sbrt.kernel.fba
Interface CatalyzedFluxome

All Superinterfaces:
Fluxome
All Known Subinterfaces:
IrrevRxnFluxome, MixedFluxome
All Known Implementing Classes:
IrrevRxnFluxomeV1, MixedFluxomeV1

public interface CatalyzedFluxome
extends Fluxome

This interface is used to represent fluxomes with catalyzed reactions.

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

Method Summary
 boolean areReqCatalysts(java.util.Collection<java.lang.String> catalysts, java.lang.String rxnName)
          Indicates if the reaction with the provided name could function if each of the catalysts in the provided collection were simultaneously absent.
 int catalysts()
          Returns the total number of catalysts contained in this fluxome.
 LogicalRelation<?> getCatalystRule(java.lang.String rxnName)
          Returns the boolean logic rule for catalysts of the reaction with the provided name.
 java.util.Map<java.lang.String,? extends LogicalRelation<?>> getCatalystRules()
          Returns the boolean logic rules for the catalysts of all reactions in this fluxome.
 java.util.Set<java.lang.String> getCatalysts()
          Returns the set of all catalysts contained in this fluxome.
 java.util.Set<java.lang.String> getCatalyzedRxnNames(java.lang.String catalyst)
          Returns the set of names of all chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.
 java.util.Map<java.lang.String,? extends ChemRxn> getCatalyzedRxns(java.lang.String catalyst)
          Returns the chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.
 boolean isCatalyst(java.lang.String s)
          Indicates if the provided string is the name of a catalyst contained in this fluxome.
 boolean isReqCatalyst(java.lang.String catalyst, java.lang.String rxnName)
          Indicates if the provided catalyst is required for the reaction with the provided name.
 CatalyzedFluxome 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.Fluxome
addedConstraints, areRxnNames, exchangeRxns, getConstraints, getExchangeRxnNames, getExchangeRxns, getFluxConstraint, getInternalRxnNames, getInternalRxns, getRxn, getRxnExprConstraint, getRxnNames, getRxns, getRxns, getSpecies, getStoichMatrix, internalRxns, isExchangeRxnName, isFluxVector, isInternalRxnName, isRxnName, isSpecies, isValid, rxns, species
 

Method Detail

getCatalyzedRxns

java.util.Map<java.lang.String,? extends ChemRxn> getCatalyzedRxns(java.lang.String catalyst)
Returns the chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.

Parameters:
catalyst - the name of the catalyst whose reactions are to be returned.
Returns:
reaction names mapped to their respective chemical reactions.

getCatalyzedRxnNames

java.util.Set<java.lang.String> getCatalyzedRxnNames(java.lang.String catalyst)
Returns the set of names of all chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.

Parameters:
catalyst - the name of the catalyst whose reaction names are to be returned.
Returns:
the set of names of all chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.

getCatalystRule

LogicalRelation<?> getCatalystRule(java.lang.String rxnName)
Returns the boolean logic rule for catalysts of the reaction with the provided name.

Parameters:
rxnName - the name of the reaction whose catalyst rule are to be returned.
Returns:
the boolean relationship of the catalysts of the specified reaction.

getCatalystRules

java.util.Map<java.lang.String,? extends LogicalRelation<?>> getCatalystRules()
Returns the boolean logic rules for the catalysts of all reactions in this fluxome.

Returns:
reaction names mapped to the boolean relationship of their catalysts.

getCatalysts

java.util.Set<java.lang.String> getCatalysts()
Returns the set of all catalysts contained in this fluxome.

Returns:
the set of all catalysts contained in this fluxome.

isCatalyst

boolean isCatalyst(java.lang.String s)
Indicates if the provided string is the name of a catalyst contained in this fluxome.

Parameters:
s - the string to test.
Returns:
true if the string is a valid catalyst; false otherwise.

catalysts

int catalysts()
Returns the total number of catalysts contained in this fluxome.

Returns:
the total number of catalysts contained in this fluxome.

isReqCatalyst

boolean isReqCatalyst(java.lang.String catalyst,
                      java.lang.String rxnName)
Indicates if the provided catalyst is required for the reaction with the provided name.

Parameters:
catalyst - the catalyst.
rxnName - the name of the reaction.
Returns:
true if the provided catalyst is required by the reaction with the provided name; false otherwise.

areReqCatalysts

boolean areReqCatalysts(java.util.Collection<java.lang.String> catalysts,
                        java.lang.String rxnName)
Indicates if the reaction with the provided name could function if each of the catalysts in the provided collection were simultaneously absent.

Parameters:
catalysts - the collection of catalysts.
rxnName - the name of the reaction.
Returns:
true if the provided catalysts are required for the specified reaction to function; false otherwise.
Throws:
java.lang.IllegalArgumentException - if rxnName is not a valid reaction name.

replaceConstraints

CatalyzedFluxome 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 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.