sbrt.kernel.fba
Interface IrrevRxnFluxome

All Superinterfaces:
CatalyzedFluxome, Fluxome
All Known Implementing Classes:
IrrevRxnFluxomeV1

public interface IrrevRxnFluxome
extends CatalyzedFluxome

This interface is used to represent fluxomes that contain only irreversible reactions. All internal reactions must be of the type IrrevRxn, and all exchange reactions must be of the types SourceRxn and SinkRxn. This sort of representation offers a variety of advantages over more commonly used models. It allows one to constrain all forward and reverse reactions independently of each other, and it also means that the flux space formed by this fluxome lies entirely in the positive orthant.

For example, an organism like yeast can consume ethanol as a food source or produce it as a waste product, depending on a variety of factors. Breaking apart the ethanol-associated exchange reactions into forward and reverse (that is, source and sink) reactions allows one to model this phenomenon in finer detail.

Author:
This interface 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.
 IrrevRxn getInternalRxn(java.lang.String rxnName)
          Returns the internal reaction in this fluxome with the provided name.
 java.util.Map<java.lang.String,IrrevRxn> getInternalRxns()
          Returns all of the internal reactions in this fluxome.
 java.util.Map<java.lang.String,IrrevRxn> getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the internal reactions with the provided names.
 SinkRxn getSinkRxn(java.lang.String rxnName)
          Returns the sink reaction in this fluxome with the provided name.
 java.util.Set<java.lang.String> getSinkRxnNames()
          Returns the names of all sink reactions in this fluxome.
 java.util.Map<java.lang.String,SinkRxn> getSinkRxns()
          Returns the set of all sink reactions in this fluxome.
 java.util.Map<java.lang.String,SinkRxn> getSinkRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the sink reactions with the provided names.
 SourceRxn getSourceRxn(java.lang.String rxnName)
          Returns the source reaction in this fluxome with the provided name.
 java.util.Set<java.lang.String> getSourceRxnNames()
          Returns the names of all source reactions in this fluxome.
 java.util.Map<java.lang.String,SourceRxn> getSourceRxns()
          Returns the set of all source reactions in this fluxome.
 java.util.Map<java.lang.String,SourceRxn> getSourceRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the source reactions with the provided names.
 boolean isSinkRxnName(java.lang.String s)
          Indicates if the provided string is the name of a sink reaction contained in this fluxome.
 boolean isSourceRxnName(java.lang.String s)
          Indicates if the provided string is the name of a source reaction contained in this fluxome.
 IrrevRxnFluxome replaceConstraints(FluxConstraints constraints, double constraintTolerance)
          Returns a copy of this fluxome, but with all constraints replaced by those provided.
 int sinkRxns()
          Returns the total number of sink reactions contained in this fluxome.
 int sourceRxns()
          Returns the total number of source reactions contained in this fluxome.
 
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, getExchangeRxns, 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,IrrevRxn> 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,IrrevRxn> 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.

getSourceRxnNames

java.util.Set<java.lang.String> getSourceRxnNames()
Returns the names of all source reactions in this fluxome.

Returns:
the names of all source reactions in this fluxome.

getSourceRxns

java.util.Map<java.lang.String,SourceRxn> getSourceRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the source reactions with the provided names.

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

getSinkRxnNames

java.util.Set<java.lang.String> getSinkRxnNames()
Returns the names of all sink reactions in this fluxome.

Returns:
the names of all sink reactions in this fluxome.

getSinkRxns

java.util.Map<java.lang.String,SinkRxn> getSinkRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the sink reactions with the provided names.

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

getSourceRxns

java.util.Map<java.lang.String,SourceRxn> getSourceRxns()
Returns the set of all source reactions in this fluxome.

Returns:
the names of all source reactions mapped to their corresponding reaction.

getSinkRxns

java.util.Map<java.lang.String,SinkRxn> getSinkRxns()
Returns the set of all sink reactions in this fluxome.

Returns:
the names of all sink reactions mapped to their corresponding reaction.

getInternalRxn

IrrevRxn 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.

getSourceRxn

SourceRxn getSourceRxn(java.lang.String rxnName)
Returns the source reaction in this fluxome with the provided name.

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

getSinkRxn

SinkRxn getSinkRxn(java.lang.String rxnName)
Returns the sink reaction in this fluxome with the provided name.

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

isSourceRxnName

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

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

isSinkRxnName

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

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

sourceRxns

int sourceRxns()
Returns the total number of source reactions contained in this fluxome.

Returns:
the total number of source reactions contained in this fluxome.

sinkRxns

int sinkRxns()
Returns the total number of sink reactions contained in this fluxome.

Returns:
the total number of sink reactions contained in this fluxome.

replaceConstraints

IrrevRxnFluxome 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).