sbrt.kernel.fba.comp
Interface CycleComputer<F extends Fluxome>

Type Parameters:
F - the fluxome type.
All Known Implementing Classes:
SlpCycleComputer

public interface CycleComputer<F extends Fluxome>

This interface is used to represent algorithms for identifying steady state cycles in stoichiometric networks.

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

Method Summary
 SparseDoubleMatrix<?,java.lang.String> getCycles(F fluxome)
          Returns the set of all steady state cycles contained in the provided fluxome.
 ProgressMonitor getProgress()
          Returns a progress monitor for this cycle computer.
 

Method Detail

getProgress

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

Returns:
a progress monitor for this cycle computer.

getCycles

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

Parameters:
fluxome - the fluxome for which all cycles will be returned.
Returns:
the cycle matrix. Column variables are reaction names, and each row represents a steady state cycle.