|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer
sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
sbrt.kernel.fba.comp.ReverseRxnFluxIntervalComputer
public class ReverseRxnFluxIntervalComputer
This class is used to compute flux intervals while constraining the fluxes of reverse reactions to their minimum. An interval is computed by minimizing and maximizing the flux of a given reaction. If a flux is unbounded, as they sometimes are, Double.NEGATIVE_INFINITY and Double.POSITIVE_INFINITY are used to denote the flux bounds.
Field Summary |
---|
Fields inherited from class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer |
---|
ZERO_CUTOFF |
Constructor Summary | |
---|---|
ReverseRxnFluxIntervalComputer(FbaOptComputer computer,
double zeroCutoff)
Constructs a new flux interval computer. |
Method Summary | |
---|---|
protected java.util.Map<java.lang.String,java.lang.Double> |
getFluxMaxima(java.util.Collection<java.lang.String> rxnNames,
MutableProgressMonitor progress)
Computes and returns the maximum fluxes of the reactions with the provided names. |
protected java.util.Map<java.lang.String,java.lang.Double> |
getFluxMinima(java.util.Collection<java.lang.String> rxnNames,
MutableProgressMonitor progress)
Computes and returns the minimum fluxes of the reactions with the provided names. |
java.util.Map<java.lang.String,Interval> |
getIntervals()
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer. |
java.util.Map<java.lang.String,Interval> |
getIntervals(java.util.Collection<java.lang.String> rxnNames)
Computes and returns the flux intervals of the reactions with the provided names. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this flux interval computer. |
Methods inherited from class sbrt.kernel.fba.comp.AbstractCvComputer |
---|
checkFluxConstraint, checkNumber, checkRxnExpr, checkRxnExprConstraint, checkRxnName, checkRxnNames, getFluxome, getRxnExpr, getRxnExpr |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.kernel.fba.comp.FluxCvComputer |
---|
getFluxome |
Constructor Detail |
---|
public ReverseRxnFluxIntervalComputer(FbaOptComputer computer, double zeroCutoff)
IrrevRxnFluxome
.
computer
- the computer with which all optimizations will be
computed.zeroCutoff
- the amount by which a computed lower bound can
exceed a computed upper bound.
java.lang.ClassCastException
- if the fluxome of the provided optimization
computer is not an IrrevRxnFluxome
.Method Detail |
---|
public ProgressMonitor getProgress()
public java.util.Map<java.lang.String,Interval> getIntervals()
public java.util.Map<java.lang.String,Interval> getIntervals(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- a collection of reaction names.
protected java.util.Map<java.lang.String,java.lang.Double> getFluxMinima(java.util.Collection<java.lang.String> rxnNames, MutableProgressMonitor progress)
rxnNames
- a collection of reaction names.progress
- the progress monitor to be incremented.
protected java.util.Map<java.lang.String,java.lang.Double> getFluxMaxima(java.util.Collection<java.lang.String> rxnNames, MutableProgressMonitor progress)
rxnNames
- a collection of reaction names.progress
- the progress monitor to be incremented.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |