public class Input extends SBase
QualitativeSpecies
.
Each Input
refers to a QualitativeSpecies
that participates in the
corresponding Transition
. In Petri nets, these are the input places of the
transition. In logical models, they are the regulators of the species
whose behaviour is defined by the transition.
Constructor and Description |
---|
Input()
Creates a new
Input with the given level, version, and package version. |
Input(Input orig)
Copy constructor for
Input . |
Input(long level)
Creates a new
Input with the given level, version, and package version. |
Input(long level,
long version)
Creates a new
Input with the given level, version, and package version. |
Input(long level,
long version,
long pkgVersion)
Creates a new
Input with the given level, version, and package version. |
Input(QualPkgNamespaces qualns)
Creates a new
Input with the given QualPkgNamespaces object. |
Modifier and Type | Method and Description |
---|---|
Input |
cloneObject()
Creates and returns a deep copy of this
Input object. |
void |
delete()
Explicitly deletes the underlying native object.
|
String |
getElementName()
Returns the XML name of this object.
|
String |
getId()
Returns the value of the 'id' attribute of this
Input . |
String |
getName()
Returns the value of the 'name' attribute of this
Input . |
String |
getQualitativeSpecies()
Returns the value of the 'qualitativeSpecies' attribute of this
Input . |
int |
getSign()
Returns the value of the 'sign' attribute of this
Input . |
int |
getThresholdLevel()
Returns the value of the 'thresholdLevel' attribute of this
Input . |
int |
getTransitionEffect()
Returns the value of the 'transitionEffect' attribute of this
Input . |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes
for this Input object have been set. |
boolean |
isSetId()
|
boolean |
isSetName()
|
boolean |
isSetQualitativeSpecies()
Predicate returning
true or false depending on whether this
Input 's 'qualitativeSpecies' attribute has been set. |
boolean |
isSetSign()
|
boolean |
isSetThresholdLevel()
Predicate returning
true or false depending on whether this
Input 's 'thresholdLevel' attribute has been set. |
boolean |
isSetTransitionEffect()
Predicate returning
true or false depending on whether this
Input 's 'transitionEffect' attribute has been set. |
void |
renameSIdRefs(String oldid,
String newid)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
int |
setId(String id)
Sets the value of the 'id' attribute of this
Input . |
int |
setName(String name)
Sets the value of the 'name' attribute of this
Input . |
int |
setQualitativeSpecies(String qualitativeSpecies)
Sets the value of the 'qualitativeSpecies' attribute of this
Input . |
int |
setSign(int sign)
Sets the value of the 'sign' attribute of this
Input . |
int |
setThresholdLevel(int thresholdLevel)
Sets the value of the 'thresholdLevel' attribute of this
Input . |
int |
setTransitionEffect(int transitionEffect)
Sets the value of the 'transitionEffect' attribute of this
Input . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
Input . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
Input . |
int |
unsetQualitativeSpecies()
Unsets the value of the 'qualitativeSpecies' attribute of this
Input . |
int |
unsetSign()
Unsets the value of the 'sign' attribute of this
Input . |
int |
unsetThresholdLevel()
Unsets the value of the 'thresholdLevel' attribute of this
Input . |
int |
unsetTransitionEffect()
Unsets the value of the 'transitionEffect' attribute of this
Input . |
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 Input(long level, long version, long pkgVersion) throws SBMLConstructorException
Input
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Input
version
- a long integer, the SBML Version to assign to this Input
pkgVersion
- a long integer, the SBML Qual Version to assign to this Input
SBMLConstructorException
public Input(long level, long version) throws SBMLConstructorException
Input
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Input
version
- a long integer, the SBML Version to assign to this Input
pkgVersion
- a long integer, the SBML Qual Version to assign to this Input
SBMLConstructorException
public Input(long level) throws SBMLConstructorException
Input
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Input
version
- a long integer, the SBML Version to assign to this Input
pkgVersion
- a long integer, the SBML Qual Version to assign to this Input
SBMLConstructorException
public Input() throws SBMLConstructorException
Input
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this Input
version
- a long integer, the SBML Version to assign to this Input
pkgVersion
- a long integer, the SBML Qual Version to assign to this Input
SBMLConstructorException
public Input(QualPkgNamespaces qualns) throws SBMLConstructorException
Input
with the given QualPkgNamespaces
object.
qualns
- the QualPkgNamespaces
objectSBMLConstructorException
public Input(Input orig) throws SBMLConstructorException
Input
.
orig
- the Input
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 Input.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 Input.delete()
themselves.
public Input cloneObject()
Input
object.
cloneObject
 in class SBase
Input
object.public String getQualitativeSpecies()
Input
.
Input
as a string.public int getTransitionEffect()
Input
.
Input
as a string.public int getSign()
Input
.
Input
as a string.public int getThresholdLevel()
Input
.
Input
as a integer.public boolean isSetId()
public boolean isSetQualitativeSpecies()
true
or false
depending on whether this
Input
's 'qualitativeSpecies' attribute has been set.
true
if this Input
's 'qualitativeSpecies' attribute has been set,
otherwise false
is returned.public boolean isSetTransitionEffect()
true
or false
depending on whether this
Input
's 'transitionEffect' attribute has been set.
true
if this Input
's 'transitionEffect' attribute has been set,
otherwise false
is returned.public boolean isSetName()
public boolean isSetSign()
true
if this Input
's 'sign' attribute has been set,
otherwise false
is returned.public boolean isSetThresholdLevel()
true
or false
depending on whether this
Input
's 'thresholdLevel' attribute has been set.
true
if this Input
's 'thresholdLevel' attribute has been set,
otherwise false
is returned.public int setId(String id)
Input
.
public int setQualitativeSpecies(String qualitativeSpecies)
Input
.
qualitativeSpecies
- String value of the 'qualitativeSpecies' attribute to be set
public int setTransitionEffect(int transitionEffect)
Input
.
transitionEffect
- String value of the 'transitionEffect' attribute to be set
public int setName(String name)
Input
.
public int setSign(int sign)
Input
.
sign
- String value of the 'sign' attribute to be set
public int setThresholdLevel(int thresholdLevel)
Input
.
thresholdLevel
- int value of the 'thresholdLevel' attribute to be set
public int unsetId()
Input
.
public int unsetQualitativeSpecies()
Input
.
public int unsetTransitionEffect()
Input
.
public int unsetName()
Input
.
public int unsetSign()
Input
.
public int unsetThresholdLevel()
Input
.
public void renameSIdRefs(String oldid, 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 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_INPUT
Input.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes
for this Input
object have been set.
hasRequiredAttributes
 in class SBase
Input
object are: