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java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<F,FbaOptimizer.Results>
sbrt.kernel.fba.proc.CvObjectiveFunctionProcess<F>
F
- the fluxome type.public final class CvObjectiveFunctionProcess<F extends Fluxome>
This class is used to perform constraint-variation objective function processes.
Constructor Summary | |
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CvObjectiveFunctionProcess(FbaOptimizer<F> computer)
Constructs a new constraint-variation objective function process. |
Method Summary | |
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F |
getFluxome()
Returns the fluxome used in this process. |
OptSense |
getOptimizationSense()
Returns the current optimization sense. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this process. |
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 |
setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
Sets the objective function input source. |
void |
setOptimizationSense(OptSense sense)
Sets the optimization sense 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 CvObjectiveFunctionProcess(FbaOptimizer<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 OptSense getOptimizationSense()
public void setOptimizationSense(OptSense sense)
sense
- an optimization sense.public void setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
objectiveSource
- a source of objective functions whose
optimal values are to be computed.public void setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
constraintSource
- a source of constraint sets whose effect upon application is
to be computed.public ProgressMonitor getProgress()
getProgress
in interface MonitoredProcess<FbaOptimizer.Results>
public void run(ResultsManager<FbaOptimizer.Results> resultsManager)
First, a set of flux constraints is retrieved from the constraint source
and applied. Then an objective function is retrieved from the objective
source. The optimal value is computed and the results are added to the
results manager. Each objective function is iterated through in the same
fashion. When the end of the objective source is reached, the flux
constraints are restored to their original value and
resultsManager.breakPoint()
is called. At this point, the next
set of flux constraints is retrieved from the constraint source. The
entire process is repeated until the end of the constraint source is
reached.
run
in interface KernelProcess<FbaOptimizer.Results>
resultsManager
- the results manager to which the results will be added.
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