jp.sbi.celldesigner.plugin
Class PluginReaction

java.lang.Object
  extended by jp.sbi.celldesigner.plugin.PluginSBase
      extended by jp.sbi.celldesigner.plugin.PluginReaction

public class PluginReaction
extends PluginSBase

This class wraps org.sbml.libsbml.Reaction for the plug-in.

Author:

Field Summary
 
Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase
sbase
 
Constructor Summary
  PluginReaction()
          Constructor
protected PluginReaction(java.lang.String id)
          Constructor
 
Method Summary
 void addGLogicGate(PluginGLogicGate pgg)
           
 void addModifier(PluginModifierSpeciesReference ref)
          Adds a PluginModifierSpeciesReference to this PluginReaction.
 void addProduct(PluginSpeciesReference ref)
          Adds Product (PluginSpeciesReference) to this PluginReaction.
 void addReactant(PluginSpeciesReference ref)
          Adds the given Reactant (PluginSpeciesReference) to this PluginReaction.
 PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations()
           
 PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations(boolean bPrintDebugInfo)
           
 boolean getFast()
           
 java.lang.String getGateType()
           
 java.lang.String getId()
           
 PluginKineticLaw getKineticLaw()
           
 java.awt.Color getLineColor()
           
 double getLineWidth()
           
 PluginListOf getListOfGLogicGates()
           
 PluginListOf getListOfModifiers()
           
 PluginListOf getListOfProducts()
           
 PluginListOf getListOfReactants()
           
 PluginModifierSpeciesReference getModifier(int index)
          Gets the PluginModifierSpeciesReference with the given index of this PluginReaction.
 java.lang.String getName()
           
 int getNumGLogicGates()
           
 int getNumModifiers()
           
 int getNumProducts()
           
 int getNumReactants()
           
 PluginSpeciesReference getProduct(int index)
          Gets the Product (PluginSpeciesReference) of this PluginReaction with the given index.
 PluginSpeciesReference getReactant(int index)
          Gets the Reactant (PluginSpeciesReference) with the given index from this PluginReaction.
 java.lang.String getReactionType()
           
 boolean getReversible()
           
static boolean havePhenotypeInSrouce(PluginSBase pSbase)
           
 void removeGLogicGate(int index)
           
 void removeGLogicGate(PluginGLogicGate pgg)
           
 void removeModifier(int index)
          Removes the PluginModifierSpeciesReference from this PluginReaction.
 void removeModifier(PluginModifierSpeciesReference ref)
          Removes a PluginModifierSpeciesReference from this PluginReaction.
 void removeProduct(int index)
          Removes the Product (PluginSpeciesReference) with the given index from this PluginReaction.
 void removeProduct(PluginSpeciesReference ref)
          Removes the given Product (PluginSpeciesReference) from this PluginReaction.
 void removeReactant(int index)
          Removes the Reactant with the given index from this PluginReaction.
 void removeReactant(PluginSpeciesReference ref)
          Removes the given Reactant (PluginSpeciesReference) from this PluginReaction.
 void setFast(boolean fast)
          Sets the fast status of this PluginReaction to the given value (boolean)
 void setGateType(java.lang.String type)
           
 void setKineticLaw(PluginKineticLaw ki)
          Sets the PluginKineticLaw of this PluginReaction.
 void setLineColor(java.awt.Color lineColor)
          Sets the lineColor of this PluginReaction.
 void setLineWidth(double lineWidth)
          Sets the line width of this PluginReaction.
 void setListOfGLogicGates(PluginListOf listOfGLogicGates)
           
 void setListOfModifiers(PluginListOf listOfModifiers)
          Sets the list of PluginModifierSpeciesReference of this PluginReaction.
 void setListOfProducts(PluginListOf listOfProducts)
          Sets the list of Products (PluginSpeciesReference) of this PluginReaction.
 void setListOfReactants(PluginListOf listOfReactants)
          Sets the list of Reactants (PluginSpeciesReference) of this PluginReaction.
 void setName(java.lang.String name)
          Sets the name of this PluginReaction.
 void setReactionType(java.lang.String type)
          Sets the type of this PluginReaction.
 void setReversible(boolean reversible)
          Sets the reversible status of this PluginReaction to the given value (boolean).
 void update(PluginReaction reaction)
          Update all properties of this PluginReaction to the same as the given PluginReaction.
 
Methods inherited from class jp.sbi.celldesigner.plugin.PluginSBase
addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, getNotes, getNotesString, getNumCVTerms, getParentSBase, getRelationFromCVTerm, setAnnotation, setAnnotationString, setCVTerm, setNotes, setNotes, setParentSBase, toSBML
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PluginReaction

public PluginReaction()
Constructor


PluginReaction

protected PluginReaction(java.lang.String id)
Constructor

Parameters:
id -
Method Detail

update

public void update(PluginReaction reaction)
Update all properties of this PluginReaction to the same as the given PluginReaction.

Parameters:
reaction -

getId

public java.lang.String getId()
Returns:
the id of this PluginReaction.

getFast

public boolean getFast()
Returns:
the fast status of this Reaction.

setFast

public void setFast(boolean fast)
Sets the fast status of this PluginReaction to the given value (boolean)

Parameters:
fast -

getReversible

public boolean getReversible()
Returns:
the reversible status of this PluginReaction.

setReversible

public void setReversible(boolean reversible)
Sets the reversible status of this PluginReaction to the given value (boolean).

Parameters:
reversible -

getName

public java.lang.String getName()
Returns:
the name of this PluginReaction.

setName

public void setName(java.lang.String name)
Sets the name of this PluginReaction.

Parameters:
name -

addReactant

public void addReactant(PluginSpeciesReference ref)
Adds the given Reactant (PluginSpeciesReference) to this PluginReaction.

Parameters:
ref - PluginSpeciesReference

removeReactant

public void removeReactant(PluginSpeciesReference ref)
Removes the given Reactant (PluginSpeciesReference) from this PluginReaction.

Parameters:
ref -

removeReactant

public void removeReactant(int index)
Removes the Reactant with the given index from this PluginReaction.

Parameters:
index -

getReactant

public PluginSpeciesReference getReactant(int index)
Gets the Reactant (PluginSpeciesReference) with the given index from this PluginReaction.

Parameters:
index -
Returns:
PluginSpeciesReference

addProduct

public void addProduct(PluginSpeciesReference ref)
Adds Product (PluginSpeciesReference) to this PluginReaction.

Parameters:
ref - Product

removeProduct

public void removeProduct(PluginSpeciesReference ref)
Removes the given Product (PluginSpeciesReference) from this PluginReaction.

Parameters:
ref -

removeProduct

public void removeProduct(int index)
Removes the Product (PluginSpeciesReference) with the given index from this PluginReaction.

Parameters:
index -

getProduct

public PluginSpeciesReference getProduct(int index)
Gets the Product (PluginSpeciesReference) of this PluginReaction with the given index.

Parameters:
index -
Returns:
PluginSpeciesReference

addModifier

public void addModifier(PluginModifierSpeciesReference ref)
Adds a PluginModifierSpeciesReference to this PluginReaction.

Parameters:
ref - PluginModifierSpeciesReference

removeModifier

public void removeModifier(PluginModifierSpeciesReference ref)
Removes a PluginModifierSpeciesReference from this PluginReaction.

Parameters:
ref -

removeModifier

public void removeModifier(int index)
Removes the PluginModifierSpeciesReference from this PluginReaction.

Parameters:
index -

getModifier

public PluginModifierSpeciesReference getModifier(int index)
Gets the PluginModifierSpeciesReference with the given index of this PluginReaction.

Parameters:
index -
Returns:
PluginModifierSpeciesReference

getKineticLaw

public PluginKineticLaw getKineticLaw()
Returns:
the PluginKineticLaw of this PluginReaction.

setKineticLaw

public void setKineticLaw(PluginKineticLaw ki)
Sets the PluginKineticLaw of this PluginReaction.

Parameters:
ki -

getLineColor

public java.awt.Color getLineColor()
Returns:
the lineColor of this PluginReaction.

setLineColor

public void setLineColor(java.awt.Color lineColor)
Sets the lineColor of this PluginReaction.

Parameters:
lineColor - the color of reaction

getLineWidth

public double getLineWidth()
Returns:
the line width of this PluginReaction.

setLineWidth

public void setLineWidth(double lineWidth)
Sets the line width of this PluginReaction.

Parameters:
lineWidth -

getListOfModifiers

public PluginListOf getListOfModifiers()
Returns:
the list of PluginModifierSpeciesReference of this PluginReaction.

setListOfModifiers

public void setListOfModifiers(PluginListOf listOfModifiers)
Sets the list of PluginModifierSpeciesReference of this PluginReaction.

Parameters:
listOfModifiers -

getListOfProducts

public PluginListOf getListOfProducts()
Returns:
the list of Products (PluginSpeciesReference) of this PluginReaction.

setListOfProducts

public void setListOfProducts(PluginListOf listOfProducts)
Sets the list of Products (PluginSpeciesReference) of this PluginReaction.

Parameters:
listOfProducts -

getListOfReactants

public PluginListOf getListOfReactants()
Returns:
the list of Reactants (PluginSpeciesReference) of this PluginReaction.

setListOfReactants

public void setListOfReactants(PluginListOf listOfReactants)
Sets the list of Reactants (PluginSpeciesReference) of this PluginReaction.

Parameters:
listOfReactants -

getReactionType

public java.lang.String getReactionType()
Returns:
the type of this PluginReaction.

setReactionType

public void setReactionType(java.lang.String type)
Sets the type of this PluginReaction.

Parameters:
type -

getNumReactants

public int getNumReactants()
Returns:
the number of Reactants of this PluginReaction.

getNumProducts

public int getNumProducts()
Returns:
the number of Products of this PluginReaction.

getNumModifiers

public int getNumModifiers()
Returns:
the number of Modifiers of this PluginReaction.

getNumGLogicGates

public int getNumGLogicGates()
Returns:
the number of GLogicGates of this PluginReaction.

addGLogicGate

public void addGLogicGate(PluginGLogicGate pgg)
Parameters:
pgg -

removeGLogicGate

public void removeGLogicGate(int index)

removeGLogicGate

public void removeGLogicGate(PluginGLogicGate pgg)

getListOfGLogicGates

public PluginListOf getListOfGLogicGates()

setListOfGLogicGates

public void setListOfGLogicGates(PluginListOf listOfGLogicGates)

getAllMyPostionInfomations

public PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations()

getAllMyPostionInfomations

public PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations(boolean bPrintDebugInfo)

getGateType

public java.lang.String getGateType()

setGateType

public void setGateType(java.lang.String type)

havePhenotypeInSrouce

public static final boolean havePhenotypeInSrouce(PluginSBase pSbase)