org.sbml.libsbml

Class Objective

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.Objective

public class Objective
extends SBase

fbc Implementation of the 'fbc' package Objective construct.

The FBC Objective class is derived from SBML SBase and inherits metaid and sboTerm, as well as the subcomponents for Annotation and Notes. An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction). In the FBC package this concept is succinctly captured in the Objective class.

Constructor Summary

Constructors

Constructor and Description
Objective() Creates a new Objective with the given level, version, and package version.
Objective(FbcPkgNamespaces fbcns) Creates a new Objective with the given FbcPkgNamespaces object.
Objective(long level) Creates a new Objective with the given level, version, and package version.
Objective(long level, long version) Creates a new Objective with the given level, version, and package version.
Objective(long level, long version, long pkgVersion) Creates a new Objective with the given level, version, and package version.
Objective(Objective source) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
int	addFluxObjective(FluxObjective member) Adds a copy of the given FluxObjective object to the list of members.
Objective	cloneObject() Creates and returns a deep copy of this Objective object.
FluxObjective	createFluxObjective() Creates a FluxObjective object, adds it to the end of the member objects list and returns a pointer to the newly created object.
void	delete() Explicitly deletes the underlying native object.
SBase	getElementByMetaId(java.lang.String metaid) Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
SBase	getElementBySId(java.lang.String id) Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
java.lang.String	getElementName() Returns the XML element name of this SBML object.
FluxObjective	getFluxObjective(long n) Returns the member with the given index.
FluxObjective	getFluxObjective(java.lang.String symbol) Returns the member with the given symbol.
java.lang.String	getId() Returns the string of the 'id' attribute of this Objective.
ListOfFluxObjectives	getListOfFluxObjectives() Returns the ListOf object that holds all members.
java.lang.String	getName() Returns the value of the 'name' attribute of this Objective.
long	getNumFluxObjectives() Returns the number of members for this objective.
int	getObjectiveType() Returns the ObjectiveType_t of the 'type' attribute of this Objective.
java.lang.String	getType() Returns the string of the 'type' attribute of this Objective.
int	getTypeCode() Returns the libSBML type code of this object instance.
boolean	isSetId() Predicate returning true or false depending on whether this Objective's 'id' attribute has been set.
boolean	isSetName() Predicate returning true or false depending on whether this Objective's 'name' attribute has been set.
boolean	isSetType() Predicate returning true or false depending on whether this Objective's 'type' attribute has been set.
FluxObjective	removeFluxObjective(long index) Removes the member with the given index from the objective.
FluxObjective	removeFluxObjective(java.lang.String symbol) Removes the member with the given symbol from the objective.
int	setId(java.lang.String id) Sets the SIdRef string of the 'id' attribute of this Objective.
int	setName(java.lang.String name) Sets the value of the 'name' attribute of this Objective.
int	setType(int type) Sets the SIdRef string of the 'type' attribute of this Objective.
int	setType(java.lang.String type) Sets the SIdRef string of the 'type' attribute of this Objective.
int	unsetId() Unsets the value of the 'id' attribute of this Objective.
int	unsetName() Unsets the value of the 'name' attribute of this Objective.
int	unsetType() Unsets the value of the 'id' attribute of this Objective.

Methods inherited from class org.sbml.libsbml.SBase

addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, 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, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Objective

public Objective()
          throws SBMLConstructorException

Creates a new Objective with the given level, version, and package version.

Throws:

SBMLConstructorException

Objective

public Objective(FbcPkgNamespaces fbcns)
          throws SBMLConstructorException

Creates a new Objective with the given FbcPkgNamespaces object.

Throws:

SBMLConstructorException

Objective

public Objective(long level)
          throws SBMLConstructorException

Creates a new Objective with the given level, version, and package version.

Throws:

SBMLConstructorException

Objective

public Objective(long level,
         long version)
          throws SBMLConstructorException

Creates a new Objective with the given level, version, and package version.

Throws:

SBMLConstructorException

Objective

public Objective(long level,
         long version,
         long pkgVersion)
          throws SBMLConstructorException

Creates a new Objective with the given level, version, and package version.

Throws:

SBMLConstructorException

Objective

public Objective(Objective source)
          throws SBMLConstructorException

Copy constructor.

Throws:

SBMLConstructorException

Method Detail

addFluxObjective

public int addFluxObjective(FluxObjective member)

Adds a copy of the given FluxObjective object to the list of members.

Parameters:

member - the FluxObjective object to be added to the list of members.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_LEVEL_MISMATCH
• LIBSBML_VERSION_MISMATCH
• LIBSBML_PKG_VERSION_MISMATCH
• LIBSBML_DUPLICATE_OBJECT_ID
• LIBSBML_OPERATION_FAILED

cloneObject

public Objective cloneObject()

Creates and returns a deep copy of this Objective object.

Overrides:

cloneObject in class SBase

Returns:

a (deep) copy of this Objective.

createFluxObjective

public FluxObjective createFluxObjective()

Creates a FluxObjective object, adds it to the end of the member objects list and returns a pointer to the newly created object.

