FbcAnd (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.FbcAssociation
  - - org.sbml.libsbml.FbcAnd

```
public class FbcAnd
extends FbcAssociation
```
fbc An &ldquoand&rdquo relationship for gene products
FbcAnd class is used in Version 2 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package to represent an 'and' relationship between two or more child FbcAssociation objects. In other words, it indicates that all of the child objects are included. Note that since the FbcAssociation class is the parent class of GeneProductRef, FbcAnd and FbcOr, a given FbcAnd can potentially include nested 'and'/'or' combinations of gene products.

See Also:

FbcAssociation, 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.

Constructor Summary

Constructors
Constructor and Description
`FbcAnd()` Creates a new `FbcAnd` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`FbcAnd(FbcAnd orig)` Copy constructor for `FbcAnd`.
`FbcAnd(FbcPkgNamespaces fbcns)` Creates a new `FbcAnd` with the given `FbcPkgNamespaces` object.
`FbcAnd(long level)` Creates a new `FbcAnd` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`FbcAnd(long level, long version)` Creates a new `FbcAnd` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`FbcAnd(long level, long version, long pkgVersion)` Creates a new `FbcAnd` 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`	`addAssociation(FbcAssociation fa)` Adds a copy the given `FbcAssociation` to this `FbcAnd`.
`FbcAnd`	`cloneObject()` Creates and returns a deep copy of this `FbcAnd` object.
`FbcAnd`	`createAnd()` Creates a new `FbcAnd` object, adds it to this `FbcAnd`'s `ListOfFbcAssociations` and returns the `FbcAnd` object created.
`GeneProductRef`	`createGeneProductRef()` Creates a new `GeneProductRef` object, adds it to this `FbcAnd`'s `ListOfFbcAssociations` and returns the `GeneProductRef` object created.
`FbcOr`	`createOr()` Creates a new `FbcOr` object, adds it to this `FbcAnd`'s `ListOfFbcAssociations` and returns the `FbcOr` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`FbcAssociation`	`getAssociation(long n)` Get the nth object from the `ListOfFbcAssociations`.
`FbcAssociation`	`getAssociation(java.lang.String sid)` Get an `FbcAssociation` from the `ListOfFbcAssociations` based on its identifier.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`ListOfFbcAssociations`	`getListOfAssociations()` Returns the `ListOfFbcAssociations` in this `FbcAnd` object.
`long`	`getNumAssociations()` Get the number of `FbcAssociation` objects in this `FbcAnd`.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required attributes for this `FbcAnd` object have been set.
`boolean`	`hasRequiredElements()` Predicate returning `true` if all the required elements for this `FbcAnd` object have been set.
`FbcAssociation`	`removeAssociation(long n)` Removes the nth `FbcAssociation` from the `ListOfFbcAssociations` within this `FbcAnd` and returns a pointer to it.
`FbcAssociation`	`removeAssociation(java.lang.String sid)` Removes the `FbcAssociation` with the given identifier from the `ListOfFbcAssociations` within this `FbcAnd` and returns a pointer to it.
`java.lang.String`	`toInfix()` Converts this `FbcAssociation` object into an infix string representation.
`java.lang.String`	`toInfix(boolean usingId)` Converts this `FbcAssociation` object into an infix string representation.

Methods inherited from class org.sbml.libsbml.FbcAssociation
isFbcAnd, isFbcOr, isGeneProductRef, parseFbcInfixAssociation, parseFbcInfixAssociation, parseFbcInfixAssociation

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, 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, removeFromParentAndDelete, 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
  - FbcAnd
```
public FbcAnd(long level,
              long version,
              long pkgVersion)
       throws SBMLConstructorException
```
    Creates a new FbcAnd with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcAnd.
    
    version - a long integer, the SBML Version to assign to this FbcAnd.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcAnd.
    
    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.
  - FbcAnd
```
public FbcAnd(long level,
              long version)
       throws SBMLConstructorException
```
    Creates a new FbcAnd with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcAnd.
    
    version - a long integer, the SBML Version to assign to this FbcAnd.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcAnd.
    
    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.
  - FbcAnd
```
public FbcAnd(long level)
       throws SBMLConstructorException
```
    Creates a new FbcAnd with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcAnd.
    
    version - a long integer, the SBML Version to assign to this FbcAnd.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcAnd.
    
    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.
  - FbcAnd
```
public FbcAnd()
       throws SBMLConstructorException
```
    Creates a new FbcAnd with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcAnd.
    
    version - a long integer, the SBML Version to assign to this FbcAnd.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcAnd.
    
    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.
  - FbcAnd
```
public FbcAnd(FbcPkgNamespaces fbcns)
       throws SBMLConstructorException
```
    Creates a new FbcAnd 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.
  - FbcAnd
```
public FbcAnd(FbcAnd orig)
       throws SBMLConstructorException
```
    Copy constructor for FbcAnd.
    
    Parameters:
    
    orig - the FbcAnd instance to copy.
    
    Throws:
    
    SBMLConstructorException
- 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 FbcAnd.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 FbcAnd.delete() themselves.
    
