java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, SBasePlugin
, TreeNodeWithChangeSupport
public class MultiSpeciesPlugin extends AbstractSBasePlugin
Constructor | Description |
---|---|
MultiSpeciesPlugin(MultiSpeciesPlugin multiSpecies) |
Creates a new
MultiSpeciesPlugin instance copied from the given MultiSpeciesPlugin . |
MultiSpeciesPlugin(Species species) |
Creates a new
MultiSpeciesPlugin instance, connected to the given 'core'
Species . |
Modifier and Type | Method | Description |
---|---|---|
boolean |
addOutwardBindingSite(OutwardBindingSite outwardBindingSite) |
Adds a new
OutwardBindingSite to the listOfOutwardBindingSites . |
boolean |
addSpeciesFeature(SpeciesFeature speciesFeature) |
Adds a new
SpeciesFeature to the listOfSpeciesFeatures . |
boolean |
addSubListOfSpeciesFeature(SubListOfSpeciesFeature SubListOfSpeciesFeature) |
Adds a new
SubListOfSpeciesFeature to the listOfSubListOfSpeciesFeatures . |
MultiSpeciesPlugin |
clone() |
Creates a new instance of
SBasePlugin from this SBasePlugin . |
OutwardBindingSite |
createOutwardBindingSite() |
Creates a new OutwardBindingSite element and adds it to the
listOfOutwardBindingSites list. |
SpeciesFeature |
createSpeciesFeature() |
Creates a new SpeciesFeature element and adds it to the
listOfSpeciesFeatures list. |
SpeciesFeature |
createSpeciesFeature(java.lang.String id) |
Creates a new
SpeciesFeature element and adds it to the
listOfSpeciesFeatures list. |
SubListOfSpeciesFeature |
createSubListOfSpeciesFeature() |
Creates a new SubListOfSpeciesFeature element and adds it to the
listOfSubListOfSpeciesFeatures list. |
SubListOfSpeciesFeature |
createSubListOfSpeciesFeature(java.lang.String id) |
Creates a new
SubListOfSpeciesFeature element and adds it to the
listOfSubListOfSpeciesFeatures list. |
boolean |
equals(java.lang.Object obj) |
|
boolean |
getAllowsChildren() |
|
SBase |
getChildAt(int childIndex) |
|
int |
getChildCount() |
|
ListOf<OutwardBindingSite> |
getListOfOutwardBindingSites() |
Returns the
listOfOutwardBindingSites . |
ListOf<SpeciesFeature> |
getListOfSpeciesFeatures() |
Returns the
listOfSpeciesFeatures . |
ListOf<SubListOfSpeciesFeature> |
getListOfSubListOfSpeciesFeatures() |
Returns the
listOfSubListOfSpeciesFeatures . |
int |
getNumOutwardBindingSites() |
Returns the number of
OutwardBindingSite s in this
MultiSpeciesPlugin . |
int |
getNumSpeciesFeatures() |
Returns the number of
SpeciesFeature s in this
MultiSpeciesPlugin . |
int |
getNumSubListOfSpeciesFeatures() |
Returns the number of
SubListOfSpeciesFeature s in this
MultiSpeciesPlugin . |
OutwardBindingSite |
getOutwardBindingSite(int i) |
Gets an element from the
listOfOutwardBindingSites at the given index. |
int |
getOutwardBindingSiteCount() |
Returns the number of
OutwardBindingSite s in this
MultiSpeciesPlugin . |
java.lang.String |
getPackageName() |
Returns the package name of this plugin object.
|
java.lang.String |
getPrefix() |
Returns the prefix of the package extension of this plugin object.
|
SpeciesFeature |
getSpeciesFeature(int i) |
Gets an element from the
listOfSpeciesFeatures at the given index. |
SpeciesFeature |
getSpeciesFeature(java.lang.String speciesFeatureId) |
Gets an element from the listOfSpeciesFeatures, with the given id.
|
int |
getSpeciesFeatureCount() |
Returns the number of
SpeciesFeature s in this
MultiSpeciesPlugin . |
java.lang.String |
getSpeciesType() |
Returns the value of
speciesType . |
SubListOfSpeciesFeature |
getSubListOfSpeciesFeature(int i) |
Gets an element from the
listOfSubListOfSpeciesFeatures at the given index. |
SubListOfSpeciesFeature |
getSubListOfSpeciesFeature(java.lang.String SubListOfSpeciesFeatureId) |
Gets an element from the listOfSubListOfSpeciesFeatures, with the given id.
