org.sbml.jsbml.ext.qual
public class QualitativeModel extends AbstractSBasePlugin
Modifier and Type | Field and Description |
---|---|
private ListOf<QualitativeSpecies> |
listOfQualitativeSpecies |
private ListOf<Transition> |
listOfTransitions |
private static long |
serialVersionUID
Generated serial version identifier.
|
extendedSBase, packageVersion
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
Constructor and Description |
---|
QualitativeModel(Model model) |
QualitativeModel(QualitativeModel qualitativeModel) |
Modifier and Type | Method and Description |
---|---|
void |
addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)
Adds a
QualitativeSpecies to the model. |
boolean |
addSpecies(QualitativeSpecies spec)
Adds a
QualitativeSpecies instance to the listOfSpecies of this Model. |
void |
addTransition(Transition transition) |
QualitativeModel |
clone() |
boolean |
containsQualitativeSpecies(QualitativeSpecies qs)
|
QualitativeSpecies |
createQualitativeSpecies()
Creates a new
QualitativeSpecies inside this QualitativeModel and returns it. |
QualitativeSpecies |
createQualitativeSpecies(java.lang.String id)
Creates a new
QualitativeSpecies inside this QualitativeModel and returns it. |
QualitativeSpecies |
createQualitativeSpecies(java.lang.String id,
Compartment c)
|
QualitativeSpecies |
createQualitativeSpecies(java.lang.String id,
java.lang.String compartment,
boolean constant)
Creates a new
QualitativeSpecies inside this QualitativeModel and returns it. |
QualitativeSpecies |
createQualitativeSpecies(java.lang.String id,
java.lang.String metaId,
Species species)
Creates a new
QualitativeSpecies , based on an existing Species ,
adds it to this QualitativeModel and returns it. |
Transition |
createTransition()
Creates a new
Transition inside this QualitativeModel and returns it. |
Transition |
createTransition(java.lang.String id)
Creates a new
Transition inside this QualitativeModel and returns it. |
Transition |
createTransition(java.lang.String id,
Input in,
Output out) |
boolean |
getAllowsChildren() |
SBase |
getChildAt(int childIndex) |
int |
getChildCount() |
java.lang.String |
getElementNamespace()
Returns the XML namespace (URI) of the package extension of this plugin object.
|
ListOf<QualitativeSpecies> |
getListOfQualitativeSpecies() |
ListOf<Transition> |
getListOfTransitions() |
Model |
getModel()
Returns the
Model |
java.lang.String |
getPackageName()
Returns the package name of this plugin object.
|
SBMLDocument |
getParent() |
SBMLDocument |
getParentSBMLObject()
Returns the parent
SBase object to which this plugin object connected. |
java.lang.String |
getPrefix()
Returns the prefix of the package extension of this plugin object.
|
QualitativeSpecies |
getQualitativeSpecies(int i)
Gets the ith
QualitativeSpecies . |
QualitativeSpecies |
getQualitativeSpecies(java.lang.String id)
Gets the
QualitativeSpecies that has the given id. |
Transition |
getTransition(int i)
Gets the ith
Transition . |
Transition |
getTransition(java.lang.String id)
Gets the
Transition that has the given id. |
java.lang.String |
getURI()
Gets the URI to which this element belongs to.
|
boolean |
isSetListOfQualitativeSpecies()
Returns
true if the listOfQualitativeSpecies is set. |
boolean |
isSetListOfTransitions()
Returns
true if the listOfTransitions is set. |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value)
Reads and sets the attribute if it is know from this
SBasePlugin . |
boolean |
removeQualitativeSpecies(QualitativeSpecies qualitativeSpecies) |
boolean |
removeTransition(Transition transition) |
void |
setListOfQualitativeSpecies(ListOf<QualitativeSpecies> listOfQualitativeSpecies) |
void |
setListOfTransitions(ListOf<Transition> listOfTransitions) |
boolean |
unsetListOfQualitativeSpecies() |
boolean |
unsetListOfTransitions() |
java.util.Map<java.lang.String,java.lang.String> |
writeXMLAttributes()
Returns a
Map containing the XML attributes of this object. |
equals, getExtendedSBase, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase
addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet
finalize, getClass, notify, notifyAll, wait, wait, wait
addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet
private static final long serialVersionUID
private ListOf<QualitativeSpecies> listOfQualitativeSpecies
private ListOf<Transition> listOfTransitions
public QualitativeModel(Model model)
model
- public QualitativeModel(QualitativeModel qualitativeModel)
qualitativeModel
- public java.lang.String getElementNamespace()
SBasePlugin
public java.lang.String getPackageName()
SBasePlugin
public java.lang.String getPrefix()
SBasePlugin
public java.lang.String getURI()
SBasePlugin
public SBMLDocument getParent()
getParent
in interface javax.swing.tree.TreeNode
getParent
in class AbstractTreeNode
public SBMLDocument getParentSBMLObject()
SBasePlugin
SBase
object to which this plugin object connected.getParentSBMLObject
in interface SBasePlugin
getParentSBMLObject
in class AbstractSBasePlugin
SBase
object to which this plugin object connected.public void addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)
QualitativeSpecies
to the model.qualitativeSpecies
- the qualitativeSpecies to add.public void addTransition(Transition transition)
transition
- public QualitativeModel clone()
clone
in interface SBasePlugin
clone
in class AbstractSBasePlugin
public boolean getAllowsChildren()
public SBase getChildAt(int childIndex)
public int getChildCount()
public Transition createTransition()
Transition
inside this QualitativeModel
and returns it.
