java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class FluxObjective extends AbstractNamedSBase implements UniqueNamedSBase
FluxObjective
class is a relatively simple container for a model
variable weighted by a signed linear coefficient.JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
FluxObjective() |
Creates an FluxObjective instance
|
FluxObjective(int level,
int version) |
Creates a FluxObjective instance with a level and version.
|
FluxObjective(java.lang.String id) |
Creates a FluxObjective instance with an id.
|
FluxObjective(java.lang.String id,
int level,
int version) |
Creates a FluxObjective instance with an id, level, and version.
|
FluxObjective(java.lang.String id,
java.lang.String name,
int level,
int version) |
Creates a FluxObjective instance with an id, name, level, and version.
|
FluxObjective(FluxObjective obj) |
Clone constructor
|
Modifier and Type | Method | Description |
---|---|---|
FluxObjective |
clone() |
clones this class
|
boolean |
equals(java.lang.Object obj) |
|
double |
getCoefficient() |
Returns the value of coefficient
|
java.lang.String |
getReaction() |
Returns the value of reaction
|
Reaction |
getReactionInstance() |
Returns the
Reaction associated with this FluxObjective . |
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
Initializes the default values using the namespace.
|
boolean |
isIdMandatory() |
Returns
true if the identifier of this
SBase is required to be defined (i.e., not null )
in the definition of SBML. |
boolean |
isSetCoefficient() |
Returns whether coefficient is set
|
boolean |
isSetReaction() |
Returns whether reaction is set
|
boolean |
isSetReactionInstance() |
Returns whether reaction is set and is a valid
Reaction in the model. |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
void |
setCoefficient(double coefficient) |
The coefficient attribute takes the value of the coefficient that the FluxObjective
takes in the context of the enclosing
Objective class. |
void |
setReaction(java.lang.String reaction) |
Sets the reaction that this
FluxObjective is associated with in the context
of the enclosing Objective class. |
void |
setReaction(Reaction reaction) |
Sets the
Reaction that this FluxObjective is associated with in the context
of the enclosing Objective class. |
boolean |
unsetCoefficient() |
Unsets the variable coefficient
|
boolean |
unsetReaction() |
Unsets the variable reaction
|
java.util.Map<java.lang.String,java.lang.String> |
writeXMLAttributes() |
Returns a map with all the attributes of this
SBase that
need to be written out in XML. |
isValidId
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm
children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet
public FluxObjective()
public FluxObjective(int level, int version)
level
- the SBML levelversion
- the SBML versionpublic FluxObjective(java.lang.String id)
id
- the idpublic FluxObjective(java.lang.String id, int level, int version)
id
- the idlevel
- the SBML levelversion
- the SBML versionpublic FluxObjective(java.lang.String id, java.lang.String name, int level, int version)
id
- the idname
- the namelevel
- the SBML levelversion
- the SBML versionpublic FluxObjective(FluxObjective obj)
obj
- the instance to clonepublic FluxObjective clone()
clone
in interface SBase
clone
in class AbstractSBase
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
public boolean equals(java.lang.Object obj)
SBase
public double getCoefficient()
public java.lang.String getReaction()
public Reaction getReactionInstance()
Reaction
associated with this FluxObjective
.Reaction
associated with this FluxObjective
or null if the reaction attribute is not a valid reaction id.public boolean isSetReactionInstance()
Reaction
in the model.Reaction
in the model.public boolean isSetReaction()
public void initDefaults()
public boolean isIdMandatory()
SBase
true
if the identifier of this
SBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
isIdMandatory
in interface SBase
isIdMandatory
in class AbstractSBase
true
if the identifier of this element must be set in
order to create a valid SBML representation. false
otherwise, i.e., if the identifier can be understood as an optional
attribute.public boolean isSetCoefficient()
public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBase
SBase
.
If the given attribute name is not recognized, nothing is done and
false
is returned.
readAttribute
in interface SBase
readAttribute
in class AbstractSBase
attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.public void setCoefficient(double coefficient)
Objective
class.coefficient
- the coefficient to setpublic void setReaction(Reaction reaction)
Reaction
that this FluxObjective
is associated with in the context
of the enclosing Objective
class.reaction
- the reaction to setpublic void setReaction(java.lang.String reaction)
FluxObjective
is associated with in the context
of the enclosing Objective
class.reaction
- the reaction to setpublic boolean unsetCoefficient()
true
, if coefficient was set before,
otherwise false
public boolean unsetReaction()
true
, if reaction was set before,
otherwise false
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBase
SBase
that
need to be written out in XML.
The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.
writeXMLAttributes
in interface SBase
writeXMLAttributes
in class AbstractSBase
Map
containing the XML attributes of this object.