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java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<F,FbaOptimizer.Results>
sbrt.kernel.fba.proc.CatalystDeletionProcess<F>
F
- the fluxome type.public final class CatalystDeletionProcess<F extends CatalyzedFluxome>
This class is used to perform catalyst deletion processes.
Constructor Summary | |
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CatalystDeletionProcess(RxnDeletionComputer<F> computer)
Constructs a new catalyst deletion process. |
Method Summary | |
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F |
getFluxome()
Returns the fluxome used by the reaction deletion computer. |
MathExpr<java.lang.String> |
getObjectiveFunction()
Returns the current objective function. |
OptSense |
getOptimizationSense()
Returns the current optimization sense. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this process. |
static java.util.Set<java.lang.String> |
getRxnNames(java.util.Set<java.lang.String> catalysts,
CatalyzedFluxome fluxome)
Returns the set of names of reactions whose activity depends on the provided set of catalysts. |
double |
getZeroCutoff()
Returns the current zero cutoff used by the reaction deletion computer. |
void |
run(ResultsManager<FbaOptimizer.Results> resultsManager)
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method. |
void |
setCatalystDelSource(java.lang.Iterable<java.util.Set<java.lang.String>> deletionSource)
Sets the catalyst deletion input source. |
void |
setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
setOptimizationSense(OptSense sense)
Sets the optimization sense to the provided value. |
void |
setZeroCutoff(double zeroCutoff)
Sets the zero cutoff to the provided value. |
Methods inherited from class sbrt.kernel.fba.proc.FbaProcess |
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toString |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public CatalystDeletionProcess(RxnDeletionComputer<F> computer)
computer
- the computer with which all results will be computed.Method Detail |
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public F getFluxome()
getFluxome
in class FbaProcess<F extends CatalyzedFluxome,FbaOptimizer.Results>
public double getZeroCutoff()
public MathExpr<java.lang.String> getObjectiveFunction()
public OptSense getOptimizationSense()
public void setObjectiveFunction(MathExpr<java.lang.String> objective)
objective
- a mathematical expression of reaction names.public void setOptimizationSense(OptSense sense)
sense
- an optimization sense.public void setCatalystDelSource(java.lang.Iterable<java.util.Set<java.lang.String>> deletionSource)
deletionSource
- a source of catalyst names sets whose effect upon
deletion is to be computed.public void setZeroCutoff(double zeroCutoff)
zeroCutoff
- the zero cutoff.public ProgressMonitor getProgress()
getProgress
in interface MonitoredProcess<FbaOptimizer.Results>
public void run(ResultsManager<FbaOptimizer.Results> resultsManager)
A set of catalyst names is retrieved from the deletion source, their effect upon deletion is computed, and the results are added to the provided results manager. This is repeated until the end of the deletion source is reached.
run
in interface KernelProcess<FbaOptimizer.Results>
resultsManager
- the results manager to which the results will be added.public static java.util.Set<java.lang.String> getRxnNames(java.util.Set<java.lang.String> catalysts, CatalyzedFluxome fluxome)
catalysts
- a set of catalyst names.fluxome
- the fluxome containing the reaction-catalyst association.
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