sbrt.kernel.fba.comp
Interface FluxIntervalComputer<F extends Fluxome>

Type Parameters:
F - the fluxome type.
All Superinterfaces:
FluxCvComputer<F>
All Known Implementing Classes:
AbstractFluxIntervalComputer, MsFluxIntervalComputer, ReverseRxnIntervalComp, SimpleFluxIntervalComputer

public interface FluxIntervalComputer<F extends Fluxome>
extends FluxCvComputer<F>

This interface is used to represent flux interval computers. Every flux in a fluxome can assume minimum and maximum values, which define an interval. Implementation of this interface must have the ability to compute these flux intervals.

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

Method Summary
 java.util.Map<java.lang.String,Interval> getIntervals()
          Computes and returns the intervals of every flux in the fluxome used by 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.
 double getTolerance()
          Returns the amount by which constraints can be violated.
 double getZeroCutoff()
          Returns the current zero cutoff.
 
Methods inherited from interface sbrt.kernel.fba.comp.FluxCvComputer
getFluxConstraint, getFluxConstraints, getFluxome, getRxnExprConstraint, getRxnExprConstraints, restoreFluxConstraint, restoreFluxConstraints, restoreFluxConstraints, restoreRxnExprConstraint, restoreRxnExprConstraints, restoreRxnExprConstraints, setFluxConstraint, setFluxConstraints, setRxnExprConstraint, setRxnExprConstraints
 

Method Detail

getIntervals

java.util.Map<java.lang.String,Interval> getIntervals()
Computes and returns the intervals of every flux in the fluxome used by this flux interval computer.

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

getIntervals

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.

getZeroCutoff

double getZeroCutoff()
Returns the current zero cutoff. The zero cutoff is a value used to decide if numerical values are close enough to zero to be considered equal to zero.

Returns:
the zero cutoff.

getTolerance

double getTolerance()
Returns the amount by which constraints can be violated.

Returns:
the amount by which constraints can be violated.

getProgress

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

Returns:
a progress monitor for this flux interval computer.