sbrt.kernel.fba.comp
Class FluxCapComputer

java.lang.Object
  extended by sbrt.kernel.fba.comp.FluxCapComputer

public class FluxCapComputer
extends java.lang.Object

This class is used to compute flux caps for use in Mahadevan-Schilling flux interval computations. A flux cap is a linear combination of fluxes that can be used to cap, or bound, an unbound flux.

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

Constructor Summary
FluxCapComputer(IrrevRxnFluxome fluxome, java.util.Collection<LinearComb<java.lang.String>> allCycles)
          Constructs a new flux cap computer from the cycles contained in the provided fluxome.
FluxCapComputer(IrrevRxnFluxome fluxome, DoubleMatrix<?,java.lang.String> cycleMatrix)
          Constructs a new flux cap computer from the cycles contained in the provided fluxome.
 
Method Summary
 java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getFluxCaps()
          Computes and returns all flux caps.
 IrrevRxnFluxome getFluxome()
          Returns the fluxome for which flux caps are computed.
 ProgressMonitor getProgress()
          Returns a progress monitor for this flux cap computer.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FluxCapComputer

public FluxCapComputer(IrrevRxnFluxome fluxome,
                       DoubleMatrix<?,java.lang.String> cycleMatrix)
Constructs a new flux cap computer from the cycles contained in the provided fluxome.

Parameters:
fluxome - the fluxome for which flux caps will be computed.
cycleMatrix - the collection of all cycles in the provided fluxome.

FluxCapComputer

public FluxCapComputer(IrrevRxnFluxome fluxome,
                       java.util.Collection<LinearComb<java.lang.String>> allCycles)
Constructs a new flux cap computer from the cycles contained in the provided fluxome.

Parameters:
fluxome - the fluxome for which flux caps will be computed.
allCycles - the collection of all cycles in the provided fluxome as linear combinations.
Method Detail

getProgress

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

Returns:
a progress monitor for this flux cap computer.

getFluxome

public IrrevRxnFluxome getFluxome()
Returns the fluxome for which flux caps are computed.

Returns:
the fluxome for which flux caps are computed.

getFluxCaps

public java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getFluxCaps()
Computes and returns all flux caps.

Returns:
reaction names mappes to their corresponding set of flux caps.