sbrt.kernel.fba
Interface MixedFluxome

All Superinterfaces:
CatalyzedFluxome, Fluxome
All Known Implementing Classes:
MixedFluxomeV1

public interface MixedFluxome
extends CatalyzedFluxome

This interface is used to represent fluxomes that contain multiple types of chemical reactions. These reaction types include: irreversible internal reactions, reversible internal reactions, source reactions, sink reactions, and reversible exchange reactions.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Method Summary
 void checkRxnName(java.lang.String reactionName)
          Ensures the provided string is a valid reaction name.
 void checkRxnNames(java.util.Collection<java.lang.String> rxnNames)
          Ensures each element of the provided collection is a valid reaction name.
 Or<And<java.lang.String>> getCatalystRule(java.lang.String rxnName)
          Returns the boolean logic statement for the catalysts of the reaction with the provided name.
 java.util.Map<java.lang.String,Or<And<java.lang.String>>> getCatalystRules()
          Returns all of the boolean logic statements regarding reaction catalysis.
 ExchangeRxn getExchangeRxn(java.lang.String rxnName)
          Returns the exchange reaction in this fluxome with the provided name.
 java.util.Map<java.lang.String,ExchangeRxn> getExchangeRxns()
          Returns all of the exchange reactions contained in this fluxome.
 java.util.Map<java.lang.String,ExchangeRxn> getExchangeRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the exchange reactions with the provided names.
 ChemRxn getInternalRxn(java.lang.String rxnName)
          Returns the internal reaction in this fluxome with the provided name.
 java.util.Map<java.lang.String,ChemRxn> getInternalRxns()
          Returns all of the internal reactions in this fluxome.
 java.util.Map<java.lang.String,ChemRxn> getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the internal reactions with the provided names.
 MixedFluxome replaceConstraints(FluxConstraints constraints, double constraintTolerance)
          Returns a copy of this fluxome, but with all constraints replaced by those provided.
 
Methods inherited from interface sbrt.kernel.fba.CatalyzedFluxome
areReqCatalysts, catalysts, getCatalysts, getCatalyzedRxnNames, getCatalyzedRxns, isCatalyst, isReqCatalyst
 
Methods inherited from interface sbrt.kernel.fba.Fluxome
addedConstraints, areRxnNames, exchangeRxns, getConstraints, getExchangeRxnNames, getFluxConstraint, getInternalRxnNames, getRxn, getRxnExprConstraint, getRxnNames, getRxns, getRxns, getSpecies, getStoichMatrix, internalRxns, isExchangeRxnName, isFluxVector, isInternalRxnName, isRxnName, isSpecies, isValid, rxns, species
 

Method Detail

checkRxnNames

void checkRxnNames(java.util.Collection<java.lang.String> rxnNames)
Ensures each element of the provided collection is a valid reaction name.

Parameters:
rxnNames - a collection of strings.
Throws:
java.lang.IllegalArgumentException - if any element of this collection is not a valid reaction name.
java.lang.NullPointerException - if the collection is null.

checkRxnName

void checkRxnName(java.lang.String reactionName)
Ensures the provided string is a valid reaction name.

Parameters:
reactionName - a potential reaction name.
Throws:
java.lang.IllegalArgumentException - if the provided string is not a valid reaction name.

getInternalRxns

java.util.Map<java.lang.String,ChemRxn> getInternalRxns()
Returns all of the internal reactions in this fluxome.

Specified by:
getInternalRxns in interface Fluxome
Returns:
reaction names mapped their reaction.

getInternalRxns

java.util.Map<java.lang.String,ChemRxn> getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the internal reactions with the provided names.

Parameters:
rxnNames - the names of the reactions to be returned.
Returns:
reaction names mapped to their reaction.

getExchangeRxns

java.util.Map<java.lang.String,ExchangeRxn> getExchangeRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the exchange reactions with the provided names.

Parameters:
rxnNames - the names of the reactions to be returned.
Returns:
reaction names mapped to their reaction.

getExchangeRxns

java.util.Map<java.lang.String,ExchangeRxn> getExchangeRxns()
Returns all of the exchange reactions contained in this fluxome.

Specified by:
getExchangeRxns in interface Fluxome
Returns:
reaction names mapped to their corresponding reaction.

getInternalRxn

ChemRxn getInternalRxn(java.lang.String rxnName)
Returns the internal reaction in this fluxome with the provided name.

Parameters:
rxnName - the name of the internal reaction to return.
Returns:
the internal reaction in this fluxome with the provided name.

getExchangeRxn

ExchangeRxn getExchangeRxn(java.lang.String rxnName)
Returns the exchange reaction in this fluxome with the provided name.

Parameters:
rxnName - the name of the exchange reaction to return.
Returns:
the exchange reaction in this fluxome with the provided name.

replaceConstraints

MixedFluxome replaceConstraints(FluxConstraints constraints,
                                double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. If a flux constraint for a particular reaction was not provided, its default value will be used.

Specified by:
replaceConstraints in interface CatalyzedFluxome
Specified by:
replaceConstraints in interface Fluxome
Parameters:
constraints - the new set of flux constraints.
constraintTolerance - the allowed amount by which constraints can violate their maximum defined intervals. These maximum defined intervals are implementation-dependent.
Returns:
a copy of this fluxome, but with all constraints replaced by those provided.

getCatalystRule

Or<And<java.lang.String>> getCatalystRule(java.lang.String rxnName)
Returns the boolean logic statement for the catalysts of the reaction with the provided name.

Specified by:
getCatalystRule in interface CatalyzedFluxome
Parameters:
rxnName - the name of the reaction for which the catalyst rules are to be returned.
Returns:
the boolean logic statement for the catalysts of the reaction with the provided name. If the specified reaction is not catalyzed, an empty (non-null) rule is returned.

getCatalystRules

java.util.Map<java.lang.String,Or<And<java.lang.String>>> getCatalystRules()
Returns all of the boolean logic statements regarding reaction catalysis.

Specified by:
getCatalystRules in interface CatalyzedFluxome
Returns:
the names of catalyzed reactions mapped to their boolean logic rules of their catalyst(s).