Transition
object created
addTransition(Transition r)
public Transition createTransition(java.lang.String id)
Transition
inside this QualitativeModel
and returns it.id
- the id of the new element to createTransition
object createdpublic Transition createTransition(java.lang.String id, Input in, Output out)
id
- in
- out
- public QualitativeSpecies createQualitativeSpecies()
QualitativeSpecies
inside this QualitativeModel
and returns it.
QualitativeSpecies
object created
addSpecies(QualitativeSpecies s)
public QualitativeSpecies createQualitativeSpecies(java.lang.String id)
QualitativeSpecies
inside this QualitativeModel
and returns it.id
- the id of the new element to createQualitativeSpecies
object createdpublic QualitativeSpecies createQualitativeSpecies(java.lang.String id, java.lang.String compartment, boolean constant)
QualitativeSpecies
inside this QualitativeModel
and returns it.id
- the id of the new element to createQualitativeSpecies
object createdpublic QualitativeSpecies createQualitativeSpecies(java.lang.String id, java.lang.String metaId, Species species)
QualitativeSpecies
, based on an existing Species
,
adds it to this QualitativeModel
and returns it.id
- the id of the new element to createmetaId
- the metaId of the new element to createspecies
- a template to copy fields fromQualitativeSpecies
object createdpublic boolean addSpecies(QualitativeSpecies spec)
QualitativeSpecies
instance to the listOfSpecies of this Model.spec
- true
if the QualitativeSpecies
was added successfully.public QualitativeSpecies createQualitativeSpecies(java.lang.String id, Compartment c)
public ListOf<QualitativeSpecies> getListOfQualitativeSpecies()
public ListOf<Transition> getListOfTransitions()
public boolean removeTransition(Transition transition)
transition
- to remove from the listOfTransitionsTRUE
if the operation was successfulpublic boolean removeQualitativeSpecies(QualitativeSpecies qualitativeSpecies)
QualitativeSpecies
- to remove from the listOfQualitativeSpeciesTRUE
if the operation was successfulpublic QualitativeSpecies getQualitativeSpecies(int i)
QualitativeSpecies
.i
- QualitativeSpecies
java.lang.IndexOutOfBoundsException
- is the index is invalid.public QualitativeSpecies getQualitativeSpecies(java.lang.String id)
QualitativeSpecies
that has the given id.id
- QualitativeSpecies
that has the given id or null if
no QualitativeSpecies
are found that match id
.public boolean containsQualitativeSpecies(QualitativeSpecies qs)
qs
- true
if qs
is already part of this QualitativeModel
public Transition getTransition(int i)
Transition
.i
- Transition
.java.lang.IndexOutOfBoundsException
- is the index is invalid.public Transition getTransition(java.lang.String id)
Transition
that has the given id.id
- Transition
that has the given id or null if
no Transition
are found that match id
.public boolean isSetListOfQualitativeSpecies()
true
if the listOfQualitativeSpecies is set.true
if the listOfQualitativeSpecies is set.public boolean isSetListOfTransitions()
true
if the listOfTransitions is set.true
if the listOfTransitions is set.public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBasePlugin
SBasePlugin
.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 setListOfQualitativeSpecies(ListOf<QualitativeSpecies> listOfQualitativeSpecies)
listOfQualitativeSpecies
- public void setListOfTransitions(ListOf<Transition> listOfTransitions)
listOfTransitions
- public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBasePlugin
Map
containing the XML attributes of this object.writeXMLAttributes
in interface SBasePlugin
writeXMLAttributes
in class AbstractSBasePlugin
Map
containing the XML attributes of this object.public boolean unsetListOfTransitions()
true
is successfulpublic boolean unsetListOfQualitativeSpecies()
true
is successful