biouml.standard.type
Class Reaction

java.lang.Object
  com.beanexplorer.beans.Option
      ru.biosoft.access.MutableDataElementSupport
          biouml.standard.type.BaseSupport
              biouml.standard.type.GenericEntity
                  biouml.standard.type.Referrer
                      biouml.standard.type.Reaction

All Implemented Interfaces:

Base, DataCollection, DataElement, FormulaDelegate, MutableDataElement, Type

Direct Known Subclasses:

Reaction

public class Reaction

extends Referrer

implements DataCollection, FormulaDelegate

Field Summary

protected VectorDataCollection	collection Primary collection.
protected boolean	fast
protected KineticLaw	kineticLaw
protected static org.apache.log4j.Category	log
static java.text.DecimalFormat	NAME_FORMAT Format to generate unique name for new reaction instance.
protected boolean	reversible

Fields inherited from class biouml.standard.type.GenericEntity

comment

Fields inherited from class biouml.standard.type.BaseSupport

title, type

Fields inherited from class ru.biosoft.access.MutableDataElementSupport

name

Fields inherited from class com.beanexplorer.beans.Option

notificationEnabled, propagationEnabled

Fields inherited from interface ru.biosoft.access.DataCollection

CHILDREN_NODE_IMAGE, CHILDREN_NODE_VISIBLE, CLASS_PROPERTY, CLASSPATH_JAR_PROPERTY, COMPARATOR_OBJECT, CONFIG_FILE_PROPERTY, CONFIG_PATH_PROPERTY, DATA_ELEMENT_CLASS_PROPERTY, DEFAULT_CONFIG_FILE, DEFAULT_CONFIG_SUFFIX, DEFAULT_FILTER_CONFIG_SUFFIX, DEFAULT_FORMAT_CONFIG_SUFFIX, DEFAULT_NODE_CONFIG_SUFFIX, DEFAULT_REPOSITORY, DESCRIPTION_PROPERTY, DISPLAY_NAME_PROPERTY, FILE_PATH_PROPERTY, FILE_PROPERTY, FILTER_PROPERTY, ID_FORMAT, IS_ROOT, JOB_CONTROL_PROPERTY, LATE_CHILDREN_INITIALIZATION, MUTABLE, NAME_PROPERTY, NEXT_CONFIG, NODE_IMAGE, NODE_VISIBLE, PRIMARY_COLLECTION, REMOVE_CHILDREN, TRANSFORMER_CLASS

Fields inherited from interface biouml.standard.type.Type

CONSTANT, DATABASE_INFO, DIAGRAM_INFO, MATH, MATH_EQUATION, MATH_EVENT, MATH_FUNCTION, MATH_STATE, MATH_TRANSITION, TYPE_CELL, TYPE_CHEMICAL_ROLE, TYPE_COMPARTMENT, TYPE_CONCEPT, TYPE_DIAGRAM_REFERENCE, TYPE_FUNCTION, TYPE_GENE, TYPE_MOLECULE, TYPE_NOTE, TYPE_NOTE_LINK, TYPE_PROCESS, TYPE_PROTEIN, TYPE_REACTION, TYPE_RELATION, TYPE_RNA, TYPE_SEMANTIC_RELATION, TYPE_STATE, TYPE_SUBSTANCE, TYPE_UNKNOWN

Constructor Summary

Reaction(DataCollection origin, java.lang.String name)

