jp.sbi.celldesigner.plugin
Class CellDesignerPlugin

java.lang.Object
  jp.sbi.celldesigner.plugin.CellDesignerPlugin

All Implemented Interfaces:

CellDesignerPlug

public abstract class CellDesignerPlugin
extends java.lang.Object
implements CellDesignerPlug

Interface class of CellDesignerPlugin.

Author:

Constructor Summary

CellDesignerPlugin()

Method Summary

void	addCellDesignerPluginMenu(PluginMenu menu) Adds the menu for this plug-in to CellDesigner.
void	addCompartmentPopupMenu(PluginMenu menu) Adds the compartment popup menu to CellDesigner.
void	addCompartmentPopupMenuSeparator() Adds the boundary to the compartment popup menu of CellDesigner.
void	addReactionPopupMenu(PluginMenu menu) Adds the reaction popup menu to CellDesigner.
void	addReactionPopupMenuSeparator() Adds the boundary to the reaction popup menu of CellDesigner.
void	addSpeciesPopupMenu(PluginMenu menu) Adds the species popup menu to CellDesigner.
void	addSpeciesPopupMenuSeparator() Adds the boundary to the species popup menu of CellDesigner.
boolean	cloneCurrModel()
protected java.lang.String	createNewAliasId() Create NewAliasId
protected java.lang.String	createNewCompartmentId() Creates NewCompartmentId
protected java.lang.String	createNewReactionId() Creates NewReactionId
protected java.lang.String	createNewSpeciesId() Creates NewSpeciesId
boolean	doCircularLayout()
boolean	exportDrawAreaToImageFile(java.lang.String strOutputFileDirName, java.lang.String strOutputFileName, java.lang.String strOutputFileExtention)
PluginListOf	getAllModels() Deprecated.
PluginListOf	getAllSpeciesNodes()
PluginModel	getModel(java.lang.String id)
PluginListOf	getSelectedAllNode()
PluginListOf	getSelectedAllNode(PluginModel pluginModel)
PluginListOf	getSelectedCompartmentNode()
PluginListOf	getSelectedCompartmentNode(PluginModel pluginModel)
PluginModel	getSelectedModel()
PluginListOf	getSelectedReactionNode()
PluginListOf	getSelectedReactionNode(PluginModel pluginModel)
PluginListOf	getSelectedSpeciesNode()
PluginListOf	getSelectedSpeciesNode(PluginModel pluginModel)
boolean	isStarted()
void	modelClosed(SBase sbase) Called when Model is closed on CellDesigner.
void	modelOpened(SBase sbase) Called when Model is opened on CellDesigner.
void	modelSelectChanged(SBase sbase) Called when the selected Model is changed on CellDesigner.
boolean	notifySBaseAdded(PluginSBase sbase) notifySBaseAdded
boolean	notifySBaseChanged(PluginSBase sbase) notifySBaseChanged
boolean	notifySBaseDeleted(PluginSBase sbase) notifySBaseDeleted
void	SBaseAdded(SBase sbase) Called when a PluginSBase is added on CellDesigner.
void	SBaseAdded(jp.sbi.celldesigner.SpeciesAlias sbase, Species parent) Called when SBase is added on CellDesigner.
void	SBaseChanged(SBase sbase) Called when some properties of PluginSBase are changed on CellDesigner.
void	SBaseChanged(jp.sbi.celldesigner.SpeciesAlias sbase, Species parent) Called when some properties of SBase are changed on CellDesigner.
void	SBaseDeleted(SBase sbase) Called when PluginSBase is deleted on CellDesigner.
void	SBaseDeleted(jp.sbi.celldesigner.SpeciesAlias sbase, Species parent) Called when SBase is deleted on CellDesigner.
boolean	SBaseSelected()
void	setStarted(boolean isStarted) Sets the start flag Note: Set true if a plugin is invoked.

