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java.lang.Object jp.sbi.celldesigner.plugin.PluginSBase jp.sbi.celldesigner.plugin.PluginReaction
public class PluginReaction
This class wraps org.sbml.libsbml.Reaction for the plug-in.
Field Summary |
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Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase |
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sbase |
Constructor Summary | |
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PluginReaction()
Constructor |
protected |
PluginReaction(java.lang.String id)
Constructor |
Method Summary | |
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void |
addGLogicGate(PluginGLogicGate pgg)
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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()
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PluginRealLineInformationDataObjOfReactionLink |
getAllMyPostionInfomations(boolean bPrintDebugInfo)
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boolean |
getFast()
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java.lang.String |
getGateType()
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java.lang.String |
getId()
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PluginKineticLaw |
getKineticLaw()
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java.awt.Color |
getLineColor()
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double |
getLineWidth()
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PluginListOf |
getListOfGLogicGates()
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PluginListOf |
getListOfModifiers()
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PluginListOf |
getListOfProducts()
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PluginListOf |
getListOfReactants()
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PluginModifierSpeciesReference |
getModifier(int index)
Gets the PluginModifierSpeciesReference with the given index of this PluginReaction. |
java.lang.String |
getName()
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int |
getNumGLogicGates()
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int |
getNumModifiers()
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int |
getNumProducts()
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int |
getNumReactants()
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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()
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boolean |
getReversible()
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static boolean |
havePhenotypeInSrouce(PluginSBase pSbase)
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void |
removeGLogicGate(int index)
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void |
removeGLogicGate(PluginGLogicGate pgg)
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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)
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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)
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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 |
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addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, getNotes, getNotesString, getNumCVTerms, getParentSBase, getRelationFromCVTerm, setAnnotation, setAnnotationString, setCVTerm, setNotes, setNotes, setParentSBase, toSBML |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PluginReaction()
protected PluginReaction(java.lang.String id)
id
- Method Detail |
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public void update(PluginReaction reaction)
reaction
- public java.lang.String getId()
public boolean getFast()
public void setFast(boolean fast)
fast
- public boolean getReversible()
public void setReversible(boolean reversible)
reversible
- public java.lang.String getName()
public void setName(java.lang.String name)
name
- public void addReactant(PluginSpeciesReference ref)
ref
- PluginSpeciesReferencepublic void removeReactant(PluginSpeciesReference ref)
ref
- public void removeReactant(int index)
index
- public PluginSpeciesReference getReactant(int index)
index
-
public void addProduct(PluginSpeciesReference ref)
ref
- Productpublic void removeProduct(PluginSpeciesReference ref)
ref
- public void removeProduct(int index)
index
- public PluginSpeciesReference getProduct(int index)
index
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public void addModifier(PluginModifierSpeciesReference ref)
ref
- PluginModifierSpeciesReferencepublic void removeModifier(PluginModifierSpeciesReference ref)
ref
- public void removeModifier(int index)
index
- public PluginModifierSpeciesReference getModifier(int index)
index
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public PluginKineticLaw getKineticLaw()
public void setKineticLaw(PluginKineticLaw ki)
ki
- public java.awt.Color getLineColor()
public void setLineColor(java.awt.Color lineColor)
lineColor
- the color of reactionpublic double getLineWidth()
public void setLineWidth(double lineWidth)
lineWidth
- public PluginListOf getListOfModifiers()
public void setListOfModifiers(PluginListOf listOfModifiers)
listOfModifiers
- public PluginListOf getListOfProducts()
public void setListOfProducts(PluginListOf listOfProducts)
listOfProducts
- public PluginListOf getListOfReactants()
public void setListOfReactants(PluginListOf listOfReactants)
listOfReactants
- public java.lang.String getReactionType()
public void setReactionType(java.lang.String type)
type
- public int getNumReactants()
public int getNumProducts()
public int getNumModifiers()
public int getNumGLogicGates()
public void addGLogicGate(PluginGLogicGate pgg)
pgg
- public void removeGLogicGate(int index)
public void removeGLogicGate(PluginGLogicGate pgg)
public PluginListOf getListOfGLogicGates()
public void setListOfGLogicGates(PluginListOf listOfGLogicGates)
public PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations()
public PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations(boolean bPrintDebugInfo)
public java.lang.String getGateType()
public void setGateType(java.lang.String type)
public static final boolean havePhenotypeInSrouce(PluginSBase pSbase)
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