTypeComponentIndex getSpeciesTypeComponentIndex(String speciesTypeComponentIndexId)
```
    Gets an element from the listOfSpeciesTypeComponentIndexes, with the given id.
    
    Parameters:
    
    speciesTypeComponentIndexId - the id of the SpeciesTypeComponentIndex element to get.
    
    Returns:
    
    an element from the listOfSpeciesTypeComponentIndexes with the given id or null.
  - getSpeciesTypeComponentIndexCount
```
public int getSpeciesTypeComponentIndexCount()
```
    Returns the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.
    
    Returns:
    
    the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.
  - getSpeciesTypeInstance
```
public SpeciesTypeInstance getSpeciesTypeInstance(int i)
```
    Gets an element from the listOfSpeciesTypeInstances at the given index.
    
    Parameters:
    
    i - the index of the SpeciesTypeInstance element to get.
    
    Returns:
    
    an element from the listOfSpeciesTypeInstances at the given index.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getSpeciesTypeInstance
```
public SpeciesTypeInstance getSpeciesTypeInstance(String speciesTypeInstanceId)
```
    Gets an element from the listOfSpeciesTypeInstances, with the given id.
    
    Parameters:
    
    speciesTypeInstanceId - the id of the SpeciesTypeInstance element to get.
    
    Returns:
    
    an element from the listOfSpeciesTypeInstances with the given id or null.
  - getSpeciesTypeInstanceCount
```
public int getSpeciesTypeInstanceCount()
```
    Returns the number of SpeciesTypeInstances in this MultiSpeciesType.
    
    Returns:
    
    the number of SpeciesTypeInstances in this MultiSpeciesType.
  - hashCode
```
public int hashCode()
```
    Specified by:
    
    hashCode in interface SBase
    
    Overrides:
    
    hashCode in class AbstractSBase
  - initDefaults
```
public void initDefaults()
```
    Initializes the default values.
  - isCompartmentMandatory
```
public boolean isCompartmentMandatory()
```
    Specified by:
    
    isCompartmentMandatory in interface CompartmentalizedSBase
  - isIdMandatory
```
public boolean isIdMandatory()
```
    Specified by:
    
    isIdMandatory in interface NamedSBase
    
    Specified by:
    
    isIdMandatory in interface SBase
    
    Overrides:
    
    isIdMandatory in class SpeciesType
  - isSetCompartment
```
public boolean isSetCompartment()
```
    Specified by:
    
    isSetCompartment in interface CompartmentalizedSBase
  - isSetCompartmentInstance
```
public boolean isSetCompartmentInstance()
```
    Specified by:
    
    isSetCompartmentInstance in interface CompartmentalizedSBase
  - isSetListOfInSpeciesTypeBonds
```
public boolean isSetListOfInSpeciesTypeBonds()
```
    Returns true if listOfInSpeciesTypeBonds contains at least one element.
    
    Returns:
    
    true if listOfInSpeciesTypeBonds contains at least one element, otherwise false.
  - isSetListOfSpeciesFeatureTypes
```
public boolean isSetListOfSpeciesFeatureTypes()
```
    Returns true if listOfSpeciesFeatureTypes contains at least one element.
    
    Returns:
    
    true if listOfSpeciesFeatureTypes contains at least one element, otherwise false.
  - isSetListOfSpeciesTypeComponentIndexes
```
public boolean isSetListOfSpeciesTypeComponentIndexes()
```
    Returns true if listOfSpeciesTypeComponentIndexes contains at least one element.
    
    Returns:
    
    true if listOfSpeciesTypeComponentIndexes contains at least one element, otherwise false.
  - isSetListOfSpeciesTypeInstances
```
public boolean isSetListOfSpeciesTypeInstances()
```
    Returns true if listOfSpeciesTypeInstances contains at least one element.
    
    Returns:
    
    true if listOfSpeciesTypeInstances contains at least one element, otherwise false.
  - readAttribute
```
public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)
```
    Specified by:
    
    readAttribute in interface SBase
    
    Overrides:
    
    readAttribute in class AbstractSBase
  - removeInSpeciesTypeBond
```
public boolean removeInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond)
```
    Removes an element from the listOfInSpeciesTypeBonds.
    
    Parameters:
    
    inSpeciesTypeBond - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeInSpeciesTypeBond
```
public InSpeciesTypeBond removeInSpeciesTypeBond(int i)
```
    Removes an element from the listOfInSpeciesTypeBonds at the given index.
