sbrt.kernel.fba.comp
Class RedundRxnRemover

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

public class RedundRxnRemover
extends java.lang.Object

This class is used to remove "redundant" reactions from fluxomes. If a fluxome contains two stoichiometrically equivalent reactions, one of them is considered redundant.

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

Constructor Summary
RedundRxnRemover()
           
 
Method Summary
static java.util.Collection<java.util.Set<java.lang.String>> getEquivRxns(Fluxome fluxome)
          Returns the equivalent reactions contained in the provided fluxome.
static IrrevRxnFluxome remove(IrrevRxnFluxome fluxome)
          Returns a fluxome for which all "redundant" reactions have been eliminated.
static MixedFluxome remove(MixedFluxome fluxome)
          Returns a fluxome for which all "redundant" reactions have been eliminated.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RedundRxnRemover

public RedundRxnRemover()
Method Detail

remove

public static MixedFluxome remove(MixedFluxome fluxome)
Returns a fluxome for which all "redundant" reactions have been eliminated.

Parameters:
fluxome - a fluxome.
Returns:
a fluxome for which all "redundant" reactions have been eliminated.
See Also:
getEquivRxns(Fluxome)

remove

public static IrrevRxnFluxome remove(IrrevRxnFluxome fluxome)
Returns a fluxome for which all "redundant" reactions have been eliminated.

Parameters:
fluxome - a fluxome.
Returns:
a fluxome for which all "redundant" reactions have been eliminated.
See Also:
getEquivRxns(Fluxome)

getEquivRxns

public static java.util.Collection<java.util.Set<java.lang.String>> getEquivRxns(Fluxome fluxome)
Returns the equivalent reactions contained in the provided fluxome.

Parameters:
fluxome - a fluxome.
Returns:
the equivalent reactions contained in the provided fluxome.