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java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<F,R>
sbrt.kernel.fba.proc.AbstractCvFbaOptProcess<F,java.util.Map<java.lang.String,Interval>>
sbrt.kernel.fba.proc.CvFluxIntervalProcess<F>
F
- the fluxome type.public final class CvFluxIntervalProcess<F extends Fluxome>
This class is used to perform constraint variation flux interval processes.
Constructor Summary | |
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CvFluxIntervalProcess(FluxIntervalComputer<F> computer)
Constructs a new constraint variation flux interval process. |
Method Summary | |
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F |
getFluxome()
Returns the fluxome used in this process. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this process. |
void |
run(ResultsManager<java.util.Map<java.lang.String,Interval>> 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 |
setReactionNames(java.util.Collection<java.lang.String> reactionNames)
Sets the names of reactions for which flux intervals are to be computed. |
Methods inherited from class sbrt.kernel.fba.proc.AbstractCvFbaOptProcess |
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restoreConstraints, setConstraints |
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 CvFluxIntervalProcess(FluxIntervalComputer<F> computer)
computer
- the computer with which all flux intervals will be computed.Method Detail |
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public F getFluxome()
getFluxome
in class FbaProcess<F extends Fluxome,java.util.Map<java.lang.String,Interval>>
public ProgressMonitor getProgress()
getProgress
in interface MonitoredProcess<java.util.Map<java.lang.String,Interval>>
public void setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
constraintSource
- a source of constraint sets whose effect upon application is
to be computed.public void setReactionNames(java.util.Collection<java.lang.String> reactionNames)
reactionNames
- the names of reactions for which flux intervals are to be
computed.public void run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
First, a set of flux constraints is retrieved from the constraint source and applied. Then the flux intervals of the reactions with the current names are computed and added to the provided results manager. Finally, the flux constraints are restored to their original values. This process is repeated until the end of the constraint source is reached.
run
in interface KernelProcess<java.util.Map<java.lang.String,Interval>>
resultsManager
- the results manager to which the results will be added.
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