    
    Parameters:
    
    i - the index where to remove the InSpeciesTypeBond.
    
    Returns:
    
    the specified element if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfInSpeciesTypeBonds)).
  - removeInSpeciesTypeBond
```
public InSpeciesTypeBond removeInSpeciesTypeBond(String inSpeciesTypeBondId)
```
    Removes an element from the listOfInSpeciesTypeBonds.
    
    Parameters:
    
    inSpeciesTypeBondId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeSpeciesFeatureType
```
public SpeciesFeatureType removeSpeciesFeatureType(int i)
```
    Removes an element from the listOfSpeciesFeatureTypes at the given index.
    
    Parameters:
    
    i - the index where to remove the SpeciesFeatureType.
    
    Returns:
    
    the specified element if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfSpeciesFeatureTypes)).
  - removeSpeciesFeatureType
```
public boolean removeSpeciesFeatureType(SpeciesFeatureType speciesFeatureType)
```
    Removes an element from the listOfSpeciesFeatureTypes.
    
    Parameters:
    
    speciesFeatureType - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeSpeciesFeatureType
```
public SpeciesFeatureType removeSpeciesFeatureType(String speciesFeatureTypeId)
```
    Removes an element from the listOfSpeciesFeatureTypes.
    
    Parameters:
    
    speciesFeatureTypeId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeSpeciesTypeComponentIndex
```
public SpeciesTypeComponentIndex removeSpeciesTypeComponentIndex(int i)
```
    Removes an element from the listOfSpeciesTypeComponentIndexes at the given index.
    
    Parameters:
    
    i - the index where to remove the SpeciesTypeComponentIndex.
    
    Returns:
    
    the specified element if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfSpeciesTypeComponentIndexes)).
  - removeSpeciesTypeComponentIndex
```
public boolean removeSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex)
```
    Removes an element from the listOfSpeciesTypeComponentIndexes.
    
    Parameters:
    
    speciesTypeComponentIndex - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeSpeciesTypeComponentIndex
```
public SpeciesTypeComponentIndex removeSpeciesTypeComponentIndex(String speciesTypeComponentIndexId)
```
    Removes an element from the listOfSpeciesTypeComponentIndexes.
    
    Parameters:
    
    speciesTypeComponentIndexId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeSpeciesTypeInstance
```
public SpeciesTypeInstance removeSpeciesTypeInstance(int i)
```
    Removes an element from the listOfSpeciesTypeInstances at the given index.
    
    Parameters:
    
    i - the index where to remove the SpeciesTypeInstance.
    
    Returns:
    
    the specified element if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfSpeciesTypeInstances)).
  - removeSpeciesTypeInstance
```
public boolean removeSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)
```
    Removes an element from the listOfSpeciesTypeInstances.
    
    Parameters:
    
    speciesTypeInstance - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeSpeciesTypeInstance
```
public SpeciesTypeInstance removeSpeciesTypeInstance(String speciesTypeInstanceId)
```
    Removes an element from the listOfSpeciesTypeInstances.
    
    Parameters:
    
    speciesTypeInstanceId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - setCompartment
```
public boolean setCompartment(Compartment compartment)
```
    Specified by:
    
    setCompartment in interface CompartmentalizedSBase
  - setCompartment
```
public boolean setCompartment(String compartment)
```
    Specified by:
    
    setCompartment in interface CompartmentalizedSBase
  - setListOfInSpeciesTypeBonds
```
public void setListOfInSpeciesTypeBonds(ListOf<InSpeciesTypeBond> listOfInSpeciesTypeBonds)
```
    Sets the given ListOf<InSpeciesTypeBond>. If listOfInSpeciesTypeBonds was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfInSpeciesTypeBonds - the list of InSpeciesTypeBond
  - setListOfSpeciesFeatureTypes
```
public void setListOfSpeciesFeatureTypes(ListOf<SpeciesFeatureType> listOfSpeciesFeatureTypes)
```
    Sets the given ListOf<SpeciesFeatureType>. If listOfSpeciesFeatureTypes was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfSpeciesFeatureTypes - the list of SpeciesFeatureType
  - setListOfSpeciesTypeComponentIndexes
```
public void setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex> listOfSpeciesTypeComponentIndexes)
```
    Sets the given ListOf<SpeciesTypeComponentIndex>. If listOfSpeciesTypeComponentIndexes was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfSpeciesTypeComponentIndexes - the list of SpeciesTypeComponentIndex
  - setListOfSpeciesTypeInstances
```
public void setListOfSpeciesTypeInstances(ListOf<SpeciesTypeInstance> listOfSpeciesTypeInstances)
```
    Sets the given ListOf<SpeciesTypeInstance>. If listOfSpeciesTypeInstances was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfSpeciesTypeInstances - the list of SpeciesTypeInstance
  - unsetCompartment
```
public boolean unsetCompartment()
```
    Specified by:
    
    unsetCompartment in interface CompartmentalizedSBase
  - unsetListOfInSpeciesTypeBonds
```
public boolean unsetListOfInSpeciesTypeBonds()
```
    Returns true if listOfInSpeciesTypeBonds contains at least one element, otherwise false.
