public class Output extends SBase
QualitativeSpecies
.
Each Output
refers to a QualitativeSpecies
that participates in (is
affected by) the corresponding Transition
. In Petri net models these are
the output places of the transition.
In a logical model, a QualitativeSpecies
should be referenced in at most
one ListOfOutputs
, (that of the Transition
defining the evolution of this
species). When a Transition
has several outputs, it is because the
referenced species share the same regulators and the same logical rules.
Constructor and Description |
---|
Output()
Creates a new
Output with the given level, version, and package version. |
Output(long level)
Creates a new
Output with the given level, version, and package version. |
Output(long level,
long version)
Creates a new
Output with the given level, version, and package version. |
Output(long level,
long version,
long pkgVersion)
Creates a new
Output with the given level, version, and package version. |
Output(Output orig)
Copy constructor for
Output . |
Output(QualPkgNamespaces qualns)
Creates a new
Output with the given QualPkgNamespaces object. |
Modifier and Type | Method and Description |
---|---|
Output |
cloneObject()
Creates and returns a deep copy of this
Output object. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML name of this object.
|
java.lang.String |
getId()
Returns the value of the 'id' attribute of this
Output . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
Output . |
int |
getOutputLevel()
Returns the value of the 'outputLevel' attribute of this
Output . |
java.lang.String |
getQualitativeSpecies()
Returns the value of the 'qualitativeSpecies' attribute of this
Output . |
int |
getTransitionEffect()
Returns the value of the 'transitionEffect' attribute of this
Output . |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes
for this Output object have been set. |
boolean |
isSetId()
|
boolean |
isSetName()
|
boolean |
isSetOutputLevel()
Predicate returning
true or false depending on whether this
Output 's 'outputLevel' attribute has been set. |
boolean |
isSetQualitativeSpecies()
Predicate returning
true or false depending on whether this
Output 's 'qualitativeSpecies' attribute has been set. |
boolean |
isSetTransitionEffect()
Predicate returning
true or false depending on whether this
Output 's 'transitionEffect' attribute has been set. |
void |
renameSIdRefs(java.lang.String oldid,
java.lang.String newid)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
int |
setId(java.lang.String id)
Sets the value of the 'id' attribute of this
Output . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
Output . |
int |
setOutputLevel(int outputLevel)
Sets the value of the 'outputLevel' attribute of this
Output . |
int |
setQualitativeSpecies(java.lang.String qualitativeSpecies)
Sets the value of the 'qualitativeSpecies' attribute of this
Output . |
int |
setTransitionEffect(int transitionEffect)
Sets the value of the 'transitionEffect' attribute of this
Output . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
Output . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
Output . |
int |
unsetOutputLevel()
Unsets the value of the 'outputLevel' attribute of this
Output . |
int |
unsetQualitativeSpecies()
Unsets the value of the 'qualitativeSpecies' attribute of this
Output . |
int |
unsetTransitionEffect()
Unsets the value of the 'transitionEffect' attribute of this
Output . |
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, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public Output(long level, long version, long pkgVersion) throws SBMLConstructorException
Output
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Output
version
- a long integer, the SBML Version to assign to this Output
pkgVersion
- a long integer, the SBML Qual Version to assign to this Output
SBMLConstructorException
public Output(long level, long version) throws SBMLConstructorException
Output
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Output
version
- a long integer, the SBML Version to assign to this Output
pkgVersion
- a long integer, the SBML Qual Version to assign to this Output
SBMLConstructorException
public Output(long level) throws SBMLConstructorException
Output
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Output
version
- a long integer, the SBML Version to assign to this Output
pkgVersion
- a long integer, the SBML Qual Version to assign to this Output
SBMLConstructorException
public Output() throws SBMLConstructorException
Output
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Output
version
- a long integer, the SBML Version to assign to this Output
pkgVersion
- a long integer, the SBML Qual Version to assign to this Output
SBMLConstructorException
public Output(QualPkgNamespaces qualns) throws SBMLConstructorException
Output
with the given QualPkgNamespaces
object.
qualns
- the QualPkgNamespaces
objectSBMLConstructorException
public Output(Output orig) throws SBMLConstructorException
Output
.
orig
- the Output
instance to copy.SBMLConstructorException
public void delete()
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 Output.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 Output.delete()
themselves.
public Output cloneObject()
Output
object.
cloneObject
 in class SBase
Output
object.public java.lang.String getId()
Output
.
public java.lang.String getQualitativeSpecies()
Output
.
Output
as a string.public int getTransitionEffect()
Output
.
Output
as a string.public java.lang.String getName()
Output
.
public int getOutputLevel()
Output
.
Output
as a integer.public boolean isSetId()
public boolean isSetQualitativeSpecies()
true
or false
depending on whether this
Output
's 'qualitativeSpecies' attribute has been set.
true
if this Output
's 'qualitativeSpecies' attribute has been set,
otherwise false
is returned.public boolean isSetTransitionEffect()
true
or false
depending on whether this
Output
's 'transitionEffect' attribute has been set.
true
if this Output
's 'transitionEffect' attribute has been set,
otherwise false
is returned.public boolean isSetName()
public boolean isSetOutputLevel()
true
or false
depending on whether this
Output
's 'outputLevel' attribute has been set.
true
if this Output
's 'outputLevel' attribute has been set,
otherwise false
is returned.public int setId(java.lang.String id)
Output
.
public int setQualitativeSpecies(java.lang.String qualitativeSpecies)
Output
.
qualitativeSpecies
- String value of the 'qualitativeSpecies' attribute to be set
public int setTransitionEffect(int transitionEffect)
Output
.
transitionEffect
- String value of the 'transitionEffect' attribute to be set
public int setName(java.lang.String name)
Output
.
public int setOutputLevel(int outputLevel)
Output
.
outputLevel
- int value of the 'outputLevel' attribute to be set
public int unsetId()
Output
.
public int unsetQualitativeSpecies()
Output
.
public int unsetTransitionEffect()
Output
.
public int unsetName()
Output
.
public int unsetOutputLevel()
Output
.
public void renameSIdRefs(java.lang.String oldid, java.lang.String newid)
Replaces all uses of a given SIdRef
type attribute value with another
value.
In SBML, object identifiers are of a data type called SId
.
In SBML Level 3, an explicit data type called SIdRef
was
introduced for attribute values that refer to SId
values in
previous Levels of SBML, this data type did not exist and attributes were
simply described to as 'referring to an identifier', but the effective
data type was the same as SIdRef
in Level 3. These and
other methods of libSBML refer to the type SIdRef
for all
Levels of SBML, even if the corresponding SBML specification did not
explicitly name the data type.
This method works by looking at all attributes and (if appropriate)
mathematical formulas in MathML content, comparing the referenced
identifiers to the value of oldid
. If any matches are found, the
matching values are replaced with newid
. The method does not
descend into child elements.
renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic java.lang.String getElementName()
getElementName
 in class SBase
public int getTypeCode()
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.
getTypeCode
 in class SBase
SBML_QUAL_OUTPUT
Output.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes
for this Output
object have been set.
hasRequiredAttributes
 in class SBase
Output
object are: