sbrt.kernel.fba.comp
Interface ExtremeCurrentComputer

All Known Implementing Classes:
SlpExCurrComputerV2

public interface ExtremeCurrentComputer

This interface is used to represent extreme current computers. An extreme current is very similar to an extreme pathway. For a fluxome containing only irreversible reactions (including exchange reactions), no extreme pathways exists, only extreme currents.

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

Method Summary
 SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor pm)
          Returns the extreme current matrix for the provided fluxome.
 ProgressMonitor getProgress()
          Returns a progress monitor for this extreme current computer.
 int getTotalOps(IrrevRxnFluxome fluxome)
          Returns the total number of "operations" required to compute the extreme currents of the provided fluxome.
 

Method Detail

getMatrix

SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome)
Returns the extreme current matrix for the provided fluxome.

Parameters:
fluxome - the fluxome for which all extreme currents will be computed.
Returns:
the extreme current matrix for the provided fluxome.

getProgress

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

Returns:
a progress monitor for this extreme current computer.

getTotalOps

int getTotalOps(IrrevRxnFluxome fluxome)
Returns the total number of "operations" required to compute the extreme currents of the provided fluxome. The number returned by this method is meant to be used with progress monitors.

Parameters:
fluxome - the fluxome for which the number of operations will be returned.
Returns:
the total number of operations required to compute the extreme currents of the provided fluxome.

getMatrix

SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome,
                                                 MutableProgressMonitor pm)
Returns the extreme current matrix for the provided fluxome.

Parameters:
fluxome - the fluxome for which all extreme currents will be computed.
pm - the progress monitor to be used during computation of extreme currents.
Returns:
the extreme current matrix for the provided fluxome.