Package de.unirostock.sems.bives.ds.rn
Class ReactionNetwork
- java.lang.Object
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- de.unirostock.sems.bives.ds.rn.ReactionNetwork
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public class ReactionNetwork extends Object
The Class ReactionNetwork representing a reaction network.A ReactionNetwork 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 ReactionNetwork- Author:
- Martin Scharm
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Constructor Summary
Constructors Constructor Description ReactionNetwork()
Instantiates a new reaction network.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description ReactionNetworkCompartment
getCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a compartment.Collection<ReactionNetworkCompartment>
getCompartments()
Gets the compartments.int
getNextCompartmentID()
Gets the next compartment id.int
getNextReactionID()
Gets the next reaction id.int
getNextSubstanceID()
Gets the next substance id.ReactionNetworkReaction
getReaction(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a reaction.Collection<ReactionNetworkReaction>
getReactions()
Gets the reactions.ReactionNetworkSubstance
getSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a substance.Collection<ReactionNetworkSubstance>
getSubstances()
Gets the substances.static String
modToString(int modification)
Convert a modification to a string representation.void
setCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node, ReactionNetworkCompartment compartment)
Adds a compartment.void
setReaction(de.unirostock.sems.xmlutils.ds.TreeNode node, ReactionNetworkReaction react)
Adds a reaction.void
setSingleDocument()
Sets the single document flag for non-comparison graphs.void
setSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node, ReactionNetworkSubstance subst)
Adds a substance.
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Method Detail
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getSubstances
public Collection<ReactionNetworkSubstance> getSubstances()
Gets the substances.- Returns:
- the substances
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getReactions
public Collection<ReactionNetworkReaction> getReactions()
Gets the reactions.- Returns:
- the reactions
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getCompartments
public Collection<ReactionNetworkCompartment> getCompartments()
Gets the compartments.- Returns:
- the compartments
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getNextSubstanceID
public int getNextSubstanceID()
Gets the next substance id.- Returns:
- the next substance id
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getNextCompartmentID
public int getNextCompartmentID()
Gets the next compartment id.- Returns:
- the next compartment id
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getNextReactionID
public int getNextReactionID()
Gets the next reaction id.- Returns:
- the next reaction id
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setReaction
public void setReaction(de.unirostock.sems.xmlutils.ds.TreeNode node, ReactionNetworkReaction react)
Adds a reaction.- Parameters:
node
- the nodereact
- the react
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setSubstance
public void setSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node, ReactionNetworkSubstance subst)
Adds a substance.- Parameters:
node
- the nodesubst
- the subst
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setCompartment
public void setCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node, ReactionNetworkCompartment compartment)
Adds a compartment.- Parameters:
node
- the nodecompartment
- the compartment
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getSubstance
public ReactionNetworkSubstance getSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a substance.- Parameters:
node
- the node- Returns:
- the substance
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getReaction
public ReactionNetworkReaction getReaction(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a reaction.- Parameters:
node
- the node- Returns:
- the reaction
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getCompartment
public ReactionNetworkCompartment getCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node)
Gets a compartment.- Parameters:
node
- the node- Returns:
- the compartment
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setSingleDocument
public void setSingleDocument()
Sets the single document flag for non-comparison graphs.
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modToString
public static String modToString(int modification)
Convert a modification to a string representation.- Parameters:
modification
- the modification- Returns:
- the textual representation
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