sbrt.kernel.fba.comp
Class MsFluxIntervalComputer<F extends IrrevRxnFluxome>

java.lang.Object
  extended by sbrt.kernel.fba.comp.AbstractCvComputer<F>
      extended by sbrt.kernel.fba.comp.AbstractFluxIntervalComputer<F>
          extended by sbrt.kernel.fba.comp.MsFluxIntervalComputer<F>
Type Parameters:
F - the fluxome type.
All Implemented Interfaces:
FluxCvComputer<F>, FluxIntervalComputer<F>

public class MsFluxIntervalComputer<F extends IrrevRxnFluxome>
extends AbstractFluxIntervalComputer<F>

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.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Field Summary
 
Fields inherited from class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
ZERO_CUTOFF
 
Constructor Summary
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.
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
 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.AbstractFluxIntervalComputer
getBoundedMax, getBoundedMax, getBoundedMaxWithRxnsMinimized, getBoundedMin, getBoundedMin, getFluxConstraint, getFluxConstraints, getInterval, getIntervals, getMaximum, getMaximum, getMaxWithRxnsMinimized, getMinimum, getMinimum, getRxnExprConstraint, getRxnExprConstraints, getTolerance, getZeroCutoff, restoreFluxConstraint, restoreFluxConstraints, restoreFluxConstraints, restoreRxnExprConstraint, restoreRxnExprConstraints, restoreRxnExprConstraints, setFluxConstraint, setFluxConstraints, setRxnExprConstraint, setRxnExprConstraints
 
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

MsFluxIntervalComputer

public 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.

Parameters:
computer - the computer with which all optimizations will be computed.
fluxCaps - the flux caps used to constrain all unbounded fluxes.

MsFluxIntervalComputer

public 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.

Parameters:
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

getProgress

public ProgressMonitor getProgress()
Returns a progress monitor for this flux interval computer.

Returns:
a progress monitor for this flux interval computer.

getIntervals

public 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.

Returns:
reaction names mapped to the computed interval of their corresponding flux.

getIntervals

public 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.

Parameters:
rxnNames - a collection of reaction names.
Returns:
reaction names mapped to the computed interval of their corresponding flux.