    Overrides:
    
    delete in class FbcAssociation
  - cloneObject
```
public FbcAnd cloneObject()
```
    Creates and returns a deep copy of this FbcAnd object.
    
    Overrides:
    
    cloneObject in class FbcAssociation
    
    Returns:
    
    a (deep) copy of this FbcAnd object.
  - getListOfAssociations
```
public ListOfFbcAssociations getListOfAssociations()
```
    Returns the ListOfFbcAssociations in this FbcAnd object.
    
    Returns:
    
    the ListOfFbcAssociations child of this FbcAnd.
  - getAssociation
```
public FbcAssociation getAssociation(long n)
```
    Get the nth object from the ListOfFbcAssociations.
    
    Parameters:
    
    n - the index number of the FbcAssociation to get.
    
    Returns:
    
    the nth FbcAssociation in the ListOfFbcAssociations within this FbcAnd.
    
    See Also:
    
    FbcAnd.getNumAssociations()
  - getAssociation
```
public FbcAssociation getAssociation(java.lang.String sid)
```
    Get an FbcAssociation from the ListOfFbcAssociations based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the FbcAssociation to get.
    
    Returns:
    
    the FbcAssociation in the ListOfFbcAssociations with the given id or null if no such FbcAssociation exists.
    
    See Also:
    
    , FbcAnd.getAssociation(long n)
  - addAssociation
```
public int addAssociation(FbcAssociation fa)
```
    Adds a copy the given FbcAssociation to this FbcAnd.
    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_OPERATION_FAILED
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
    LIBSBML_NAMESPACES_MISMATCH
  - getNumAssociations
```
public long getNumAssociations()
```
    Get the number of FbcAssociation objects in this FbcAnd.
    
    Returns:
    
    the number of FbcAssociation objects in this FbcAnd.
  - toInfix
```
public java.lang.String toInfix(boolean usingId)
```
    Converts this FbcAssociation object into an infix string representation.
    
    Overrides:
    
    toInfix in class FbcAssociation
    
    Returns:
    
    the association as infix string.
  - toInfix
```
public java.lang.String toInfix()
```
    Converts this FbcAssociation object into an infix string representation.
    
    Overrides:
    
    toInfix in class FbcAssociation
    
    Returns:
    
    the association as infix string.
  - createAnd
```
public FbcAnd createAnd()
```
    Creates a new FbcAnd object, adds it to this FbcAnd's ListOfFbcAssociations and returns the FbcAnd object created.
    
    Returns:
    
    a new FbcAnd object instance.
    
    See Also:
    
    FbcAnd.addAssociation(FbcAssociation fa)
  - createOr
```
public FbcOr createOr()
```
    Creates a new FbcOr object, adds it to this FbcAnd's ListOfFbcAssociations and returns the FbcOr object created.
    
    Returns:
    
    a new FbcOr object instance.
    
    See Also:
    
    FbcAnd.addAssociation(FbcAssociation fa)
  - createGeneProductRef
```
public GeneProductRef createGeneProductRef()
```
    Creates a new GeneProductRef object, adds it to this FbcAnd's ListOfFbcAssociations and returns the GeneProductRef object created.
    
    Returns:
    
    a new GeneProductRef object instance.
    
    See Also:
    
    FbcAnd.addAssociation(FbcAssociation fa)
  - removeAssociation
```
public FbcAssociation removeAssociation(long n)
```
    Removes the nth FbcAssociation from the ListOfFbcAssociations within this FbcAnd and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the FbcAssociation to remove.
    
    See Also:
    
    FbcAnd.getNumAssociations()
  - removeAssociation
```
public FbcAssociation removeAssociation(java.lang.String sid)
```
    Removes the FbcAssociation with the given identifier from the ListOfFbcAssociations within this FbcAnd 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 FbcAnd, the XML element name is always 'fbcAnd'.
    
    Overrides:
    
    getElementName in class FbcAssociation
    
    Returns:
    
    the name of this element, i.e. 'fbcAnd'.
  - 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 FbcAssociation
    
    Returns:
    
    the SBML type code for this object: SBML_FBC_AND (default).
    
    See Also:
    
    FbcAnd.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().
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this FbcAnd object have been set. Will always return true, since FbcOr has no required attributes.
    
    Overrides:
    
    hasRequiredAttributes in class FbcAssociation
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
  - hasRequiredElements
```
public boolean hasRequiredElements()
```
    Predicate returning true if all the required elements for this FbcAnd object have been set.
    
    Overrides:
    
    hasRequiredElements in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required elements for this object have been defined.
    
    "Note:"
    
    An FbcAnd object must have at least two FbcAssociation children.

Class FbcAnd

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.FbcAssociation

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

FbcAnd

FbcAnd

FbcAnd

FbcAnd

FbcAnd

FbcAnd

Method Detail

delete

cloneObject

getListOfAssociations

getAssociation

getAssociation

addAssociation

getNumAssociations

toInfix

toInfix

createAnd

createOr

createGeneProductRef

removeAssociation

removeAssociation

getElementName

getTypeCode

hasRequiredAttributes

hasRequiredElements