org.sbml.libsbml

Class Port

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.CompBase

org.sbml.libsbml.SBaseRef

org.sbml.libsbml.Port

public class Port
extends SBaseRef

comp Implementation of the Port construct from the &ldquocomp&rdquo package.

The Port class was introduced by the SBML Level 3 'Hierarchical Model Composition' package (&ldquocomp&rdquo) to allow a Model to define a standard interface between it and other models that might use it as a submodel. It derives from the SBaseRef class, and the elements defined there refer to elements in the same parent Model as the Port object. A Port object instance therefore uses those attributes to define a port for a component in a model. When other SBaseRef or SBaseRef-derived classes refer to a Port object using a 'portRef' attribute, the element being referenced is the element the Port object itself points to.

In the present formulation of the Hierarchical Model Composition package, the use of ports is not enforced, nor is there any mechanism to restrict which ports may be used in what ways&mdashthey are only an advisory construct. Future versions of this SBML package may provide additional functionality to support explicit restrictions on port use. For the present definition of Hierarchical Model Composition, users of models containing ports are encouraged to respect the modeler's intention in defining ports, and use the port definitions to interact with components through their ports (when they have ports defined) rather than interact directly with the components.

The required attribute 'id' is used to give an identifier to a Port object so that other objects can refer to it. The attribute has type PortSId and is essentially identical to the SBML primitive type SId, except that its namespace is limited to the identifiers of Port objects defined within a Model object. In parallel, the PortSId type has a companion type, PortSIdRef, that corresponds to the SBML primitive type SIdRef the value space of PortSIdRef is limited to PortSId values.

Constructor Summary

Constructors

Constructor and Description
Port() Creates a new Port with the given level, version, and package version.
Port(CompPkgNamespaces compns) Creates a new Port with the given CompPkgNamespaces object.
Port(long level) Creates a new Port with the given level, version, and package version.
Port(long level, long version) Creates a new Port with the given level, version, and package version.
Port(long level, long version, long pkgVersion) Creates a new Port with the given level, version, and package version.
Port(Port source) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
SBase	cloneObject() Creates and returns a deep copy of this Port object.
void	delete() Explicitly deletes the underlying native object.
java.lang.String	getElementName() Returns the XML element name of this SBML object.
java.lang.String	getId() Returns the value of the 'id' attribute of this Port.
java.lang.String	getName() Returns the value of the 'name' attribute of this Port.
int	getTypeCode() Returns the libSBML type code of this object instance.
boolean	hasRequiredAttributes() Returns true if the 'id' attribute is set, and if exactly one of the optional attributes of SBaseRef (portRef, idRef, metaIdRef, and unitRef)are set.
boolean	isSetId() Predicate returning true or false depending on whether this Port's 'id' attribute has been set.
boolean	isSetName() Predicate returning true or false depending on whether this Port's 'name' attribute has been set.
void	renameMetaIdRefs(java.lang.String oldid, java.lang.String newid) Renames the metaIdRef attribute on this element if the oldid matches.
void	renameSIdRefs(java.lang.String oldid, java.lang.String newid) Renames the idRef attribute on this element if the oldid matches.
void	renameUnitSIdRefs(java.lang.String oldid, java.lang.String newid) Renames the unitRef attribute on this element if the oldid matches.
int	saveReferencedElement() Finds and stores the referenced object by finding its Model parent, calling 'getReferencedElementFrom()' on that model, and storing the result.
int	setId(java.lang.String id) Sets the value of the 'id' attribute of this Port.
int	setName(java.lang.String name) Sets the value of the 'name' attribute of this Port.
int	setPortRef(java.lang.String id) Overrides SBaseRef.setPortRef to always fail, because Port objects themselves cannot refer to model elements by PortSId.
int	unsetId() Unsets the value of the 'id' attribute of this Port.
int	unsetName() Unsets the value of the 'name' attribute of this Port.

Methods inherited from class org.sbml.libsbml.SBaseRef

clearReferencedElement, createSBaseRef, getElementByMetaId, getElementBySId, getIdRef, getMetaIdRef, getNumReferents, getPortRef, getReferencedElement, getReferencedElementFrom, getSBaseRef, getUnitRef, isSetIdRef, isSetMetaIdRef, isSetPortRef, isSetSBaseRef, isSetUnitRef, performDeletion, removeFromParentAndDelete, setIdRef, setMetaIdRef, setSBaseRef, setUnitRef, unsetIdRef, unsetMetaIdRef, unsetPortRef, unsetSBaseRef, unsetUnitRef

Methods inherited from class org.sbml.libsbml.CompBase

getPackageName, getPackageURI, getPackageVersion, getParentModel

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, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, 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

Port

public Port()
     throws SBMLConstructorException

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

Parameters:

level - the SBML Level

version - the Version within the SBML Level

pkgVersion - the version of the package

Throws:

SBMLConstructorException

Port

public Port(CompPkgNamespaces compns)
     throws SBMLConstructorException

Creates a new Port with the given CompPkgNamespaces object.

