sbrt.kernel.fba.proc
Class SvInitialPointProcess<F extends Fluxome>

java.lang.Object
  extended by sbrt.kernel.fba.proc.FbaProcess<F,R>
      extended by sbrt.kernel.fba.proc.AbstractCvFbaOptProcess<F,InitialPointComputer.Results>
          extended by sbrt.kernel.fba.proc.SvInitialPointProcess<F>
Type Parameters:
F - the fluxome type.
All Implemented Interfaces:
KernelProcess<InitialPointComputer.Results>, MonitoredProcess<InitialPointComputer.Results>

public final class SvInitialPointProcess<F extends Fluxome>
extends AbstractCvFbaOptProcess<F,InitialPointComputer.Results>
implements MonitoredProcess<InitialPointComputer.Results>

This class is used to perform flux space variation initial point processes. Initial points are required for random flux vector processes.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.
See Also:
CdHarFluxVectorProcess

Constructor Summary
SvInitialPointProcess(InitialPointComputer<F> computer)
          Constructs a new constraint variation initial point process.
 
Method Summary
 F getFluxome()
          Returns the fluxome used in this initial point process.
 ProgressMonitor getProgress()
          Returns a progress monitor for this process.
 void run(ResultsManager<InitialPointComputer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
 void setIntervalSource(java.lang.Iterable<FluxConstraints> intervalSource)
          Sets the flux interval input source.
 
Methods inherited from class sbrt.kernel.fba.proc.AbstractCvFbaOptProcess
restoreConstraints, setConstraints
 
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

SvInitialPointProcess

public SvInitialPointProcess(InitialPointComputer<F> computer)
Constructs a new constraint variation initial point process.

Parameters:
computer - the computer with which initial points will be computed.
Method Detail

getFluxome

public F getFluxome()
Returns the fluxome used in this initial point process.

Specified by:
getFluxome in class FbaProcess<F extends Fluxome,InitialPointComputer.Results>
Returns:
the fluxome used in this initial point process.

setIntervalSource

public void setIntervalSource(java.lang.Iterable<FluxConstraints> intervalSource)
Sets the flux interval input source.

Parameters:
intervalSource - a source of flux intervals.

getProgress

public ProgressMonitor getProgress()
Returns a progress monitor for this process.

Specified by:
getProgress in interface MonitoredProcess<InitialPointComputer.Results>
Returns:
a progress monitor for this process.

run

public void run(ResultsManager<InitialPointComputer.Results> resultsManager)
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.

First, a set of flux intervals is retrieved from the interval source and applied as constraints. Then the initial point is 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.

Specified by:
run in interface KernelProcess<InitialPointComputer.Results>
Parameters:
resultsManager - the results manager to which the results will be added.