Methods inherited from class java.lang.Object

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

Methods inherited from interface jp.sbi.celldesigner.plugin.CellDesignerPlug

addPluginMenu

Constructor Detail

CellDesignerPlugin

public CellDesignerPlugin()

Method Detail

addCellDesignerPluginMenu

public void addCellDesignerPluginMenu(PluginMenu menu)

Adds the menu for this plug-in to CellDesigner.

Parameters:

PluginMenu -

addSpeciesPopupMenu

public void addSpeciesPopupMenu(PluginMenu menu)

Adds the species popup menu to CellDesigner.

Parameters:

PluginMenu -

addSpeciesPopupMenuSeparator

public void addSpeciesPopupMenuSeparator()

Adds the boundary to the species popup menu of CellDesigner.

addReactionPopupMenu

public void addReactionPopupMenu(PluginMenu menu)

Adds the reaction popup menu to CellDesigner.

Parameters:

PluginMenu -

addReactionPopupMenuSeparator

public void addReactionPopupMenuSeparator()

Adds the boundary to the reaction popup menu of CellDesigner.

addCompartmentPopupMenu

public void addCompartmentPopupMenu(PluginMenu menu)

Adds the compartment popup menu to CellDesigner.

Parameters:

PluginMenu -

addCompartmentPopupMenuSeparator

public void addCompartmentPopupMenuSeparator()

Adds the boundary to the compartment popup menu of CellDesigner.

getSelectedModel

public PluginModel getSelectedModel()

Returns:

The model selected on CellDesigner

getModel

public PluginModel getModel(java.lang.String id)

Returns:

the model with the given id or null if no such model exists.

getAllModels

@Deprecated
public PluginListOf getAllModels()

Deprecated.

Returns:

the list of all models opened on CellDesigner.

getSelectedSpeciesNode

public PluginListOf getSelectedSpeciesNode()

Returns:

the list of species selected on CellDesigner.

getSelectedSpeciesNode

public PluginListOf getSelectedSpeciesNode(PluginModel pluginModel)

Parameters:

pluginModel -

Returns:

the list of species selected on celldesigner

getAllSpeciesNodes

public PluginListOf getAllSpeciesNodes()

Returns:

the list of all species selected on CellDesigner.

getSelectedReactionNode

public PluginListOf getSelectedReactionNode()

Returns:

the list of reactions selected on CellDesigner.

getSelectedReactionNode

public PluginListOf getSelectedReactionNode(PluginModel pluginModel)

Parameters:

pluginModel -

Returns:

the list of reactions selected on CellDesigner.

getSelectedCompartmentNode

public PluginListOf getSelectedCompartmentNode()

Returns:

the list of compartments selected on CellDesigner.

getSelectedCompartmentNode

public PluginListOf getSelectedCompartmentNode(PluginModel pluginModel)

Parameters:

pluginModel -

Returns:

the list of compartments selected on CellDesigner.

getSelectedAllNode

public PluginListOf getSelectedAllNode()

Returns:

the list of all nodes selected on CellDesigner.

getSelectedAllNode

public PluginListOf getSelectedAllNode(PluginModel pluginModel)

Parameters:

pluginModel -

Returns:

the list of all nodes selected on CellDesigner

createNewSpeciesId

protected java.lang.String createNewSpeciesId()

Creates NewSpeciesId

Returns:

the new species id, or NULL if model is null.

createNewCompartmentId

protected java.lang.String createNewCompartmentId()

Creates NewCompartmentId

Returns:

the new compartment id

createNewReactionId

protected java.lang.String createNewReactionId()

Creates NewReactionId

Returns:

the new reaction id

createNewAliasId

protected java.lang.String createNewAliasId()

Create NewAliasId

Returns:

the new alias id

SBaseAdded

public void SBaseAdded(SBase sbase)

Description copied from interface: CellDesignerPlug

Called when a PluginSBase is added on CellDesigner.