    
    Returns:
    
    true if listOfInSpeciesTypeBonds contains at least one element, otherwise false.
  - unsetListOfSpeciesFeatureTypes
```
public boolean unsetListOfSpeciesFeatureTypes()
```
    Returns true if listOfSpeciesFeatureTypes contains at least one element, otherwise false.
    
    Returns:
    
    true if listOfSpeciesFeatureTypes contains at least one element, otherwise false.
  - unsetListOfSpeciesTypeComponentIndexes
```
public boolean unsetListOfSpeciesTypeComponentIndexes()
```
    Returns true if listOfSpeciesTypeComponentIndexes contains at least one element, otherwise false.
    
    Returns:
    
    true if listOfSpeciesTypeComponentIndexes contains at least one element, otherwise false.
  - unsetListOfSpeciesTypeInstances
```
public boolean unsetListOfSpeciesTypeInstances()
```
    Returns true if listOfSpeciesTypeInstances contains at least one element, otherwise false.
    
    Returns:
    
    true if listOfSpeciesTypeInstances contains at least one element, otherwise false.
  - writeXMLAttributes
```
public Map<String,String> writeXMLAttributes()
```
    Specified by:
    
    writeXMLAttributes in interface SBase
    
    Overrides:
    
    writeXMLAttributes in class AbstractSBase

Class MultiSpeciesType

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.SpeciesType

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.NamedSBase

Methods inherited from interface org.sbml.jsbml.SBase

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Methods inherited from interface javax.swing.tree.TreeNode

Constructor Detail

MultiSpeciesType

MultiSpeciesType

MultiSpeciesType

MultiSpeciesType

MultiSpeciesType

MultiSpeciesType

Method Detail

addInSpeciesTypeBond

addSpeciesFeatureType

addSpeciesTypeComponentIndex

addSpeciesTypeInstance

clone

createInSpeciesTypeBond

createInSpeciesTypeBond

createSpeciesFeatureType

createSpeciesFeatureType

createSpeciesTypeComponentIndex

createSpeciesTypeComponentIndex

createSpeciesTypeInstance

createSpeciesTypeInstance

equals

getChildAt

getChildCount

getCompartment

getCompartmentInstance

getElementName

getInSpeciesTypeBond

getInSpeciesTypeBond

getInSpeciesTypeBondCount

getListOfInSpeciesTypeBonds

getListOfSpeciesFeatureTypes

getListOfSpeciesTypeComponentIndexes

getListOfSpeciesTypeInstances

getNumInSpeciesTypeBonds

getNumSpeciesFeatureTypes

getNumSpeciesTypeComponentIndexes

getNumSpeciesTypeInstances

getSpeciesFeatureType

getSpeciesFeatureType

getSpeciesFeatureTypeCount

getSpeciesTypeComponentIndex

getSpeciesTypeComponentIndex

getSpeciesTypeComponentIndexCount

getSpeciesTypeInstance

getSpeciesTypeInstance

getSpeciesTypeInstanceCount

hashCode

initDefaults

isCompartmentMandatory

isIdMandatory

isSetCompartment

isSetCompartmentInstance

isSetListOfInSpeciesTypeBonds

isSetListOfSpeciesFeatureTypes

isSetListOfSpeciesTypeComponentIndexes

isSetListOfSpeciesTypeInstances

readAttribute

removeInSpeciesTypeBond

removeInSpeciesTypeBond

removeInSpeciesTypeBond

removeSpeciesFeatureType

removeSpeciesFeatureType

removeSpeciesFeatureType

removeSpeciesTypeComponentIndex