de.unirostock.sems.bives.ds.rn

Class ReactionNetwork

java.lang.Object

de.unirostock.sems.bives.ds.rn.ReactionNetwork

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

Constructor Summary

Constructors

Constructor and Description
ReactionNetwork() Instantiates a new reaction network.

Method Summary

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ReactionNetwork

public ReactionNetwork()

Instantiates a new reaction network.

Method Detail

getSubstances

public Collection<ReactionNetworkSubstance> getSubstances()

Gets the substances.

Returns:

the substances

getReactions

public Collection<ReactionNetworkReaction> getReactions()

Gets the reactions.

Returns:

the reactions

getCompartments

public Collection<ReactionNetworkCompartment> getCompartments()

Gets the compartments.

Returns:

the compartments

getNextSubstanceID

public int getNextSubstanceID()

Gets the next substance id.

Returns:

the next substance id

getNextCompartmentID

public int getNextCompartmentID()

Gets the next compartment id.

Returns:

the next compartment id

getNextReactionID

public int getNextReactionID()

Gets the next reaction id.

Returns:

the next reaction id

setReaction

public void setReaction(de.unirostock.sems.xmlutils.ds.TreeNode node,
                        ReactionNetworkReaction react)

Adds a reaction.

Parameters:

node - the node

react - the react

setSubstance

public void setSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node,
                         ReactionNetworkSubstance subst)

Adds a substance.

Parameters:

node - the node

subst - the subst

setCompartment

public void setCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node,
                           ReactionNetworkCompartment compartment)

Adds a compartment.

Parameters:

node - the node

compartment - the compartment

getSubstance

public ReactionNetworkSubstance getSubstance(de.unirostock.sems.xmlutils.ds.TreeNode node)

Gets a substance.

Parameters:

node - the node

Returns:

the substance

getReaction

public ReactionNetworkReaction getReaction(de.unirostock.sems.xmlutils.ds.TreeNode node)

Gets a reaction.

Parameters:

node - the node

Returns:

the reaction

getCompartment

public ReactionNetworkCompartment getCompartment(de.unirostock.sems.xmlutils.ds.TreeNode node)

Gets a compartment.

Parameters:

node - the node

Returns:

the compartment

setSingleDocument

public void setSingleDocument()

Sets the single document flag for non-comparison graphs.

modToString

public static String modToString(int modification)

Convert a modification to a string representation.

Parameters:

modification - the modification

Returns:

the textual representation