ListOfFbcAssociations (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.ListOf
  - - org.sbml.libsbml.ListOfFbcAssociations

```
public class ListOfFbcAssociations
extends ListOf
```
fbc A list of FbcAssociation objects.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The ListOfFbcAssociations is a container of FbcAssociation objects for the FbcAnd and FbcOr classes. Unlike the ListOf___ classes in SBML, the ListOfFbcAssociations is not a class that appears in the &ldquofbc&rdquo Version 2 specification, and instead is used internally in libSBML as a convenience class to store arbitrary numbers of FbcAssociation objects. Also unlike other ListOf___ classes, the FbcAnd and FbcOr classes require at least two child FbcAssociation objects, so valid ListOfFbcAssociations libsbml objects will always contain two or more children. These children will have element names associated with their derived class, not the base FbcAssociation class: <fbc:and>, <fbc:or>, and <fbc:geneProductRef>.

See Also:

FbcAssociation, FbcAnd, FbcOr, GeneProductRef

"Note:"

This class of objects was introduced in Version 2 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) specification. In Version 1 of &ldquofbc&rdquo, the information encoded by this class can be stored instead using the Association and GeneAssociation annotation classes. Please see the Version 1 and Version 2 &ldquofbc&rdquo specifications for more details.

"Warning:"

It is important to be clear that ListOfFbcAssociations is not written out in the XML output produced by libSBML&mdashthe constructs only exist in software to enable software applications to manipulate FbcAssociation objects in a way that mirrors how other lists of components in SBML are manipulated. ListOfFbcAssociations is abstracted away when an SBML &ldquofbc&rdquo model file is actually written out in the final XML form.

Constructor Summary

Constructors
Constructor and Description
`ListOfFbcAssociations()` Creates a new `ListOfFbcAssociations` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`ListOfFbcAssociations(FbcPkgNamespaces fbcns)` Creates a new `ListOfFbcAssociations` with the given `FbcPkgNamespaces` object.
`ListOfFbcAssociations(long level)` Creates a new `ListOfFbcAssociations` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`ListOfFbcAssociations(long level, long version)` Creates a new `ListOfFbcAssociations` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`ListOfFbcAssociations(long level, long version, long pkgVersion)` Creates a new `ListOfFbcAssociations` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addFbcAssociation(FbcAssociation fa)` Adds a copy the given `FbcAssociation` object to this `ListOfFbcAssociations`.
`ListOfFbcAssociations`	`cloneObject()` Creates and returns a deep copy of this `ListOfFbcAssociations` object.
`FbcAnd`	`createAnd()` Creates a new `FbcAnd` object.
`GeneProductRef`	`createGeneProductRef()` Creates a new `GeneProductRef` object.
`FbcOr`	`createOr()` Creates a new `FbcOr` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`FbcAssociation`	`get(long n)` Get a `FbcAssociation` from the `ListOfFbcAssociations`.
`FbcAssociation`	`get(java.lang.String sid)` Get a `FbcAssociation` from the `ListOfFbcAssociations` based on its identifier.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`int`	`getItemTypeCode()` Returns the libSBML type code for the objects contained in this `ListOf`.
`long`	`getNumFbcAssociations()` Get the number of `FbcAssociation` objects in this `ListOfFbcAssociations`.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`FbcAssociation`	`remove(long n)` Removes the nth `FbcAssociation`
`FbcAssociation`	`remove(java.lang.String sid)` Removes the `FbcAssociation` with the given identifier

Methods inherited from class org.sbml.libsbml.ListOf
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, insert, insertAndOwn, removeFromParentAndDelete, size

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - ListOfFbcAssociations
```
public ListOfFbcAssociations(long level,
                             long version,
                             long pkgVersion)
                      throws SBMLConstructorException
```
    Creates a new ListOfFbcAssociations with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFbcAssociations.
    
    version - a long integer, the SBML Version to assign to this ListOfFbcAssociations.
    
    pkgVersion - a long integer, the SBML &ldquofbc&rdquo package Version to assign to this ListOfFbcAssociations.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfFbcAssociations
```
public ListOfFbcAssociations(long level,
                             long version)
                      throws SBMLConstructorException
```
    Creates a new ListOfFbcAssociations with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFbcAssociations.
    
    version - a long integer, the SBML Version to assign to this ListOfFbcAssociations.
    
    pkgVersion - a long integer, the SBML &ldquofbc&rdquo package Version to assign to this ListOfFbcAssociations.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfFbcAssociations
```
public ListOfFbcAssociations(long level)
                      throws SBMLConstructorException
```
    Creates a new ListOfFbcAssociations with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFbcAssociations.
    
    version - a long integer, the SBML Version to assign to this ListOfFbcAssociations.
    
    pkgVersion - a long integer, the SBML &ldquofbc&rdquo package Version to assign to this ListOfFbcAssociations.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfFbcAssociations
```
public ListOfFbcAssociations()
                      throws SBMLConstructorException
```
    Creates a new ListOfFbcAssociations with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFbcAssociations.
    
    version - a long integer, the SBML Version to assign to this ListOfFbcAssociations.
    
