charite.christo.metannogen
Class MReactionCollection

java.lang.Object
  charite.christo.metannogen.MReactionCollection

All Implemented Interfaces:

ChCustomDictionaryProvider, ReactionCollection

public class MReactionCollection
extends Object
implements ReactionCollection, ChCustomDictionaryProvider

Method Summary

Class	getClazz()
Object[]	getCustomDictionaryWords() For JOrtho
EC_Class[]	getEC_Classes()
String	getID() The ID like "KEGG" or "EHM".
String[]	getListOfCompartments() List of all compartments in this network.
Map<String,EC_Class>	getMapEC2EC_Class()
Map<String,MReaction>	getMapId2Reaction()
Map<String,MSpecies>	getMapId2Species()
Map<String,MObject[]>	getMapName2ReactionOrSpecies()
String	getName()
String	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
Pathway[]	getPathwayObjects()
MReaction[]	getReactions() Flat list of reactions.
MReaction[]	getReactionsGroupped() List of reactions.
MReaction[]	getReactionsMappedSorted()
MReaction[]	getReactionsWithMetabolite(String m) Search for reactions with a certain metabolite.
MSpecies[]	getSpecies()
String[]	getSubstratesAndProducts() List of all metabolites in this network.
static void	loadDatasets(String f)
static Map	newDictionary(ByteArray ba)
static Map	newDictionary(File f)
void	setEC_Classes(EC_Class[] ee)
void	setID(String s)
MReactionCollection	setIsMutable(boolean b)
void	setMetaboliteObjects(MSpecies[] cc)
void	setMetabolites(MSpecies[] mm)
void	setPathwayObjects(Pathway[] pp)
void	setReactions(MReaction[] rr, long optionFlags)
Pathway	withoutPathway()

Methods inherited from class java.lang.Object

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

Method Detail

getClazz

public Class getClazz()

getOptions

public long getOptions()

Description copied from interface: ReactionCollection

See Reaction#UNIQUE, FILTER_REJECTED_DATASETS, FILTER_NOT_EXCLUDED

Specified by:

getOptions in interface ReactionCollection

getReactionsGroupped

public MReaction[] getReactionsGroupped()

Description copied from interface: ReactionCollection

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();.

Specified by:

getReactionsGroupped in interface ReactionCollection

setReactions

public void setReactions(MReaction[] rr,
                         long optionFlags)

setIsMutable

public MReactionCollection setIsMutable(boolean b)

getReactionsMappedSorted

public MReaction[] getReactionsMappedSorted()

getSpecies

public MSpecies[] getSpecies()

setMetabolites

public void setMetabolites(MSpecies[] mm)

getListOfCompartments

public String[] getListOfCompartments()

Description copied from interface: ReactionCollection

List of all compartments in this network.

Specified by:

getListOfCompartments in interface ReactionCollection

getReactions

public final MReaction[] getReactions()

Description copied from interface: ReactionCollection

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

Specified by:

getReactions in interface ReactionCollection

getReactionsWithMetabolite

public MReaction[] getReactionsWithMetabolite(String m)

Description copied from interface: ReactionCollection

Search for reactions with a certain metabolite.

Specified by:

getReactionsWithMetabolite in interface ReactionCollection

getSubstratesAndProducts

public String[] getSubstratesAndProducts()

Description copied from interface: ReactionCollection

List of all metabolites in this network.

Specified by:

getSubstratesAndProducts in interface ReactionCollection

loadDatasets

public static void loadDatasets(String f)

getNameForID

public String getNameForID(String id)

Description copied from interface: ReactionCollection

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

Specified by:

getNameForID in interface ReactionCollection

newDictionary

public static Map newDictionary(File f)

newDictionary

public static Map newDictionary(ByteArray ba)

getID

public String getID()

Description copied from interface: ReactionCollection

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

Specified by:

getID in interface ReactionCollection

setID

public void setID(String s)

getName

public String getName()

setMetaboliteObjects

public void setMetaboliteObjects(MSpecies[] cc)

withoutPathway

public Pathway withoutPathway()

getPathwayObjects

public Pathway[] getPathwayObjects()

setPathwayObjects

public void setPathwayObjects(Pathway[] pp)

getEC_Classes

public EC_Class[] getEC_Classes()

setEC_Classes

public void setEC_Classes(EC_Class[] ee)

getMapEC2EC_Class

public Map<String,EC_Class> getMapEC2EC_Class()

getMapId2Reaction

public Map<String,MReaction> getMapId2Reaction()

getMapId2Species

public Map<String,MSpecies> getMapId2Species()

getMapName2ReactionOrSpecies

public Map<String,MObject[]> getMapName2ReactionOrSpecies()

getCustomDictionaryWords

public Object[] getCustomDictionaryWords()

Description copied from interface: ChCustomDictionaryProvider

For JOrtho

Specified by:

getCustomDictionaryWords in interface ChCustomDictionaryProvider