|
int |
getSubListOfSpeciesFeatureCount() |
Returns the number of
SubListOfSpeciesFeature s in this
MultiSpeciesPlugin . |
java.lang.String |
getURI() |
Gets the URI to which this element belongs to.
|
int |
hashCode() |
|
boolean |
isSetListOfOutwardBindingSites() |
Returns
true if listOfOutwardBindingSites is not null. |
boolean |
isSetListOfSpeciesFeatures() |
Returns
true if listOfSpeciesFeatures is not null. |
boolean |
isSetListOfSubListOfSpeciesFeatures() |
Returns
true if listOfSubListOfSpeciesFeatures contains at least
one element. |
boolean |
isSetSpeciesType() |
Returns whether
speciesType 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 . |
OutwardBindingSite |
removeOutwardBindingSite(int i) |
Removes an element from the
listOfOutwardBindingSites at the given index. |
boolean |
removeOutwardBindingSite(OutwardBindingSite outwardBindingSite) |
Removes an element from the
listOfOutwardBindingSites . |
SpeciesFeature |
removeSpeciesFeature(int i) |
Removes an element from the
listOfSpeciesFeatures at the given index. |
SpeciesFeature |
removeSpeciesFeature(java.lang.String speciesFeatureId) |
Removes an element from the
listOfSpeciesFeatures . |
boolean |
removeSpeciesFeature(SpeciesFeature speciesFeature) |
Removes an element from the
listOfSpeciesFeatures . |
SubListOfSpeciesFeature |
removeSubListOfSpeciesFeature(int i) |
Removes an element from the
listOfSubListOfSpeciesFeatures at the given index. |
SubListOfSpeciesFeature |
removeSubListOfSpeciesFeature(java.lang.String SubListOfSpeciesFeatureId) |
Removes an element from the
listOfSubListOfSpeciesFeatures . |
boolean |
removeSubListOfSpeciesFeature(SubListOfSpeciesFeature SubListOfSpeciesFeature) |
Removes an element from the
listOfSubListOfSpeciesFeatures . |
void |
setListOfOutwardBindingSites(ListOf<OutwardBindingSite> listOfOutwardBindingSites) |
Sets the given
ListOf<OutwardBindingSite> . |
void |
setListOfSpeciesFeatures(ListOf<SpeciesFeature> listOfSpeciesFeatures) |
Sets the given
ListOf<SpeciesFeature> . |
void |
setListOfSubListOfSpeciesFeatures(ListOf<SubListOfSpeciesFeature> listOfSubListOfSpeciesFeatures) |
Sets the given
ListOf<SubListOfSpeciesFeature> . |
void |
setSpeciesType(java.lang.String speciesType) |
Sets the value of speciesType
|
boolean |
unsetListOfOutwardBindingSites() |
|
boolean |
unsetListOfSpeciesFeatures() |
|
boolean |
unsetListOfSubListOfSpeciesFeatures() |
|
boolean |
unsetSpeciesType() |
Unsets the variable speciesType.
|
java.util.Map<java.lang.String,java.lang.String> |
writeXMLAttributes() |
Returns a
Map containing the XML attributes of this object. |
fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getElementNamespace, getExtendedSBase, getLevel, getPackageVersion, getParentSBMLObject, getSBMLDocument, getVersion, isSetExtendedSBase, isSetPackageVersion, removeFromParent, setExtendedSBase, setNamespace, setPackageVersion
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getParent, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet
public MultiSpeciesPlugin(Species species)
MultiSpeciesPlugin
instance, connected to the given 'core'
Species
.species
- the core species that is extendedpublic MultiSpeciesPlugin(MultiSpeciesPlugin multiSpecies)
MultiSpeciesPlugin
instance copied from the given MultiSpeciesPlugin
.multiSpecies
- the element to copy/clone.public java.lang.String getPackageName()
SBasePlugin
public java.lang.String getPrefix()
SBasePlugin
public java.lang.String getURI()
SBasePlugin
SBasePlugin.getElementNamespace()
public MultiSpeciesPlugin clone()
SBasePlugin
SBasePlugin
from this SBasePlugin
.clone
in interface SBasePlugin
clone
in class AbstractSBasePlugin
SBasePlugin
from this SBasePlugin
.public boolean isSetListOfOutwardBindingSites()
true
if listOfOutwardBindingSites
is not null.true
if listOfOutwardBindingSites
is not null, false
otherwise.public ListOf<OutwardBindingSite> getListOfOutwardBindingSites()
listOfOutwardBindingSites
.
