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java.lang.Objectsbrt.kernel.fba.comp.SlpCycleComputer
public class SlpCycleComputer
This class is used to identify the steady state cycles in stoichiometric networks. This is accomplished by removing all exchange reactions from a network and then identifying the extreme currents of the sub-network. Those extreme currents are necessarily cycles, and are also the set of all Type III extreme pathways of the sub-network.
Constructor Summary | |
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SlpCycleComputer(ExtremeCurrentComputer computer)
Constructs a new steady state cycle computer from the given extreme current computer. |
Method Summary | |
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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 steady state cycle computer. |
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 SlpCycleComputer(ExtremeCurrentComputer computer)
computer
- the computer with which all extreme currents will be identified.Method Detail |
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public ProgressMonitor getProgress()
getProgress
in interface CycleComputer<IrrevRxnFluxome>
public SparseDoubleMatrix<?,java.lang.String> getCycles(IrrevRxnFluxome fluxome)
getCycles
in interface CycleComputer<IrrevRxnFluxome>
fluxome
- the fluxome for which all cycles will be identified.
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