Method Summary

void	addDataCollectionListener(DataCollectionListener l) Add a listener to the list that's notified each time a change to the data collection occurs.
void	close() Closes data collection, releases all resources.
boolean	contains(DataElement de) Returns true if this data collection contains the specified element, false otherwise
boolean	contains(java.lang.String name) Returns true if this data collection contains the element with the specified name, false otherwise
DataElement	get(java.lang.String name) Returns the DataElement with the specified name.
java.lang.String	getCompleteName() Returns complete name of data collection.
java.lang.Class	getDataElementType() Returns the type of DataElements stored in the data collection.
java.lang.String	getFormula()
DataCollectionInfo	getInfo() Returns additional info for this data collection.
KineticLaw	getKineticLaw()
java.util.List	getNameList() Returns an unmodifiable view of the data element name list.
int	getSize() Returns the number of elements in this data collection.
SpecieReference[]	getSpecieReferences()
java.lang.String	getSpecieTitle(java.lang.Integer index, java.lang.Object obj)
java.lang.String	getType()
void	init()
boolean	isFast()
boolean	isMutable() Returns true if this data collection is mutable, false otherwise.
boolean	isPropagationEnabled()
boolean	isReversible()
java.util.Iterator	iterator() Returns an iterator over the data elements in this collection.
void	propagateElementChanged(DataCollection source, DataCollectionEvent primaryEvent)
void	propagateElementWillChange(DataCollection source, DataCollectionEvent primaryEvent)
DataElement	put(DataElement obj) Adds the specified data element to the collection.
void	release(java.lang.String dataElementName) Release DataElement with the specified name from the DataCollection cache.
void	remove(java.lang.String name) Removes the specified data element from the collection, if present.
void	removeDataCollectionListener(DataCollectionListener l) Remove a listener from the list that's notified each time a change to the data collection occurs.
void	setFast(boolean fast)
void	setKineticLaw(KineticLaw kineticLaw)
void	setPropagationEnabled(boolean propagationEnabled)
void	setReversible(boolean reversible)
void	setSpecieReferences(SpecieReference[] species) Should be used only to load initial set of specie references.

Methods inherited from class biouml.standard.type.Referrer

getDatabaseReferences, getDescription, getLiteratureReferences, setDatabaseReferences, setDescription, setLiteratureReferences

Methods inherited from class biouml.standard.type.GenericEntity

getComment, getDate, setComment, setDate

Methods inherited from class biouml.standard.type.BaseSupport

getTitle, setTitle

Methods inherited from class ru.biosoft.access.MutableDataElementSupport

getName, getOrigin, toString

Methods inherited from class com.beanexplorer.beans.Option

addPropertyChangeListener, copyListenersTo, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getParent, isNotificationEnabled, removePropertyChangeListener, setNotificationEnabled, setParent

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ru.biosoft.access.DataCollection

isNotificationEnabled, setNotificationEnabled

Methods inherited from interface ru.biosoft.access.DataElement

getName, getOrigin

Methods inherited from interface biouml.model.dynamics.FormulaDelegate

addPropertyChangeListener, removePropertyChangeListener

Methods inherited from interface ru.biosoft.access.MutableDataElement

addPropertyChangeListener, removePropertyChangeListener

Field Detail

log

protected static org.apache.log4j.Category log

NAME_FORMAT

public static java.text.DecimalFormat NAME_FORMAT

Format to generate unique name for new reaction instance.

kineticLaw

protected KineticLaw kineticLaw

reversible

protected boolean reversible

fast

protected boolean fast

collection

protected VectorDataCollection collection

Primary collection.

Constructor Detail

Reaction

public Reaction(DataCollection origin,
                java.lang.String name)

Method Detail

getType

public java.lang.String getType()

Specified by:

getType in interface Base

Overrides:

getType in class BaseSupport

getSpecieTitle

public java.lang.String getSpecieTitle(java.lang.Integer index,
                                       java.lang.Object obj)

getSpecieReferences

public SpecieReference[] getSpecieReferences()

setSpecieReferences

public void setSpecieReferences(SpecieReference[] species)

Should be used only to load initial set of specie references.

getKineticLaw

public KineticLaw getKineticLaw()

setKineticLaw

public void setKineticLaw(KineticLaw kineticLaw)

isReversible

public boolean isReversible()

setReversible

public void setReversible(boolean reversible)

isFast

public boolean isFast()

setFast

public void setFast(boolean fast)

getFormula

public java.lang.String getFormula()

Specified by:

getFormula in interface FormulaDelegate

getInfo

public DataCollectionInfo getInfo()

Description copied from interface: DataCollection

Returns additional info for this data collection. Can return null.

Specified by:

getInfo in interface DataCollection

Returns:

Additional info for this data collection.

See Also:

DataCollectionInfo

getSize

public int getSize()

Description copied from interface: DataCollection

Returns the number of elements in this data collection.

Specified by:

getSize in interface DataCollection

Returns:

Size of this data collection.

getDataElementType

public java.lang.Class getDataElementType()

Description copied from interface: DataCollection

Returns the type of DataElements stored in the data collection.

Specified by:

getDataElementType in interface DataCollection

Returns:

Type of DataElements stored in the data collection.

isMutable

public boolean isMutable()

Description copied from interface: DataCollection

Returns true if this data collection is mutable, false otherwise.

Specified by:

isMutable in interface DataCollection

Returns:

true if primary data collection is mutable,
false otherwise..

contains

public boolean contains(java.lang.String name)

Description copied from interface: DataCollection

Returns true if this data collection contains the element with the specified name, false otherwise

Specified by:

contains in interface DataCollection

Parameters:

name - name of data element

Returns:

true if this data collection contains the element with specified name,
false otherwise

contains

public boolean contains(DataElement de)

Description copied from interface: DataCollection

Returns true if this data collection contains the specified element, false otherwise

Specified by:

contains in interface DataCollection

Parameters:

de - specified data element

Returns:

true if this data collection contains the element wit specified name,
false otherwise

iterator

public java.util.Iterator iterator()

Description copied from interface: DataCollection

Returns an iterator over the data elements in this collection. There are no guarantees concerning the order in which the elements are returned. If the data collection is modified while an iteration over it is in progress, the results of the iteration are undefined.

Specified by:

iterator in interface DataCollection

getNameList

public java.util.List getNameList()

Description copied from interface: DataCollection

Returns an unmodifiable view of the data element name list. Query operations on the returned list "read through" to the internal name list, and attempts to modify the returned list, whether direct or via its iterator, result in an UnsupportedOperationException. The returned list is backed by the data collection, so changes to the data collection are reflected in the returned list. The name list can be sorted or unsorted depending on the DataCollection implementing class.

Specified by:

getNameList in interface DataCollection

Returns:

list of names

get

public DataElement get(java.lang.String name)
                throws java.lang.Exception

Description copied from interface: DataCollection

Returns the DataElement with the specified name. Returns null if the data collection contains no data element for this name.

Specified by:

get in interface DataCollection

Throws:

java.lang.Exception

put

public DataElement put(DataElement obj)
                throws java.lang.Exception

Description copied from interface: DataCollection

Adds the specified data element to the collection. If the data collection previously contained the specified element, the old value is replaced.

Specified by:

put in interface DataCollection

Returns:

previous version of the data element, or null if there was no one.

Throws:

java.lang.Exception

See Also:

DataCollection.isMutable()

remove

public void remove(java.lang.String name)
            throws java.lang.Exception

Description copied from interface: DataCollection

Removes the specified data element from the collection, if present. Notifies all listeners if the data element was removed.

Specified by:

remove in interface DataCollection

Returns:

the removed data element.

Throws:

java.lang.Exception - If error occured.

See Also:

DataCollection.isMutable()

addDataCollectionListener

public void addDataCollectionListener(DataCollectionListener l)

Description copied from interface: DataCollection

Add a listener to the list that's notified each time a change to the data collection occurs.

Specified by:

addDataCollectionListener in interface DataCollection

Parameters:

l - the DataCollectionListener

removeDataCollectionListener

public void removeDataCollectionListener(DataCollectionListener l)

Description copied from interface: DataCollection

Remove a listener from the list that's notified each time a change to the data collection occurs.

Specified by:

removeDataCollectionListener in interface DataCollection

Parameters:

l - the DataCollectionListener

getCompleteName

public java.lang.String getCompleteName()

Description copied from interface: DataCollection

Returns complete name of data collection.

Specified by:

getCompleteName in interface DataCollection

Returns:

Full name of DataCollection in the tree hierarchy.

close

public void close()
           throws java.lang.Exception

Description copied from interface: DataCollection

Closes data collection, releases all resources. This method invalidates DataCollection instance.

Specified by:

close in interface DataCollection

Throws:

java.lang.Exception - If error occured.

init

public void init()

release

public void release(java.lang.String dataElementName)

Description copied from interface: DataCollection

Release DataElement with the specified name from the DataCollection cache.

Specified by:

release in interface DataCollection

isPropagationEnabled

public boolean isPropagationEnabled()

Specified by:

isPropagationEnabled in interface DataCollection

setPropagationEnabled

public void setPropagationEnabled(boolean propagationEnabled)

Specified by:

setPropagationEnabled in interface DataCollection

propagateElementWillChange

public void propagateElementWillChange(DataCollection source,
                                       DataCollectionEvent primaryEvent)

Specified by:

propagateElementWillChange in interface DataCollection

propagateElementChanged

public void propagateElementChanged(DataCollection source,
                                    DataCollectionEvent primaryEvent)

Specified by:

propagateElementChanged in interface DataCollection