Creates it if it does not already exist.listOfOutwardBindingSites
.public void setListOfOutwardBindingSites(ListOf<OutwardBindingSite> listOfOutwardBindingSites)
ListOf<OutwardBindingSite>
.
If listOfOutwardBindingSites
was defined before and contains some
elements, they are all unset.listOfOutwardBindingSites
- the list of OutwardBindingSite
to set.public boolean unsetListOfOutwardBindingSites()
true
if listOfOutwardBindingSites
contains at least
one element, otherwise false
.public boolean addOutwardBindingSite(OutwardBindingSite outwardBindingSite)
OutwardBindingSite
to the listOfOutwardBindingSites
.
The listOfOutwardBindingSites is initialized if necessary.
outwardBindingSite
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean removeOutwardBindingSite(OutwardBindingSite outwardBindingSite)
listOfOutwardBindingSites
.outwardBindingSite
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public OutwardBindingSite removeOutwardBindingSite(int i)
listOfOutwardBindingSites
at the given index.i
- the index where to remove the OutwardBindingSite
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfOutwardBindingSites)
).public OutwardBindingSite createOutwardBindingSite()
listOfOutwardBindingSites
list.listOfOutwardBindingSites
public OutwardBindingSite getOutwardBindingSite(int i)
listOfOutwardBindingSites
at the given index.i
- the index of the OutwardBindingSite
element to get.java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size).public int getOutwardBindingSiteCount()
OutwardBindingSite
s in this
MultiSpeciesPlugin
.OutwardBindingSite
s in this
MultiSpeciesPlugin
.public int getNumOutwardBindingSites()
OutwardBindingSite
s in this
MultiSpeciesPlugin
.OutwardBindingSite
s in this
MultiSpeciesPlugin
.getOutwardBindingSiteCount()
public boolean isSetListOfSpeciesFeatures()
true
if listOfSpeciesFeatures
is not null.true
if listOfSpeciesFeatures
is not null, otherwise false
.public ListOf<SpeciesFeature> getListOfSpeciesFeatures()
listOfSpeciesFeatures
.
Creates it if it does not already exist.listOfSpeciesFeatures
.public void setListOfSpeciesFeatures(ListOf<SpeciesFeature> listOfSpeciesFeatures)
ListOf<SpeciesFeature>
.
If listOfSpeciesFeatures
was defined before and contains some
elements, they are all unset.listOfSpeciesFeatures
- the list of SpeciesFeature
to set.public boolean unsetListOfSpeciesFeatures()
true
if listOfSpeciesFeatures
contains at least
one element, otherwise false
.public boolean addSpeciesFeature(SpeciesFeature speciesFeature)
SpeciesFeature
to the listOfSpeciesFeatures
.
The listOfSpeciesFeatures is initialized if necessary.
speciesFeature
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean removeSpeciesFeature(SpeciesFeature speciesFeature)
listOfSpeciesFeatures
.speciesFeature
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public SpeciesFeature removeSpeciesFeature(java.lang.String speciesFeatureId)
listOfSpeciesFeatures
.speciesFeatureId
- the id of the element to be removed from the list.null
.public SpeciesFeature removeSpeciesFeature(int i)
listOfSpeciesFeatures
at the given index.i
- the index where to remove the SpeciesFeature
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfSpeciesFeatures)
).public SpeciesFeature createSpeciesFeature()
listOfSpeciesFeatures
list.listOfSpeciesFeatures
public SpeciesFeature createSpeciesFeature(java.lang.String id)
SpeciesFeature
element and adds it to the
listOfSpeciesFeatures
list.id
- the identifier that is to be applied to the new element.SpeciesFeature
element, which is the last
element in the listOfSpeciesFeatures
.public SpeciesFeature getSpeciesFeature(int i)
listOfSpeciesFeatures
at the given index.i
- the index of the SpeciesFeature
element to get.java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size).public SpeciesFeature getSpeciesFeature(java.lang.String speciesFeatureId)
speciesFeatureId
- the id of the SpeciesFeature
element to get.null
.public int getSpeciesFeatureCount()
SpeciesFeature
s in this
MultiSpeciesPlugin
.SpeciesFeature
s in this
MultiSpeciesPlugin
.public int getNumSpeciesFeatures()
SpeciesFeature
s in this
MultiSpeciesPlugin
.SpeciesFeature
s in this
MultiSpeciesPlugin
.getSpeciesFeatureCount()
public boolean isSetListOfSubListOfSpeciesFeatures()
true
if listOfSubListOfSpeciesFeatures
contains at least
one element.true
if listOfSubListOfSpeciesFeatures
contains at least
one element, otherwise false
.public ListOf<SubListOfSpeciesFeature> getListOfSubListOfSpeciesFeatures()
listOfSubListOfSpeciesFeatures
.
