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java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer<F>
sbrt.kernel.fba.comp.AbstractFluxIntervalComputer<F>
sbrt.kernel.fba.comp.MsFluxIntervalComputer<F>
F
- the fluxome type.public class MsFluxIntervalComputer<F extends IrrevRxnFluxome>
This class is used to compute Mahadevan-Schilling flux intervals. The first description of these intervals can be found in the paper: R. Mahadevan, C. H. Schilling, "Effects of Alternate Optimal Solutions in Constraint-based Genome Scale Metabolic Models", Metabolic Engineering, 2003, 5:264-276.
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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MsFluxIntervalComputer(FbaOptimizer<F> computer,
java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps)
Constructs a new Mahadevan-Schilling flux interval computer. |
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MsFluxIntervalComputer(FbaOptimizer<F> computer,
java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps,
double zeroCutoff)
Constructs a new Mahadevan-Schilling 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. |
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 MsFluxIntervalComputer(FbaOptimizer<F> computer, java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps)
computer
- the computer with which all optimizations will be
computed.fluxCaps
- the flux caps used to constrain all unbounded fluxes.public MsFluxIntervalComputer(FbaOptimizer<F> computer, java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps, double zeroCutoff)
computer
- the computer with which all optimizations will be
computed.fluxCaps
- the flux caps used to constrain all unbounded fluxes.zeroCutoff
- the zero cutoff used by this flux interval computer.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.
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