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java.lang.Objectsbrt.kernel.fba.comp.MsCycleComputer
public class MsCycleComputer
This class is used to identify the steady state cycles (Type III extreme pathways) in a fluxome. It is an implementation of the algorithm described by Mahadevan and Schilling (MS).
Constructor Summary | |
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MsCycleComputer(ProgramSolver<java.lang.Object,java.lang.Object> solver,
ExtremeCurrentComputer computer)
Constructs a new steady state cycle computer from the provided linear program solver and extreme current computer. |
Method Summary | |
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SparseDoubleMatrix<?,java.lang.String> |
getCycles(IrrevRxnFluxome fluxome)
Returns the set of all steady state cycles (Type III extreme pathways) contained in the provided fluxome. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this cycle computer. |
IrrevRxnFluxome |
getSubFluxome(IrrevRxnFluxome fluxome)
Returns the sub-fluxome resulting from linear programming. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MsCycleComputer(ProgramSolver<java.lang.Object,java.lang.Object> solver, ExtremeCurrentComputer computer)
solver
- the linear program solver with which all optimizations will
be computed.computer
- the computer with which all extreme currents will be
computed.Method Detail |
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public ProgressMonitor getProgress()
getProgress
in interface CycleComputer
public SparseDoubleMatrix<?,java.lang.String> getCycles(IrrevRxnFluxome fluxome)
getCycles
in interface CycleComputer
fluxome
- the fluxome for which all cycles will be identified.
public IrrevRxnFluxome getSubFluxome(IrrevRxnFluxome fluxome)
fluxome
- the fluxome for which a sub-fluxome will be returned.
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