|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<FbaOptComputer.Results>
sbrt.kernel.fba.proc.CvFbaOptimizationExperiment
public final class CvFbaOptimizationExperiment
This class is used to perform constraint-variation FBA optimization experiments.
Constructor Summary | |
---|---|
CvFbaOptimizationExperiment(FbaOptComputer computer)
Constructs a new constraint-variation FBA optimization experiment. |
Method Summary | |
---|---|
Fluxome |
getFluxome()
Returns the fluxome used in this experiment. |
MathExpr<java.lang.String> |
getObjectiveFunction()
Returns the current objective function. |
OptimizationSense |
getOptimizationSense()
Returns the current optimization sense. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this experiment. |
void |
run(ResultsManager<FbaOptComputer.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 |
setObjectiveFunction(MathExpr<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 |
---|
toString |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public CvFbaOptimizationExperiment(FbaOptComputer computer)
computer
- the computer with which all results will be computed.Method Detail |
---|
public Fluxome getFluxome()
getFluxome
in class FbaProcess<FbaOptComputer.Results>
public MathExpr<java.lang.String> getObjectiveFunction()
public OptimizationSense getOptimizationSense()
public void setObjectiveFunction(MathExpr<java.lang.String> objective)
objective
- a mathematical expression of reaction names.public void setOptimizationSense(OptimizationSense sense)
sense
- an optimization sense.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<FbaOptComputer.Results>
public void run(ResultsManager<FbaOptComputer.Results> resultsManager)
ResultsManager.addData(Object)
method.A set of flux constraints is retrieved from the constraint source, their effect 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<FbaOptComputer.Results>
resultsManager
- the results manager
to which the results will be added.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |