public abstract class CellDesignerPlugin extends java.lang.Object implements CellDesignerPlug
Constructor and Description |
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CellDesignerPlugin() |
Modifier and Type | Method and Description |
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void |
addCellDesignerPluginMenu(PluginMenu menu)
Adds the menu for this plug-in to CellDesigner.
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void |
addCompartmentPopupMenu(PluginMenu menu)
Adds the compartment popup menu to CellDesigner.
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void |
addCompartmentPopupMenuSeparator()
Adds the boundary to the compartment popup menu of CellDesigner.
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void |
addReactionPopupMenu(PluginMenu menu)
Adds the reaction popup menu to CellDesigner.
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void |
addReactionPopupMenuSeparator()
Adds the boundary to the reaction popup menu of CellDesigner.
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void |
addSpeciesPopupMenu(PluginMenu menu)
Adds the species popup menu to CellDesigner.
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void |
addSpeciesPopupMenuSeparator()
Adds the boundary to the species popup menu of CellDesigner.
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boolean |
cloneCurrModel() |
protected java.lang.String |
createNewAliasId()
Create NewAliasId
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protected java.lang.String |
createNewCompartmentId()
Creates NewCompartmentId
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protected java.lang.String |
createNewReactionId()
Creates NewReactionId
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protected java.lang.String |
createNewSpeciesId()
Creates NewSpeciesId
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boolean |
doCircularLayout()
Runs circular layout.
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boolean |
exportDrawAreaToImageFile(java.lang.String strOutputFileDirName,
java.lang.String strOutputFileName,
java.lang.String strOutputFileExtention) |
PluginListOf |
getAllModels()
Deprecated.
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PluginListOf |
getAllSpeciesNodes() |
PluginModel |
getModel(java.lang.String id) |
javax.swing.JMenu |
getPluginMenu() |
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(org.sbml.libsbml.SBase sbase)
Called when Model is closed on CellDesigner.
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void |
modelOpened(org.sbml.libsbml.SBase sbase)
Called when Model is opened on CellDesigner.
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void |
modelSelectChanged(org.sbml.libsbml.SBase sbase)
Called when the selected Model is changed on CellDesigner.
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boolean |
notifySBaseAdded(PluginSBase sbase)
notifySBaseAdded
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boolean |
notifySBaseChanged(PluginSBase sbase)
notifySBaseChanged
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boolean |
notifySBaseDeleted(PluginSBase sbase)
notifySBaseDeleted
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void |
SBaseAdded(org.sbml.libsbml.SBase sbase)
Called when SBase is added on CellDesigner.
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void |
SBaseAdded(jp.sbi.celldesigner.SpeciesAlias sbase,
org.sbml.libsbml.Species parent)
Called when SBase is added on CellDesigner.
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void |
SBaseChanged(org.sbml.libsbml.SBase sbase)
Called when some properties of SBase are changed on CellDesigner.
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void |
SBaseChanged(jp.sbi.celldesigner.SpeciesAlias sbase,
org.sbml.libsbml.Species parent)
Called when some properties of SBase are changed on CellDesigner.
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void |
SBaseDeleted(org.sbml.libsbml.SBase sbase)
Called when SBase is deleted on CellDesigner.
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void |
SBaseDeleted(jp.sbi.celldesigner.SpeciesAlias sbase,
org.sbml.libsbml.Species parent)
Called when SBase is deleted on CellDesigner.
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boolean |
SBaseSelected()
Notifies CelLDesigner when SBase is selected.
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void |
setStarted(boolean isStarted)
Sets the start flag
Note: Set true if a plugin is invoked. |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addPluginMenu, modelClosed, modelOpened, modelSelectChanged, SBaseAdded, SBaseChanged, SBaseDeleted
public void addCellDesignerPluginMenu(PluginMenu menu)
menu
- PluginMenupublic javax.swing.JMenu getPluginMenu()
public void addSpeciesPopupMenu(PluginMenu menu)
menu
- PluginMenupublic void addSpeciesPopupMenuSeparator()
public void addReactionPopupMenu(PluginMenu menu)
menu
- PluginMenupublic void addReactionPopupMenuSeparator()
public void addCompartmentPopupMenu(PluginMenu menu)
menu
- PluginMenupublic void addCompartmentPopupMenuSeparator()
public PluginModel getSelectedModel()
public PluginModel getModel(java.lang.String id)
id
- Model ID@Deprecated public PluginListOf getAllModels()
public PluginListOf getSelectedSpeciesNode()
public PluginListOf getSelectedSpeciesNode(PluginModel pluginModel)
pluginModel
- PluginModelpublic PluginListOf getAllSpeciesNodes()
public PluginListOf getSelectedReactionNode()
public PluginListOf getSelectedReactionNode(PluginModel pluginModel)
pluginModel
- PluginModelpublic PluginListOf getSelectedCompartmentNode()
public PluginListOf getSelectedCompartmentNode(PluginModel pluginModel)
pluginModel
- PluginModelpublic PluginListOf getSelectedAllNode()
public PluginListOf getSelectedAllNode(PluginModel pluginModel)
pluginModel
- PluginModelprotected java.lang.String createNewSpeciesId()
protected java.lang.String createNewCompartmentId()
protected java.lang.String createNewReactionId()
protected java.lang.String createNewAliasId()
public void SBaseAdded(org.sbml.libsbml.SBase sbase)
CellDesignerPlug
SBaseAdded
in interface CellDesignerPlug
sbase
- SBasepublic void SBaseAdded(jp.sbi.celldesigner.SpeciesAlias sbase, org.sbml.libsbml.Species parent)
CellDesignerPlug
SBaseAdded
in interface CellDesignerPlug
sbase
- SpeciesAliasparent
- Speciespublic void SBaseChanged(org.sbml.libsbml.SBase sbase)
CellDesignerPlug
SBaseChanged
in interface CellDesignerPlug
sbase
- SBasepublic void SBaseChanged(jp.sbi.celldesigner.SpeciesAlias sbase, org.sbml.libsbml.Species parent)
CellDesignerPlug
SBaseChanged
in interface CellDesignerPlug
sbase
- SpeciesAliasparent
- Speciespublic void SBaseDeleted(org.sbml.libsbml.SBase sbase)
CellDesignerPlug
SBaseDeleted
in interface CellDesignerPlug
sbase
- SBasepublic void SBaseDeleted(jp.sbi.celldesigner.SpeciesAlias sbase, org.sbml.libsbml.Species parent)
CellDesignerPlug
SBaseDeleted
in interface CellDesignerPlug
sbase
- SpeciesAliasparent
- Speciespublic void modelOpened(org.sbml.libsbml.SBase sbase)
CellDesignerPlug
modelOpened
in interface CellDesignerPlug
sbase
- SBasepublic void modelSelectChanged(org.sbml.libsbml.SBase sbase)
CellDesignerPlug
modelSelectChanged
in interface CellDesignerPlug
sbase
- SBasepublic void modelClosed(org.sbml.libsbml.SBase sbase)
CellDesignerPlug
modelClosed
in interface CellDesignerPlug
sbase
- SBasepublic boolean notifySBaseAdded(PluginSBase sbase)
notifySBaseAdded
in interface CellDesignerPlug
sbase
- PluginSBasepublic boolean notifySBaseChanged(PluginSBase sbase)
notifySBaseChanged
in interface CellDesignerPlug
sbase
- PluginSBasepublic boolean notifySBaseDeleted(PluginSBase sbase)
notifySBaseDeleted
in interface CellDesignerPlug
sbase
- PluginSBasepublic boolean isStarted()
isStarted
in interface CellDesignerPlug
public void setStarted(boolean isStarted)
SBaseAdded(PluginSBase) SBaseChanged(PluginSBase) SBaseDeleted(PluginSBase) modelOpened(PluginSBase) modelSelectChanged(PluginSBase) modelClosed(PluginSBase)
isStarted
- true if plug is starting, false otherwise.public boolean exportDrawAreaToImageFile(java.lang.String strOutputFileDirName, java.lang.String strOutputFileName, java.lang.String strOutputFileExtention)
public boolean doCircularLayout()
public boolean cloneCurrModel()
public boolean SBaseSelected()
CellDesignerPlug
SBaseSelected
in interface CellDesignerPlug