|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.comp.SlpExCurrComputerV2
public class SlpExCurrComputerV2
This class is an implementation of an algorithm for identifying extreme currents in stoichiometric networks. This algorithm was described in the paper: C. Schilling, D. Letscher and B. O. Palsson, Theory for systemic definition of metabolic pathways and their use in intrepreting metabolic function from a pathway-oriented perspective. Journal of Theoretical Biology 203 (2000), pp. 285-301. This algorithm was intended for computing extreme pathways, but it has been modified here to compute extreme currents instead. A brief mention of extreme currents can be found in the paper cited above.
Constructor Summary | |
---|---|
SlpExCurrComputerV2()
Constructs a new extreme current computer. |
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. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public SlpExCurrComputerV2()
Method Detail |
---|
public ProgressMonitor getProgress()
getProgress
in interface ExtremeCurrentComputer
public int getTotalOps(IrrevRxnFluxome fluxome)
getTotalOps
in interface ExtremeCurrentComputer
fluxome
- the fluxome for which the number of operations will be returned.
public SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome)
getMatrix
in interface ExtremeCurrentComputer
fluxome
- the fluxome for which all extreme currents will be
computed.
public SparseDoubleMatrix<?,java.lang.String> getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor pm)
getMatrix
in interface ExtremeCurrentComputer
fluxome
- the fluxome for which all extreme currents will be computed.pm
- the progress monitor to be used during computation of extreme
currents.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |