sbrt.ext.metatool
Class MetatoolCycleComputer

java.lang.Object
  extended by sbrt.ext.metatool.MetatoolCycleComputer
All Implemented Interfaces:
CycleComputer

public class MetatoolCycleComputer
extends java.lang.Object
implements CycleComputer

This class is used to run metatool to compute steady state cycles.

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

Constructor Summary
MetatoolCycleComputer(java.io.File executable)
          Constructs a new metatool steady state cycle 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 cycle computer.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MetatoolCycleComputer

public MetatoolCycleComputer(java.io.File executable)
Constructs a new metatool steady state cycle computer.

Parameters:
executable - the full name of the metatool executable.
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.

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