Returns:

a newly created FluxObjective object

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 Objective.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 Objective.delete() themselves.

Overrides:

delete in class SBase

getElementByMetaId

public SBase getElementByMetaId(java.lang.String metaid)

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.

Overrides:

getElementByMetaId in class SBase

Parameters:

metaid - string representing the metaid of objects to find

Returns:

a pointer to the SBase element with the given metaid.

getElementBySId

public SBase getElementBySId(java.lang.String id)

Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.

Overrides:

getElementBySId in class SBase

Parameters:

id - string representing the id of objects to find

Returns:

a pointer to the SBase element with the given id.

getElementName

public java.lang.String getElementName()

Returns the XML element name of this SBML object.

Overrides:

getElementName in class SBase

Returns:

the string of the name of this element.

getFluxObjective

public FluxObjective getFluxObjective(long n)

Returns the member with the given index. If the index is invalid, null is returned.

Parameters:

n - the index number of the FluxObjective to get.

Returns:

the nth FluxObjective in the ListOfFluxObjectives.

getFluxObjective

public FluxObjective getFluxObjective(java.lang.String symbol)

Returns the member with the given symbol. If the index is invalid, null is returned.

Parameters:

symbol - a string representing the symbol attribute of the FluxObjective to get.

Returns:

FluxObjective in the ListOfFluxObjectives with the given symbol or null if no such FluxObjective exists.

getId

public java.lang.String getId()

Returns the string of the 'id' attribute of this Objective.

Overrides:

getId in class SBase

Returns:

the string of the 'id' attribute of this Objective.

getListOfFluxObjectives

public ListOfFluxObjectives getListOfFluxObjectives()

Returns the ListOf object that holds all members.

Returns:

the ListOf object that holds all members.

getName

public java.lang.String getName()

Returns the value of the 'name' attribute of this Objective.

Overrides:

getName in class SBase

Returns:

the value of the 'name' attribute of this Objective.

getNumFluxObjectives

public long getNumFluxObjectives()

Returns the number of members for this objective.

Returns:

the number of members for this objective.

getObjectiveType

public int getObjectiveType()

Returns the ObjectiveType_t of the 'type' attribute of this Objective.

Returns:

the ObjectiveType_t of the 'type' attribute of this Objective.

getType

public java.lang.String getType()

Returns the string of the 'type' attribute of this Objective.

Returns:

the string of the 'type' attribute of this Objective.

getTypeCode

public int getTypeCode()

Returns the libSBML type code of this object instance.

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 &ldquoSBML_&rdquo. 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 SBase

Returns:

the SBML type code for this object: SBML_FBC_OBJECTIVE

See Also:

Objective.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().

isSetId

public boolean isSetId()

Predicate returning true or false depending on whether this Objective's 'id' attribute has been set.

Overrides:

isSetId in class SBase

Returns:

true if this Objective's 'id' attribute has been set, otherwise false is returned.

isSetName

public boolean isSetName()

Predicate returning true or false depending on whether this Objective's 'name' attribute has been set.

Overrides:

isSetName in class SBase

Returns:

true if this Objective's 'id' attribute has been set, otherwise false is returned.

isSetType

public boolean isSetType()

Predicate returning true or false depending on whether this Objective's 'type' attribute has been set.

Returns:

true if this Objective's 'type' attribute has been set, otherwise false is returned.

removeFluxObjective

public FluxObjective removeFluxObjective(long index)

Removes the member with the given index from the objective. A pointer to the member that was removed is returned. If no member has been removed, null is returned.

Parameters:

index - the index of the FluxObjective object to remove

Returns:

the FluxObjective object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

removeFluxObjective

public FluxObjective removeFluxObjective(java.lang.String symbol)

Removes the member with the given symbol from the objective. A pointer to the member that was removed is returned. If no member has been removed, null is returned.

Parameters:

symbol - the symbol attribute of the FluxObjective object to remove

Returns:

the FluxObjective object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

setId

public int setId(java.lang.String id)

Sets the SIdRef string of the 'id' attribute of this Objective.

Overrides:

setId in class SBase

Parameters:

id - a SIdRef string to be set.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setName

public int setName(java.lang.String name)

Sets the value of the 'name' attribute of this Objective.

Overrides:

setName in class SBase

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setType

public int setType(int type)

Sets the SIdRef string of the 'type' attribute of this Objective.

Parameters:

type - a SIdRef string to be set.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setType

public int setType(java.lang.String type)

Sets the SIdRef string of the 'type' attribute of this Objective.

Parameters:

type - a SIdRef string to be set.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

unsetId

public int unsetId()

Unsets the value of the 'id' attribute of this Objective.

Overrides:

unsetId in class SBase

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

unsetName

public int unsetName()

Unsets the value of the 'name' attribute of this Objective.

Overrides:

unsetName in class SBase

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

unsetType

public int unsetType()

Unsets the value of the 'id' attribute of this Objective.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED