Output (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.Output

```
public class Output
extends SBase
```
qual The output from a 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 Summary

Constructors
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.

Method Summary

All Methods Instance Methods Concrete Methods
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()` Predicate returning `true` or `false` depending on whether this `Output`'s 'id' attribute has been set.
`boolean`	`isSetName()` Predicate returning `true` or `false` depending on whether this `Output`'s 'name' attribute has been set.
`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`.

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, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - Output
```
public Output(long level,
              long version,
              long pkgVersion)
       throws SBMLConstructorException
```
    Creates a new Output with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - Output
```
public Output(long level,
              long version)
       throws SBMLConstructorException
```
    Creates a new Output with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - Output
```
public Output(long level)
       throws SBMLConstructorException
```
    Creates a new Output with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - Output
```
public Output()
       throws SBMLConstructorException
```
    Creates a new Output with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - Output
```
public Output(QualPkgNamespaces qualns)
       throws SBMLConstructorException
```
    Creates a new Output with the given QualPkgNamespaces object.
    
    Parameters:
    
    qualns - the QualPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
  - Output
```
public Output(Output orig)
       throws SBMLConstructorException
```
    Copy constructor for Output.
    
    Parameters:
    
    orig - the Output 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 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.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public Output cloneObject()
```
    Creates and returns a deep copy of this Output object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this Output object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this Output.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the value of the 'id' attribute of this Output as a string.
  - getQualitativeSpecies
```
public java.lang.String getQualitativeSpecies()
```
    Returns the value of the 'qualitativeSpecies' attribute of this Output.
    
    Returns:
    
    the value of the 'qualitativeSpecies' attribute of this Output as a string.
  - getTransitionEffect
```
public int getTransitionEffect()
```
    Returns the value of the 'transitionEffect' attribute of this Output.
    
    Returns:
    
    the value of the 'transitionEffect' attribute of this Output as a string.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this Output.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this Output as a string.
  - getOutputLevel
```
public int getOutputLevel()
```
    Returns the value of the 'outputLevel' attribute of this Output.
    
    Returns:
    
    the value of the 'outputLevel' attribute of this Output as a integer.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true or false depending on whether this Output's 'id' attribute has been set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if this Output's 'id' attribute has been set, otherwise false is returned.
  - isSetQualitativeSpecies
```
public boolean isSetQualitativeSpecies()
```
    Predicate returning true or false depending on whether this Output's 'qualitativeSpecies' attribute has been set.
    
    Returns:
    
    true if this Output's 'qualitativeSpecies' attribute has been set, otherwise false is returned.
  - isSetTransitionEffect
```
public boolean isSetTransitionEffect()
```
    Predicate returning true or false depending on whether this Output's 'transitionEffect' attribute has been set.
    
    Returns:
    
    true if this Output's 'transitionEffect' attribute has been set, otherwise false is returned.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true or false depending on whether this Output's 'name' attribute has been set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this Output's 'name' attribute has been set, otherwise false is returned.
  - isSetOutputLevel
```
public boolean isSetOutputLevel()
```
    Predicate returning true or false depending on whether this Output's 'outputLevel' attribute has been set.
    
    Returns:
    
    true if this Output's 'outputLevel' attribute has been set, otherwise false is returned.
  - setId
```
public int setId(java.lang.String id)
```
    Sets the value of the 'id' attribute of this Output.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    id - String value of the 'id' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setQualitativeSpecies
```
public int setQualitativeSpecies(java.lang.String qualitativeSpecies)
```
    Sets the value of the 'qualitativeSpecies' attribute of this Output.
    Parameters:
    
    qualitativeSpecies - String value of the 'qualitativeSpecies' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setTransitionEffect
```
public int setTransitionEffect(int transitionEffect)
```
    Sets the value of the 'transitionEffect' attribute of this Output.
    Parameters:
    
    transitionEffect - String value of the 'transitionEffect' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function 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 Output.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - String value of the 'name' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setOutputLevel
```
public int setOutputLevel(int outputLevel)
```
    Sets the value of the 'outputLevel' attribute of this Output.
    Parameters:
    
    outputLevel - int value of the 'outputLevel' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this Output.
    Overrides:
    
    unsetId in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetQualitativeSpecies
```
public int unsetQualitativeSpecies()
```
    Unsets the value of the 'qualitativeSpecies' attribute of this Output.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetTransitionEffect
```
public int unsetTransitionEffect()
```
    Unsets the value of the 'transitionEffect' attribute of this Output.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this Output.
    Overrides:
    
    unsetName in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetOutputLevel
```
public int unsetOutputLevel()
```
    Unsets the value of the 'outputLevel' attribute of this Output.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - renameSIdRefs
```
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 SIdRefin 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.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML name of this object.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element.
  - 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 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 SBase
    
    Returns:
    
    the SBML type code for this object: SBML_QUAL_OUTPUT
    
    See Also:
    
    Output.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 Output object have been set.
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
    
    "Note:"
    The required attributes for a Output object are:
    
    'qualitativeSpecies'
    'transitionEffect'

Class Output

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

Output

Output

Output

Output

Output

Output

Method Detail

delete

cloneObject

getId

getQualitativeSpecies

getTransitionEffect

getName

getOutputLevel

isSetId

isSetQualitativeSpecies

isSetTransitionEffect

isSetName

isSetOutputLevel

setId

setQualitativeSpecies

setTransitionEffect

setName

setOutputLevel

unsetId

unsetQualitativeSpecies

unsetTransitionEffect

unsetName

unsetOutputLevel

renameSIdRefs

getElementName

getTypeCode

hasRequiredAttributes