sbrt.kernel.fba.comp
Class SlpCycleComputer

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

public class SlpCycleComputer
extends java.lang.Object
implements CycleComputer<IrrevRxnFluxome>

This class is used to identify the steady state cycles in stoichiometric networks. This is accomplished by removing all exchange reactions from a network and then identifying the extreme currents of the sub-network. Those extreme currents are necessarily cycles, and are also the set of all Type III extreme pathways of the sub-network.

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

Constructor Summary
SlpCycleComputer(ExtremeCurrentComputer computer)
          Constructs a new steady state cycle computer from the given extreme current computer.
 
Method Summary
 SparseDoubleMatrix<?,java.lang.String> getCycles(IrrevRxnFluxome fluxome)
          Returns the set of all steady state cycles contained in the provided fluxome.
 ProgressMonitor getProgress()
          Returns a progress monitor for this steady state cycle computer.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SlpCycleComputer

public SlpCycleComputer(ExtremeCurrentComputer computer)
Constructs a new steady state cycle computer from the given extreme current computer.

Parameters:
computer - the computer with which all extreme currents will be identified.
Method Detail

getProgress

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

Specified by:
getProgress in interface CycleComputer<IrrevRxnFluxome>
Returns:
a progress monitor for this steady state cycle computer.

getCycles

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

Specified by:
getCycles in interface CycleComputer<IrrevRxnFluxome>
Parameters:
fluxome - the fluxome for which all cycles will be identified.
Returns:
the extreme current matrix. The column variables are the names of all internal reactions, and each row corresponds to a steady state cycle.