Specified by:

SBaseAdded in interface CellDesignerPlug

Parameters:

sbase -

SBaseAdded

public void SBaseAdded(jp.sbi.celldesigner.SpeciesAlias sbase,
                       Species parent)

Description copied from interface: CellDesignerPlug

Called when SBase is added on CellDesigner.

Specified by:

SBaseAdded in interface CellDesignerPlug

Parameters:

sbase -

parent -

SBaseChanged

public void SBaseChanged(SBase sbase)

Description copied from interface: CellDesignerPlug

Called when some properties of PluginSBase are changed on CellDesigner.

Specified by:

SBaseChanged in interface CellDesignerPlug

Parameters:

sbase -

SBaseChanged

public void SBaseChanged(jp.sbi.celldesigner.SpeciesAlias sbase,
                         Species parent)

Description copied from interface: CellDesignerPlug

Called when some properties of SBase are changed on CellDesigner.

Specified by:

SBaseChanged in interface CellDesignerPlug

Parameters:

sbase -

parent -

SBaseDeleted

public void SBaseDeleted(SBase sbase)

Description copied from interface: CellDesignerPlug

Called when PluginSBase is deleted on CellDesigner.

Specified by:

SBaseDeleted in interface CellDesignerPlug

Parameters:

sbase -

SBaseDeleted

public void SBaseDeleted(jp.sbi.celldesigner.SpeciesAlias sbase,
                         Species parent)

Description copied from interface: CellDesignerPlug

Called when SBase is deleted on CellDesigner.

Specified by:

SBaseDeleted in interface CellDesignerPlug

Parameters:

sbase -

parent -

modelOpened

public void modelOpened(SBase sbase)

Description copied from interface: CellDesignerPlug

Called when Model is opened on CellDesigner.

Specified by:

modelOpened in interface CellDesignerPlug

Parameters:

sbase -

modelSelectChanged

public void modelSelectChanged(SBase sbase)

Description copied from interface: CellDesignerPlug

Called when the selected Model is changed on CellDesigner.

Specified by:

modelSelectChanged in interface CellDesignerPlug

Parameters:

sbase -

modelClosed

public void modelClosed(SBase sbase)

Description copied from interface: CellDesignerPlug

Called when Model is closed on CellDesigner.

Specified by:

modelClosed in interface CellDesignerPlug

Parameters:

sbase -

notifySBaseAdded

public boolean notifySBaseAdded(PluginSBase sbase)

notifySBaseAdded

Specified by:

notifySBaseAdded in interface CellDesignerPlug

Parameters:

sbase -

notifySBaseChanged

public boolean notifySBaseChanged(PluginSBase sbase)

notifySBaseChanged

Specified by:

notifySBaseChanged in interface CellDesignerPlug

Parameters:

sbase -

notifySBaseDeleted

public boolean notifySBaseDeleted(PluginSBase sbase)

notifySBaseDeleted

Specified by:

notifySBaseDeleted in interface CellDesignerPlug

Parameters:

sbase -

isStarted

public boolean isStarted()

Specified by:

isStarted in interface CellDesignerPlug

Returns:

true if this plugin is starting, false otherwise.

setStarted

public void setStarted(boolean isStarted)

Sets the start flag
Note: Set true if a plugin is invoked. If the parameter is false, the plugin can't receive any events from CellDesigner, or call the follwing methods:

 SBaseAdded(PluginSBase)
 SBaseChanged(PluginSBase)
 SBaseDeleted(PluginSBase)
 modelOpened(PluginSBase)
 modelSelectChanged(PluginSBase)
 modelClosed(PluginSBase)
 

Parameters:

true - if plug is starting, false otherwise.

exportDrawAreaToImageFile

public boolean exportDrawAreaToImageFile(java.lang.String strOutputFileDirName,
                                         java.lang.String strOutputFileName,
                                         java.lang.String strOutputFileExtention)

doCircularLayout

public boolean doCircularLayout()

cloneCurrModel

public boolean cloneCurrModel()

SBaseSelected

public boolean SBaseSelected()

Specified by:

SBaseSelected in interface CellDesignerPlug