FbcOr (LibSBML Java API)

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

```
public class FbcOr
extends FbcAssociation
```
fbc An &ldquoor&rdquo relationship for gene products
FbcOr class is used in Version 2 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package to represent an 'or' 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 GeneProducRef, FbcOr and FbcOr, a given FbcOr can potentially include nested 'and'/'or' combinations of gene products.

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

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

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, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - FbcOr
```
public FbcOr(long level,
             long version,
             long pkgVersion)
      throws SBMLConstructorException
```
    Creates a new FbcOr with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcOr
    
    version - a long integer, the SBML Version to assign to this FbcOr
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcOr
    
    Throws:
    
    SBMLConstructorException
  - FbcOr
```
public FbcOr(long level,
             long version)
      throws SBMLConstructorException
```
    Creates a new FbcOr with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcOr
    
    version - a long integer, the SBML Version to assign to this FbcOr
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcOr
    
    Throws:
    
    SBMLConstructorException
  - FbcOr
```
public FbcOr(long level)
      throws SBMLConstructorException
```
    Creates a new FbcOr with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcOr
    
    version - a long integer, the SBML Version to assign to this FbcOr
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcOr
    
    Throws:
    
    SBMLConstructorException
  - FbcOr
```
public FbcOr()
      throws SBMLConstructorException
```
    Creates a new FbcOr with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this FbcOr
    
    version - a long integer, the SBML Version to assign to this FbcOr
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this FbcOr
    
    Throws:
    
    SBMLConstructorException
  - FbcOr
```
public FbcOr(FbcPkgNamespaces fbcns)
      throws SBMLConstructorException
```
    Creates a new FbcOr with the given FbcPkgNamespaces object.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
  - FbcOr
```
public FbcOr(FbcOr orig)
      throws SBMLConstructorException
```
    Copy constructor for FbcOr.
    
    Parameters:
    
    orig - the FbcOr 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 FbcOr.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 FbcOr.delete() themselves.
    
    Overrides:
    
    delete in class FbcAssociation
  - cloneObject
```
public FbcOr cloneObject()
```
    Creates and returns a deep copy of this FbcOr object.
    
    Overrides:
    
    cloneObject in class FbcAssociation
    
    Returns:
    
    a (deep) copy of this FbcOr object.
  - getListOfAssociations
```
public ListOfFbcAssociations getListOfAssociations()
```
    Returns the 'ListOfFbcAssociations' in this FbcOr object.
    
    Returns:
    
    the 'ListOfFbcAssociations' attribute of this FbcOr.
  - getAssociation
```
public FbcAssociation getAssociation(long n)
```
    Get a Association from the ListOfFbcAssociations.
    
    Parameters:
    
    n - the index number of the Association to get.
    
    Returns:
    
    the nth Association in the ListOfFbcAssociations within this FbcOr.
    
    See Also:
    
    FbcOr.getNumAssociations()
  - getAssociation
```
public FbcAssociation getAssociation(java.lang.String sid)
```
    Get a Association from the ListOfFbcAssociations based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Association to get.
    
    Returns:
    
    the Association in the ListOfFbcAssociations with the given id or null if no such Association exists.
    
    See Also:
    
    , FbcOr.getAssociation(long n)
  - addAssociation
```
public int addAssociation(FbcAssociation fa)
```
    Adds a copy the given 'FbcAssociation' to this FbcOr.
    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
  - getNumAssociations
```
public long getNumAssociations()
```
    Get the number of FbcAssociation objects in this FbcOr.
    
    Returns:
    
    the number of FbcAssociation objects in this FbcOr
  - 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 FbcOrs ListOfFbcAssociations and returns the FbcAnd object created.
    
    Returns:
    
    a new FbcAnd object instance
    
    See Also:
    
    FbcOr.addAssociation(FbcAssociation fa)
  - createOr
```
public FbcOr createOr()
```
    Creates a new FbcOr object, adds it to this FbcOrs ListOfFbcAssociations and returns the FbcOr object created.
    
    Returns:
    
    a new FbcOr object instance
    
    See Also:
    
    FbcOr.addAssociation(FbcAssociation fa)
  - createGeneProductRef
```
public GeneProductRef createGeneProductRef()
```
    Creates a new GeneProductRef object, adds it to this FbcOrs ListOfFbcAssociations and returns the GeneProductRef object created.
    
    Returns:
    
    a new GeneProductRef object instance
    
    See Also:
    
    FbcOr.addAssociation(FbcAssociation fa)
  - removeAssociation
```
public FbcAssociation removeAssociation(long n)
```
    Removes the nth Association from the ListOfFbcAssociations within this FbcOr. and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the Association to remove.
    
    See Also:
    
    FbcOr.getNumAssociations()
  - removeAssociation
```
public FbcAssociation removeAssociation(java.lang.String sid)
```
    Removes the Association with the given identifier from the ListOfFbcAssociations within this FbcOr 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 Association to remove.
    
    Returns:
    
    the Association 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 FbcOr, the XML element name is always 'fbcOr'.
    
    Overrides:
    
    getElementName in class FbcAssociation
    
    Returns:
    
    the name of this element, i.e. 'fbcOr'.
  - 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 getPackageName() method on the object.
    
    Overrides:
    
    getTypeCode in class FbcAssociation
    
    Returns:
    
    the SBML type code for this object: SBML_FBC_OR (default).
    
    See Also:
    
    FbcOr.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy 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 FbcOr object have been set.
    
    Overrides:
    
    hasRequiredAttributes in class FbcAssociation
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
    
    "Note:"
    
    The required attributes for a FbcOr object are:
  - hasRequiredElements
```
public boolean hasRequiredElements()
```
    Predicate returning true if all the required elements for this FbcOr 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:"
    
    The required elements for a FbcOr object are:

Class FbcOr

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

FbcOr

FbcOr

FbcOr

FbcOr

FbcOr

FbcOr

Method Detail

delete

cloneObject

getListOfAssociations

getAssociation

getAssociation

addAssociation

getNumAssociations

toInfix

createAnd

createOr

createGeneProductRef

removeAssociation

removeAssociation

getElementName

getTypeCode

hasRequiredAttributes

hasRequiredElements