public class CRNReaction extends CRNEntity
docA, docB, id, labelA, labelB, singleDoc
DELETE, INSERT, MODIFIED, UNMODIFIED
Constructor and Description |
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CRNReaction(CRN crn,
String labelA,
String labelB,
de.unirostock.sems.xmlutils.ds.DocumentNode docA,
de.unirostock.sems.xmlutils.ds.DocumentNode docB,
CRNCompartment compartmentA,
CRNCompartment compartmentB,
boolean reversible)
Instantiates a new cRN reaction.
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Modifier and Type | Method and Description |
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void |
addInputA(CRNSubstance subst,
SBOTerm sbo)
Add a reactant of this reaction in its original version.
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void |
addInputB(CRNSubstance subst,
SBOTerm sbo)
Add a reactant of this reaction in its modified version.
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void |
addModA(CRNSubstance subst,
SBOTerm sbo)
Adds the modifier of this reaction in its original version.
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void |
addModB(CRNSubstance subst,
SBOTerm sbo)
Add a modifier of this reaction in its modified version.
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void |
addOutputA(CRNSubstance subst,
SBOTerm sbo)
Add a product of this reaction in its original version.
|
void |
addOutputB(CRNSubstance subst,
SBOTerm sbo)
Add a product of this reaction in its modified version.
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CRNCompartment |
getCompartment()
Gets the compartment.
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Collection<CRNSubstanceRef> |
getInputs()
Gets the reactants.
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int |
getModification()
Gets the modification of this entity.
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Collection<CRNSubstanceRef> |
getModifiers()
Gets the modifiers.
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Collection<CRNSubstanceRef> |
getOutputs()
Gets the products.
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String |
getSBO()
Gets the sbo.
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boolean |
isReversible()
Checks if is reversible.
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void |
setCompartmentA(CRNCompartment compartment)
Sets the compartment in original version.
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void |
setCompartmentB(CRNCompartment compartment)
Sets the compartment in modified version.
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void |
setSingleDocument()
Sets the single document flag.
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public CRNReaction(CRN crn, String labelA, String labelB, de.unirostock.sems.xmlutils.ds.DocumentNode docA, de.unirostock.sems.xmlutils.ds.DocumentNode docB, CRNCompartment compartmentA, CRNCompartment compartmentB, boolean reversible)
crn
- the chemical reaction networklabelA
- the label of that reaction in the original documentlabelB
- the label of that reaction in the modified documentdocA
- the original documentdocB
- the modified documentcompartmentA
- the compartment acompartmentB
- the compartment breversible
- the reversible flagpublic void setCompartmentA(CRNCompartment compartment)
compartment
- the compartment in original versionpublic void setCompartmentB(CRNCompartment compartment)
compartment
- the compartment in modified versionpublic CRNCompartment getCompartment()
public void addInputA(CRNSubstance subst, SBOTerm sbo)
subst
- the substancesbo
- the SBOTerm describing the interactionpublic void addOutputA(CRNSubstance subst, SBOTerm sbo)
subst
- the substancesbo
- the SBOTerm describing the interactionpublic void addModA(CRNSubstance subst, SBOTerm sbo) throws BivesUnsupportedException
subst
- the substancesbo
- the SBOTerm describing the modificationBivesUnsupportedException
- if one edges contains two types of modificationspublic void addInputB(CRNSubstance subst, SBOTerm sbo)
subst
- the substancesbo
- the SBOTerm describing the interactionpublic void addOutputB(CRNSubstance subst, SBOTerm sbo)
subst
- the substancesbo
- the SBOTerm describing the interactionpublic void addModB(CRNSubstance subst, SBOTerm sbo) throws BivesUnsupportedException
subst
- the substancesbo
- the SBOTerm describing the modificationBivesUnsupportedException
- if one edges contains two types of modificationspublic Collection<CRNSubstanceRef> getInputs()
public Collection<CRNSubstanceRef> getOutputs()
public Collection<CRNSubstanceRef> getModifiers()
public String getSBO()
public boolean isReversible()
public void setSingleDocument()
setSingleDocument
in class CRNEntity
public int getModification()
CRNEntity
getModification
in class CRNEntity
Copyright © 2014 SEMS project @ University of Rostock. All rights reserved.