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public interface Fluxome
This interface is used to represent fluxomes for use in Flux Balance Analysis. A fluxome is a set of biochemical reactions whose rates (i.e. fluxes) may be subject to constraint. A fluxome is composed of
• chemical species | |
• the chemical reactions in which those chemical species participate | |
• the constraints on the fluxes of those reactions, and |
Two basic types of reactions exist in a fluxome: internal reactions and exchange reactions. Each reaction has a unique identifier, that is, a name. Each reaction also has an associated flux constraint, which is either assigned explicitly or by default.
A flux constraint can be represented as α ≤ V ≤ β, where α and β are the lower and upper flux bounds, respectively, and V is the flux under consideration. For a particular type of fluxome, the allowed flux constraints may have a defined range. That is to say, the allowed values of α and β may differ between fluxomes of different types or even between reactions of different type within the same fluxome. For example, a popular type of fluxome uses the following convention: 0 ≤ α ≤ ∞, α ≤ β ≤ ∞ for internal reactions and -∞ ≤ α ≤ &infin, α ≤ β ≤ ∞ for exchange reactions. This interface provides a way to maintain the integrity of these definitions or conventions using isValid(Interval, String, double).
Method Summary | |
---|---|
int |
addedConstraints()
Returns the total number of constraints added to this fluxome. |
boolean |
areRxnNames(java.util.Collection<java.lang.String> c)
Indicates if every string in the provided collection is the name of a reaction contained in this fluxome. |
int |
exchangeRxns()
Returns the total number of exchange reactions contained in this fluxome. |
FluxConstraints |
getConstraints()
Returns the set of all constraints for fluxes and mathematical expressions of fluxes in this fluxome. |
java.util.Set<java.lang.String> |
getExchangeRxnNames()
Returns the set of names of all exchange reactions contained in this fluxome. |
java.util.Map<java.lang.String,? extends ExchangeRxn> |
getExchangeRxns()
Returns all of the exchange reactions contained in this fluxome. |
Interval |
getFluxConstraint(java.lang.String reactionName)
Returns the flux constraint for the reaction with the provided name. |
java.util.Set<java.lang.String> |
getInternalRxnNames()
Returns the set of names of all internal chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,? extends ChemRxn> |
getInternalRxns()
Returns the set of all internal chemical reactions contained in this fluxome. |
ChemRxn |
getRxn(java.lang.String reactionName)
Returns the chemical reaction in this fluxome with the provided name. |
Interval |
getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint corresponding to the provided mathematical expression of reaction names. |
java.util.Set<java.lang.String> |
getRxnNames()
Returns the set of names of all chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
getRxns()
Returns the set of all chemical reactions contained in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
getRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the chemical reactions with the provided names. |
java.util.Set<java.lang.String> |
getSpecies()
Returns the set of names of all chemical species participating in reactions contained in this fluxome. |
SparseDoubleMatrix<java.lang.String,java.lang.String> |
getStoichMatrix()
Returns the stoichiometry matrix of this fluxome. |
int |
internalRxns()
Returns the total number of internal reactions contained in this fluxome. |
boolean |
isExchangeRxnName(java.lang.String s)
Indicates if the provided string is the name of an exchange reaction contained in this fluxome. |
boolean |
isFluxVector(java.util.Map<java.lang.String,java.lang.Double> fluxVector,
double tolerance)
Indicates if the provided flux vector lies within the feasible space of this fluxome, given the provided tolerance value. |
boolean |
isInternalRxnName(java.lang.String s)
Indicates if the provided string is the name of an internal reaction contained in this fluxome. |
boolean |
isRxnName(java.lang.String s)
Indicates if the provided string is the name of a reaction contained in this fluxome. |
boolean |
isSpecies(java.lang.String s)
Indicates if the provided string is the name of a chemical species contained in this fluxome. |
boolean |
isValid(Interval constraint,
java.lang.String rxnName,
double tolerance)
Indicates if the provided interval is a valid flux constraint for the reaction with the provided name. |
Fluxome |
replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
int |
rxns()
Returns the total number of chemical reactions contained in this fluxome. |
int |
species()
Returns the total number of chemical species contained in this fluxome. |
Method Detail |
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java.util.Map<java.lang.String,ChemRxn> getRxns()
java.util.Map<java.lang.String,ChemRxn> getRxns(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- the names of the reactions to be returned.
java.util.Map<java.lang.String,? extends ChemRxn> getInternalRxns()
java.util.Map<java.lang.String,? extends ExchangeRxn> getExchangeRxns()
ChemRxn getRxn(java.lang.String reactionName)
reactionName
- the name of the chemical reaction to be returned.
java.util.Set<java.lang.String> getRxnNames()
java.util.Set<java.lang.String> getInternalRxnNames()
java.util.Set<java.lang.String> getExchangeRxnNames()
java.util.Set<java.lang.String> getSpecies()
Interval getFluxConstraint(java.lang.String reactionName)
reactionName
- the name of the reaction whose flux constraint is
to be returned.
Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
rxnNameExpr
- the mathematical expression of
reaction names whose constraint is to be returned.
FluxConstraints getConstraints()
SparseDoubleMatrix<java.lang.String,java.lang.String> getStoichMatrix()
boolean isRxnName(java.lang.String s)
s
- the string to test.
true
if the string is a valid reaction name;
false
otherwise.boolean isInternalRxnName(java.lang.String s)
s
- the string to test.
true
if the string is a valid internal reaction name;
false
otherwise.boolean isExchangeRxnName(java.lang.String s)
s
- the string to test.
true
if the string is a valid exchange reaction name;
false
otherwise.boolean areRxnNames(java.util.Collection<java.lang.String> c)
c
- a collection of strings.
true
if every string is a valid reaction name;
false
otherwise.boolean isSpecies(java.lang.String s)
s
- the string to test.
true
if the string is a valid chemical species;
false
otherwise.boolean isFluxVector(java.util.Map<java.lang.String,java.lang.Double> fluxVector, double tolerance)
fluxVector
- reaction names mapped to flux values.tolerance
- the amount by which a computed value is allowed to
violate a defined constraint. This should be small positive number, like
1E-9 for example.
true
if the vector satisfies all constraints;
false
otherwise.boolean isValid(Interval constraint, java.lang.String rxnName, double tolerance)
constraint
- the flux constraint to test.rxnName
- the name of the reaction.tolerance
- the allowed amount by which the provided
constraint can violate its maximum defined interval. This
maximum defined interval is implementation-dependent.
true
if the constraint is valid;
false
otherwise.
java.lang.IllegalArgumentException
- if the provided reaction
name does not exist in this fluxome.int rxns()
int internalRxns()
int exchangeRxns()
int species()
int addedConstraints()
replaceConstraints(FluxConstraints, double)
Fluxome replaceConstraints(FluxConstraints constraints, double constraintTolerance)
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.
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