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public interface IrrevRxnFluxome
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.
Method Summary | |
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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 |
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areReqCatalysts, catalysts, getCatalysts, getCatalyzedRxnNames, getCatalyzedRxns, isCatalyst, isReqCatalyst |
Methods inherited from interface sbrt.kernel.fba.Fluxome |
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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 |
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void checkRxnNames(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- a collection of strings.
java.lang.IllegalArgumentException
- if any element of this collection
is not a valid reaction name.
java.lang.NullPointerException
- if the collection is null.void checkRxnName(java.lang.String reactionName)
reactionName
- a potential reaction name.
java.lang.IllegalArgumentException
- if the provided string
is not a valid reaction name.java.util.Map<java.lang.String,IrrevRxn> getInternalRxns()
getInternalRxns
in interface Fluxome
java.util.Map<java.lang.String,IrrevRxn> getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- the names of the reactions to be returned.
java.util.Set<java.lang.String> getSourceRxnNames()
java.util.Map<java.lang.String,SourceRxn> getSourceRxns(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- the names of the reactions to be returned.
java.util.Set<java.lang.String> getSinkRxnNames()
java.util.Map<java.lang.String,SinkRxn> getSinkRxns(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- the names of the reactions to be returned.
java.util.Map<java.lang.String,SourceRxn> getSourceRxns()
java.util.Map<java.lang.String,SinkRxn> getSinkRxns()
IrrevRxn getInternalRxn(java.lang.String rxnName)
rxnName
- the name of the internal reaction to return.
SourceRxn getSourceRxn(java.lang.String rxnName)
rxnName
- the name of the source reaction to return.
SinkRxn getSinkRxn(java.lang.String rxnName)
rxnName
- the name of the sink reaction to return.
boolean isSourceRxnName(java.lang.String s)
s
- the string to test.
true
if the string is a valid source reaction name;
false
otherwise.boolean isSinkRxnName(java.lang.String s)
s
- the string to test.
true
if the string is a valid sink reaction name;
false
otherwise.int sourceRxns()
int sinkRxns()
IrrevRxnFluxome replaceConstraints(FluxConstraints constraints, double constraintTolerance)
replaceConstraints
in interface CatalyzedFluxome
replaceConstraints
in interface Fluxome
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.
Or<And<java.lang.String>> getCatalystRule(java.lang.String rxnName)
getCatalystRule
in interface CatalyzedFluxome
rxnName
- the name of the reaction for which the catalyst rules
are to be returned.
java.util.Map<java.lang.String,Or<And<java.lang.String>>> getCatalystRules()
getCatalystRules
in interface CatalyzedFluxome
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