sbrt.ext.metatool
Class MetatoolExtCurrComputer

java.lang.Object
  extended by sbrt.ext.metatool.MetatoolExtCurrComputer
All Implemented Interfaces:
ExtremeCurrentComputer

public class MetatoolExtCurrComputer
extends java.lang.Object
implements ExtremeCurrentComputer

This class is used to run metatool to compute steady state cycles. This class is an implementation of ExtremeCurrentComputer, but fluxomes with exchange reactions are currently not supported by this class. Therefore, this type of extreme current computer only computes steady state cycles.

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

Constructor Summary
MetatoolExtCurrComputer(java.io.File executable)
          Constructs a new metatool steady state cycle computer.
 
Method Summary
 SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome)
          Returns the set of all steady state cycles contained in the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor progress)
          Returns the set of all steady state cycles contained in the provided fluxome.
 ProgressMonitor getProgress()
          Returns a progress monitor for this cycle computer.
 int getTotal(IrrevRxnFluxome fluxome)
          Returns 3.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MetatoolExtCurrComputer

public MetatoolExtCurrComputer(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 ExtremeCurrentComputer
Returns:
a progress monitor for this cycle computer.

getTotal

public int getTotal(IrrevRxnFluxome fluxome)
Returns 3.

Specified by:
getTotal in interface ExtremeCurrentComputer
Parameters:
fluxome - the fluxome for which the number of operations will be returned.
Returns:
3.

getMatrix

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

Specified by:
getMatrix in interface ExtremeCurrentComputer
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.
Throws:
java.lang.UnsupportedOperationException - if the provided fluxome contains exchange reactions.

getMatrix

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

Specified by:
getMatrix in interface ExtremeCurrentComputer
Parameters:
fluxome - the fluxome for which all cycles will be returned.
progress - the progress monitor to be used during computation of extreme currents.
Returns:
the extreme current matrix. Column variables are reaction names, and each row represents a steady state cycle.
Throws:
java.lang.UnsupportedOperationException - if the provided fluxome contains exchange reactions.