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java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer<F>
sbrt.kernel.fba.comp.AbstractFluxIntervalComputer<F>
sbrt.kernel.fba.comp.SimpleFluxIntervalComputer<F>
F
- the fluxome type.public class SimpleFluxIntervalComputer<F extends Fluxome>
This class is used to compute flux intervals in the simplest possible way. An
interval is computed by minimizing and maximizing the flux of a given
reaction. If a flux is unbounded in a particular direction, as they sometimes are,
Double.NEGATIVE_INFINITY
or
Double.POSITIVE_INFINITY
are used to denote the flux bounds.
Field Summary |
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Fields inherited from class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer |
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ZERO_CUTOFF |
Constructor Summary | |
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SimpleFluxIntervalComputer(FbaOptimizer<F> computer,
double zeroCutoff)
Constructs a new flux interval computer. |
Method Summary | |
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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. |
java.util.Map<java.lang.String,java.lang.Double> |
getMaximumFluxes(java.util.Collection<java.lang.String> rxnNames,
MutableProgressMonitor progress)
Computes and returns the maximum fluxes 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 |
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checkFluxConstraint, checkNumber, checkRxnExpr, checkRxnExprConstraint, checkRxnName, checkRxnNames, getFluxome, getRxnExpr, getRxnExpr |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.kernel.fba.comp.FluxCvComputer |
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getFluxome |
Constructor Detail |
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public SimpleFluxIntervalComputer(FbaOptimizer<F> computer, double zeroCutoff)
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.Method Detail |
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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.
public java.util.Map<java.lang.String,java.lang.Double> getMaximumFluxes(java.util.Collection<java.lang.String> rxnNames, MutableProgressMonitor progress)
rxnNames
- a collection of reaction names.progress
- the progress monitor to be incremented.
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