sbrt.kernel.fba.comp
Class MsFluxomeReducer

java.lang.Object
  extended by sbrt.kernel.fba.comp.MsFluxomeReducer
All Implemented Interfaces:
FluxomeReducer<IrrevRxnFluxome>

public class MsFluxomeReducer
extends java.lang.Object
implements FluxomeReducer<IrrevRxnFluxome>

This class is used to reduce the size of fluxomes for the purpose of identifying the steady state cycles they contain. It is an implementation of the algorithm described by Mahadevan and Schilling (MS).

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

Constructor Summary
MsFluxomeReducer(ProgramSolver<java.lang.Object,java.lang.Object> solver)
          Constructs a fluxome reducer from the provided linear program solver.
 
Method Summary
 ProgressMonitor getProgress()
          Returns a progress monitor for this fluxome reducer.
 IrrevRxnFluxome makeFluxome(IrrevRxnFluxome fluxome)
          Returns the sub-fluxome resulting from network reduction.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MsFluxomeReducer

public MsFluxomeReducer(ProgramSolver<java.lang.Object,java.lang.Object> solver)
Constructs a fluxome reducer from the provided linear program solver.

Parameters:
solver - the linear program solver with which all optimizations will be computed.
Method Detail

getProgress

public ProgressMonitor getProgress()
Returns a progress monitor for this fluxome reducer.

Specified by:
getProgress in interface FluxomeReducer<IrrevRxnFluxome>
Returns:
a progress monitor for this fluxome reducer.

makeFluxome

public IrrevRxnFluxome makeFluxome(IrrevRxnFluxome fluxome)
Returns the sub-fluxome resulting from network reduction.

Specified by:
makeFluxome in interface FluxomeReducer<IrrevRxnFluxome>
Parameters:
fluxome - the fluxome for which a sub-fluxome will be returned.
Returns:
the sub-fluxome resulting from network reduction.