    pkgVersion - a long integer, the SBML &ldquofbc&rdquo package Version to assign to this ListOfFbcAssociations.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfFbcAssociations
```
public ListOfFbcAssociations(FbcPkgNamespaces fbcns)
                      throws SBMLConstructorException
```
    Creates a new ListOfFbcAssociations with the given FbcPkgNamespaces object.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
- Method Detail
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the ListOfFbcAssociations.delete() method on the libSBML object.
    This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke ListOfFbcAssociations.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfFbcAssociations cloneObject()
```
    Creates and returns a deep copy of this ListOfFbcAssociations object.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    a (deep) copy of this ListOfFbcAssociations object.
  - get
```
public FbcAssociation get(long n)
```
    Get a FbcAssociation from the ListOfFbcAssociations.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the FbcAssociation to get.
    
    Returns:
    
    the nth FbcAssociation in this ListOfFbcAssociations.
    
    See Also:
    
    ListOf.size(), ListOfFbcAssociations.getNumFbcAssociations()
  - get
```
public FbcAssociation get(java.lang.String sid)
```
    Get a FbcAssociation from the ListOfFbcAssociations based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the FbcAssociation to get.
    
    Returns:
    
    FbcAssociation in this ListOfFbcAssociations with the given id or null if no such FbcAssociation exists.
    
    See Also:
    
    ListOfFbcAssociations.get(long n), ListOf.size()
  - addFbcAssociation
```
public int addFbcAssociation(FbcAssociation fa)
```
    Adds a copy the given FbcAssociation object to this ListOfFbcAssociations.
    Parameters:
    
    fa - the FbcAssociation object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getNumFbcAssociations
```
public long getNumFbcAssociations()
```
    Get the number of FbcAssociation objects in this ListOfFbcAssociations.
    
    Returns:
    
    the number of FbcAssociation objects in this ListOfFbcAssociations.
  - createAnd
```
public FbcAnd createAnd()
```
    Creates a new FbcAnd object.
    This method creates a new FbcAssociation object of subclass FbcAnd, adds it to the ListOfFbcAssociations, and returns the FbcAssociation object created.
    
    Returns:
    
    a new FbcAssociation object instance.
    
    See Also:
    
    ListOfFbcAssociations.createOr(), ListOfFbcAssociations.createGeneProductRef(), ListOfFbcAssociations.addFbcAssociation(FbcAssociation fa)
  - createOr
```
public FbcOr createOr()
```
    Creates a new FbcOr object.
    This method creates a new FbcAssociation object of subclass FbcOr, adds it to the ListOfFbcAssociations, and returns the FbcAssociation object created.
    
    Returns:
    
    a new FbcAssociation object instance.
    
    See Also:
    
    ListOfFbcAssociations.createAnd(), ListOfFbcAssociations.createGeneProductRef(), ListOfFbcAssociations.addFbcAssociation(FbcAssociation fa)
  - createGeneProductRef
```
public GeneProductRef createGeneProductRef()
```
    Creates a new GeneProductRef object.
    This method creates a new FbcAssociation object of subclass GeneProductRef, adds it to the ListOfFbcAssociations, and returns the FbcAssociation object created.
    
    Returns:
    
    a new FbcAssociation object instance.
    
    See Also:
    
    ListOfFbcAssociations.createOr(), ListOfFbcAssociations.createAnd(), ListOfFbcAssociations.addFbcAssociation(FbcAssociation fa)
  - remove
```
public FbcAssociation remove(long n)
```
    Removes the nth FbcAssociation
    This method removes the nth object from this ListOfFbcAssociations and returns a pointer to it.
    
    Overrides:
    
    remove in class ListOf
    
    Parameters:
    
    n - the index of the FbcAssociation to remove.
    
    See Also:
    
    ListOf.size()
  - remove
```
public FbcAssociation remove(java.lang.String sid)
```
    Removes the FbcAssociation with the given identifier
    This method searches for and removes the FbcAssociation object with the given identifier sid, and returns a pointer to it. The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.
    
    Parameters:
    
    sid - the identifier of the FbcAssociation to remove.
    
    Returns:
    
    the FbcAssociation removed. As mentioned above, the caller owns the returned item.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For ListOfFbcAssociations, the XML element name is always 'listOfFbcAssociations'.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the name of this element.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code for this SBML object.
    
    LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. Note that different Level 3 package plug-ins may use overlapping type codes to identify the package to which a given object belongs, call the SBase.getPackageName() method on the object.
    
    Overrides:
    
    getTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for this object: SBML_LIST_OF (default).
    
    See Also:
    
    ListOfFbcAssociations.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - getItemTypeCode
```
public int getItemTypeCode()
```
    Returns the libSBML type code for the objects contained in this ListOf.
    
    LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. Note that different Level 3 package plug-ins may use overlapping type codes to identify the package to which a given object belongs, call the SBase.getPackageName() method on the object.
    
    Overrides:
    
    getItemTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for the objects contained in this ListOf instance: SBML_FBC_ASSOCIATION (default).
    
    See Also:
    
    ListOfFbcAssociations.getElementName(), SBase.getPackageName()

Class ListOfFbcAssociations

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.ListOf

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

ListOfFbcAssociations

ListOfFbcAssociations

ListOfFbcAssociations

ListOfFbcAssociations

ListOfFbcAssociations

Method Detail

delete

cloneObject

get

get

addFbcAssociation

getNumFbcAssociations

createAnd

createOr

createGeneProductRef

remove

remove

getElementName

getTypeCode

getItemTypeCode