sbrt.kernel.fba.comp
Class WwCycleComputer

java.lang.Object
  extended by sbrt.kernel.fba.comp.WwCycleComputer
All Implemented Interfaces:
CycleComputer

public class WwCycleComputer
extends java.lang.Object
implements CycleComputer

This class is used to identify the steady state cycles (Type III extreme pathways) in a fluxome. It is an implementation of the algorithm described by Wright and Wagner (WW).

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

Constructor Summary
WwCycleComputer(ProgramSolver<java.lang.Object,java.lang.Object> solver, ExtremeCurrentComputer computer)
          Constructs a new steady state cycle computer from the provided linear program solver and extreme current computer.
 
Method Summary
 SparseDoubleMatrix<?,java.lang.String> getCycles(IrrevRxnFluxome fluxome)
          Returns the set of all steady state cycles (Type III extreme pathways) contained in the provided fluxome.
 ProgressMonitor getProgress()
          Returns a progress monitor for this cycle computer.
 IrrevRxnFluxome getSubFluxome(IrrevRxnFluxome fluxome)
          Returns the sub-fluxome resulting from linear programming.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

WwCycleComputer

public WwCycleComputer(ProgramSolver<java.lang.Object,java.lang.Object> solver,
                       ExtremeCurrentComputer computer)
Constructs a new steady state cycle computer from the provided linear program solver and extreme current computer.

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

getProgress

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

Specified by:
getProgress in interface CycleComputer
Returns:
a progress monitor for this cycle computer.

getSubFluxome

public IrrevRxnFluxome getSubFluxome(IrrevRxnFluxome fluxome)
Returns the sub-fluxome resulting from linear programming.

Parameters:
fluxome - the fluxome for which a sub-fluxome will be returned.
Returns:
the sub-fluxome resulting from linear programming.

getCycles

public SparseDoubleMatrix<?,java.lang.String> getCycles(IrrevRxnFluxome fluxome)
Returns the set of all steady state cycles (Type III extreme pathways) contained in the provided fluxome.

Specified by:
getCycles in interface CycleComputer
Parameters:
fluxome - the fluxome for which all cycles will be identified.
Returns:
the extreme current matrix. Column variables are reaction names, and each row represents a steady state cycle.