Creates it if it does not already exist.listOfSubListOfSpeciesFeatures
.public void setListOfSubListOfSpeciesFeatures(ListOf<SubListOfSpeciesFeature> listOfSubListOfSpeciesFeatures)
ListOf<SubListOfSpeciesFeature>
.
If listOfSubListOfSpeciesFeatures
was defined before and contains some
elements, they are all unset.listOfSubListOfSpeciesFeatures
- the list of SubListOfSpeciesFeature
spublic boolean unsetListOfSubListOfSpeciesFeatures()
true
if listOfSubListOfSpeciesFeatures
contains at least
one element, otherwise false
.public boolean addSubListOfSpeciesFeature(SubListOfSpeciesFeature SubListOfSpeciesFeature)
SubListOfSpeciesFeature
to the listOfSubListOfSpeciesFeatures
.
The listOfSubListOfSpeciesFeatures is initialized if necessary.
SubListOfSpeciesFeature
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean removeSubListOfSpeciesFeature(SubListOfSpeciesFeature SubListOfSpeciesFeature)
listOfSubListOfSpeciesFeatures
.SubListOfSpeciesFeature
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public SubListOfSpeciesFeature removeSubListOfSpeciesFeature(java.lang.String SubListOfSpeciesFeatureId)
listOfSubListOfSpeciesFeatures
.SubListOfSpeciesFeatureId
- the id of the element to be removed from the list.null
.public SubListOfSpeciesFeature removeSubListOfSpeciesFeature(int i)
listOfSubListOfSpeciesFeatures
at the given index.i
- the index where to remove the SubListOfSpeciesFeature
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfSubListOfSpeciesFeatures)
).public SubListOfSpeciesFeature createSubListOfSpeciesFeature()
listOfSubListOfSpeciesFeatures
list.listOfSubListOfSpeciesFeatures
public SubListOfSpeciesFeature createSubListOfSpeciesFeature(java.lang.String id)
SubListOfSpeciesFeature
element and adds it to the
listOfSubListOfSpeciesFeatures
list.id
- the identifier that is to be applied to the new element.SubListOfSpeciesFeature
element, which is the last
element in the listOfSubListOfSpeciesFeatures
.public SubListOfSpeciesFeature getSubListOfSpeciesFeature(int i)
listOfSubListOfSpeciesFeatures
at the given index.i
- the index of the SubListOfSpeciesFeature
element to get.java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size).public SubListOfSpeciesFeature getSubListOfSpeciesFeature(java.lang.String SubListOfSpeciesFeatureId)
SubListOfSpeciesFeatureId
- the id of the SubListOfSpeciesFeature
element to get.null
.public int getSubListOfSpeciesFeatureCount()
SubListOfSpeciesFeature
s in this
MultiSpeciesPlugin
.SubListOfSpeciesFeature
s in this
MultiSpeciesPlugin
.public int getNumSubListOfSpeciesFeatures()
SubListOfSpeciesFeature
s in this
MultiSpeciesPlugin
.SubListOfSpeciesFeature
s in this
MultiSpeciesPlugin
.getSubListOfSpeciesFeatureCount()
public java.lang.String getSpeciesType()
speciesType
.speciesType
.public boolean isSetSpeciesType()
speciesType
is set.speciesType
is set.public void setSpeciesType(java.lang.String speciesType)
speciesType
- the value of speciesType to be set.public boolean unsetSpeciesType()
true
if speciesType was set before, otherwise false
.public boolean getAllowsChildren()
public SBase getChildAt(int childIndex)
public int getChildCount()
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 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 int hashCode()
hashCode
in interface SBasePlugin
hashCode
in class AbstractSBasePlugin
public boolean equals(java.lang.Object obj)
equals
in interface SBasePlugin
equals
in class AbstractSBasePlugin