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java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<F,FbaOptimizer.Results>
sbrt.kernel.fba.proc.RxnDeletionProcess<F>
F
- a type of fluxome.public final class RxnDeletionProcess<F extends Fluxome>
This class is used to perform reaction deletion processes.
Constructor Summary | |
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RxnDeletionProcess(RxnDeletionComputer<F> computer)
Constructs a new reaction 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. |
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 |
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 |
setRxnDeletionSource(java.lang.Iterable<java.util.Set<java.lang.String>> deletionSource)
Sets the reaction deletion input source. |
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 RxnDeletionProcess(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 Fluxome,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 setRxnDeletionSource(java.lang.Iterable<java.util.Set<java.lang.String>> deletionSource)
deletionSource
- a source of reaction 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 reaction 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.
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