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java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<FbaOptComputer.Results>
sbrt.kernel.fba.proc.FbaOptimizationProcess
public final class FbaOptimizationProcess
This class is used to perform basic Flux Balance Analysis optimization.
Constructor Summary | |
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FbaOptimizationProcess(FbaOptComputer computer)
Constructs a new FBA optimization experiment. |
Method Summary | |
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Fluxome |
getFluxome()
Returns the fluxome used in this experiment. |
LinearComb<java.lang.String> |
getObjectiveFunction()
Returns the current objective function. |
OptimizationSense |
getOptimizationSense()
Returns the current optimization sense. |
void |
run(ResultsManager<FbaOptComputer.Results> resultsManager)
Computes the optimal value of the current objective function and adds the results to the provided results manager via its ResultsManager.addData(Object) method. |
void |
setObjectiveFunction(LinearComb<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
setOptimizationSense(OptimizationSense 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 FbaOptimizationProcess(FbaOptComputer computer)
computer
- the computer with which all optimizations will be performed.Method Detail |
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public Fluxome getFluxome()
getFluxome
in class FbaProcess<FbaOptComputer.Results>
public LinearComb<java.lang.String> getObjectiveFunction()
public OptimizationSense getOptimizationSense()
public void setObjectiveFunction(LinearComb<java.lang.String> objective)
objective
- a mathematical expression of reaction names.public void setOptimizationSense(OptimizationSense sense)
sense
- an optimization sense.public void run(ResultsManager<FbaOptComputer.Results> resultsManager)
ResultsManager.addData(Object)
method.
resultsManager
- the results manager to which the computed results will be
added.
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