Package org.sbml.jsbml.ext.fbc

Class GeneProduct

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.fbc.GeneProduct

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class GeneProduct
extends AbstractNamedSBase
implements UniqueNamedSBase

Defines a single gene product.

Introduced to FBC in version 2.

Since:

1.1

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

Constructor	Description
GeneProduct()	Creates a new GeneProduct instance.
GeneProduct(int level, int version)	Creates a new GeneProduct instance.
GeneProduct(java.lang.String id)	Creates a new GeneProduct instance.
GeneProduct(java.lang.String id, int level, int version)	Creates a new GeneProduct instance.
GeneProduct(java.lang.String id, java.lang.String name, int level, int version)	Creates a new GeneProduct instance.
GeneProduct(GeneProduct nsb)	Creates a new GeneProduct instance.

Method Summary

Modifier and Type	Method	Description
GeneProduct	clone()	Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object obj)	Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getAssociatedSpecies()	Returns the value of associatedSpecies.
java.lang.String	getLabel()	Returns the value of label
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	isSetAssociatedSpecies()	Returns whether associatedSpecies is set.
boolean	isSetLabel()	Returns whether label is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)	Sets the given attribute in this SBase.
void	setAssociatedSpecies(java.lang.String associatedSpecies)	Sets the value of associatedSpecies
void	setLabel(java.lang.String label)	Sets the value of label
boolean	unsetAssociatedSpecies()	Unsets the variable associatedSpecies.
boolean	unsetLabel()	Unsets the variable label
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.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

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

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

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

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

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

Constructor Detail

GeneProduct

public GeneProduct()

Creates a new GeneProduct instance.

GeneProduct

public GeneProduct(GeneProduct nsb)

Creates a new GeneProduct instance.

Parameters:

nsb - the instance to clone

GeneProduct

public GeneProduct(int level,
                   int version)

Creates a new GeneProduct instance.

Parameters:

level - the SBML level

version - the SBML version

GeneProduct

public GeneProduct(java.lang.String id)

Creates a new GeneProduct instance.

Parameters:

id - the id

GeneProduct

public GeneProduct(java.lang.String id,
                   int level,
                   int version)

Creates a new GeneProduct instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

GeneProduct

public GeneProduct(java.lang.String id,
                   java.lang.String name,
                   int level,
                   int version)

Creates a new GeneProduct instance.

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Method Detail

getAssociatedSpecies

public java.lang.String getAssociatedSpecies()

Returns the value of associatedSpecies.

Returns:

the value of associatedSpecies.

isSetAssociatedSpecies

public boolean isSetAssociatedSpecies()

Returns whether associatedSpecies is set.

Returns:

whether associatedSpecies is set.

setAssociatedSpecies

public void setAssociatedSpecies(java.lang.String associatedSpecies)

Sets the value of associatedSpecies

Parameters:

associatedSpecies - the value of associatedSpecies to be set.

unsetAssociatedSpecies

public boolean unsetAssociatedSpecies()

Unsets the variable associatedSpecies.

Returns:

true if associatedSpecies was set before, otherwise false.

clone

public GeneProduct clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

equals

public boolean equals(java.lang.Object obj)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

obj - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getLabel

public java.lang.String getLabel()

Returns the value of label

Returns:

the value of label

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

Returns:

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.

isSetLabel

public boolean isSetLabel()

Returns whether label is set

Returns:

whether label is set

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setLabel

public void setLabel(java.lang.String label)

Sets the value of label

Parameters:

label -

unsetLabel

public boolean unsetLabel()

Unsets the variable label

Returns:

true, if label was set before, otherwise false

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this 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.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.