public class CRN extends Object
A CRN contains compartments, which may contain species and reactions.
There may be directed connections between species and reactions representing relationships like reactants, products, modifiers etc.
see also ChemicalReactionNetwork
Constructor and Description |
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CRN()
Instantiates a new chemical reaction network.
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Modifier and Type | Method and Description |
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CRNCompartment |
getCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a compartment.
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Collection<CRNCompartment> |
getCompartments()
Gets the compartments.
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int |
getNextCompartmentID()
Gets the next compartment id.
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int |
getNextReactionID()
Gets the next reaction id.
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int |
getNextSubstanceID()
Gets the next substance id.
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CRNReaction |
getReaction(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a reaction.
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Collection<CRNReaction> |
getReactions()
Gets the reactions.
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CRNSubstance |
getSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a substance.
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Collection<CRNSubstance> |
getSubstances()
Gets the substances.
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static String |
modToString(int modification)
Convert a modification to a string representation.
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void |
setCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node,
CRNCompartment compartment)
Adds a compartment.
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void |
setReaction(de.unirostock.sems.xmlutils.ds.TreeNode node,
CRNReaction react)
Adds a reaction.
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void |
setSingleDocument()
Sets the single document flag for non-comparison graphs.
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void |
setSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node,
CRNSubstance subst)
Adds a substance.
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public Collection<CRNSubstance> getSubstances()
public Collection<CRNReaction> getReactions()
public Collection<CRNCompartment> getCompartments()
public int getNextSubstanceID()
public int getNextCompartmentID()
public int getNextReactionID()
public void setReaction(de.unirostock.sems.xmlutils.ds.TreeNode node, CRNReaction react)
node
- the nodereact
- the reactpublic void setSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node, CRNSubstance subst)
node
- the nodesubst
- the substpublic void setCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node, CRNCompartment compartment)
node
- the nodecompartment
- the compartmentpublic CRNSubstance getSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node)
node
- the nodepublic CRNReaction getReaction(de.unirostock.sems.xmlutils.ds.TreeNode node)
node
- the nodepublic CRNCompartment getCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node)
node
- the nodepublic void setSingleDocument()
public static String modToString(int modification)
modification
- the modificationCopyright © 2014 SEMS project @ University of Rostock. All rights reserved.