charite.christo.metannogen
Interface ReactionCollection

All Known Implementing Classes:

MReactionCollection

public interface ReactionCollection

Method Summary

String	getID() The ID like "KEGG" or "EHM".
String[]	getListOfCompartments() List of all compartments in this network.
CharSequence	getNameForID(String ID) Return a human readable name of the metabolite or reaction with this ID or null if no object with this ID exists.
long	getOptions() See Reaction#UNIQUE, FILTER_REJECTED_DATASETS, FILTER_NOT_EXCLUDED
Reaction[]	getReactions() Flat list of reactions.
Reaction[]	getReactionsGroupped() List of reactions.
Reaction[]	getReactionsWithMetabolite(String metabolite) Search for reactions with a certain metabolite.
String[]	getSubstratesAndProducts() List of all metabolites in this network.

Method Detail

getOptions

long getOptions()

See Reaction#UNIQUE, FILTER_REJECTED_DATASETS, FILTER_NOT_EXCLUDED

getReactions

Reaction[] getReactions()

Flat list of reactions. The list may contain Reactions with the same stoichiometry but differing by compartment.

getReactionsGroupped

Reaction[] getReactionsGroupped()

List of reactions. If there are identical Reactions differing only by compartment, then only one of those is include. The others are obtained with Reaction#getReactionsWithThisStoichiometry();.

getReactionsWithMetabolite

Reaction[] getReactionsWithMetabolite(String metabolite)

Search for reactions with a certain metabolite.

getSubstratesAndProducts

String[] getSubstratesAndProducts()

List of all metabolites in this network.

getListOfCompartments

String[] getListOfCompartments()

List of all compartments in this network.

getID

String getID()

The ID like "KEGG" or "EHM". If loaded from an SBML file then the ID is the file name.

getNameForID

CharSequence getNameForID(String ID)

Return a human readable name of the metabolite or reaction with this ID or null if no object with this ID exists.