Parameters:

compns - the namespace to use

Throws:

SBMLConstructorException

Port

public Port(long level)
     throws SBMLConstructorException

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

Parameters:

level - the SBML Level

version - the Version within the SBML Level

pkgVersion - the version of the package

Throws:

SBMLConstructorException

Port

public Port(long level,
    long version)
     throws SBMLConstructorException

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

Parameters:

level - the SBML Level

version - the Version within the SBML Level

pkgVersion - the version of the package

Throws:

SBMLConstructorException

Port

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

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

Parameters:

level - the SBML Level

version - the Version within the SBML Level

pkgVersion - the version of the package

Throws:

SBMLConstructorException

Port

public Port(Port source)
     throws SBMLConstructorException

Copy constructor.

Throws:

SBMLConstructorException

Method Detail

cloneObject

public SBase cloneObject()

Creates and returns a deep copy of this Port object.

Overrides:

cloneObject in class SBaseRef

Returns:

a (deep) copy of this Port 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 Port.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 Port.delete() themselves.

Overrides:

delete in class SBaseRef

getElementName

public java.lang.String getElementName()

Returns the XML element name of this SBML object.

Overrides:

getElementName in class SBaseRef

Returns:

the string of the name of this element.

getId

public java.lang.String getId()

Returns the value of the 'id' attribute of this Port.

Overrides:

getId in class SBase

Returns:

the value of the 'id' attribute of this Port.

getName

public java.lang.String getName()

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

Overrides:

getName in class SBase

Returns:

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

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 SBaseRef

Returns:

the SBML type code for this object: SBML_COMP_PORT

See Also:

Port.getElementName(), CompBase.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()

Returns true if the 'id' attribute is set, and if exactly one of the optional attributes of SBaseRef (portRef, idRef, metaIdRef, and unitRef)are set.

Overrides:

hasRequiredAttributes in class SBaseRef

Returns:

boolean: 'true' if the attributes are correctly set 'false' if not.

isSetId

public boolean isSetId()

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

Overrides:

isSetId in class SBase

Returns:

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

isSetName

public boolean isSetName()

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

Overrides:

isSetName in class SBase

Returns:

true if this Port's 'name' attribute has been set, otherwise false is returned.

renameMetaIdRefs

public void renameMetaIdRefs(java.lang.String oldid,
                    java.lang.String newid)

Renames the metaIdRef attribute on this element if the oldid matches.

Overrides:

renameMetaIdRefs in class SBase

Parameters:

oldid - the old identifier

newid - the new identifier

renameSIdRefs

public void renameSIdRefs(java.lang.String oldid,
                 java.lang.String newid)

Renames the idRef attribute on this element if the oldid matches.

Overrides:

renameSIdRefs in class SBaseRef

Parameters:

oldid - the old identifier

newid - the new identifier

renameUnitSIdRefs

public void renameUnitSIdRefs(java.lang.String oldid,
                     java.lang.String newid)

Renames the unitRef attribute on this element if the oldid matches.

Overrides:

renameUnitSIdRefs in class SBase

Parameters:

oldid - the old identifier

newid - the new identifier

saveReferencedElement

public int saveReferencedElement()

Finds and stores the referenced object by finding its Model parent, calling 'getReferencedElementFrom()' on that model, and storing the result.

Overrides:

saveReferencedElement in class SBaseRef

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

setId

public int setId(java.lang.String id)

Sets the value of the 'id' attribute of this Port.

This method fails if the id is not a valid syntax for an SId.

Overrides:

setId in class SBase

Parameters:

id - the identifier for the port

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 Port.

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

setPortRef

public int setPortRef(java.lang.String id)

Overrides SBaseRef.setPortRef to always fail, because Port objects themselves cannot refer to model elements by PortSId.

Overrides:

setPortRef in class SBaseRef

Parameters:

id - the identifier to set for the port reference

Returns:

integer value indicating failure of the function. The possible value returned by this function is:

• LIBSBML_OPERATION_FAILED

unsetId

public int unsetId()

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

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 Port.

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