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

java.lang.Object
  extended by sbrt.kernel.fba.proc.FbaProcess<F,R>
      extended by sbrt.kernel.fba.proc.AbstractCvFbaOptProcess<F,java.util.Map<java.lang.String,Interval>>
          extended by sbrt.kernel.fba.proc.CvFluxIntervalProcess<F>
Type Parameters:
F - the fluxome type.
All Implemented Interfaces:
KernelProcess<java.util.Map<java.lang.String,Interval>>, MonitoredProcess<java.util.Map<java.lang.String,Interval>>

public final class CvFluxIntervalProcess<F extends Fluxome>
extends AbstractCvFbaOptProcess<F,java.util.Map<java.lang.String,Interval>>
implements MonitoredProcess<java.util.Map<java.lang.String,Interval>>

This class is used to perform constraint variation flux interval processes.

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

Constructor Summary
CvFluxIntervalProcess(FluxIntervalComputer<F> computer)
          Constructs a new constraint variation flux interval process.
 
Method Summary
 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
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

CvFluxIntervalProcess

public CvFluxIntervalProcess(FluxIntervalComputer<F> computer)
Constructs a new constraint variation flux interval process.

Parameters:
computer - the computer with which all flux intervals will be computed.
Method Detail

getFluxome

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

Specified by:
getFluxome in class FbaProcess<F extends Fluxome,java.util.Map<java.lang.String,Interval>>
Returns:
the fluxome used in this process.

getProgress

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

Specified by:
getProgress in interface MonitoredProcess<java.util.Map<java.lang.String,Interval>>
Returns:
a progress monitor for this process.

setConstraintSource

public void setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source.

Parameters:
constraintSource - a source of constraint sets whose effect upon application is to be computed.

setReactionNames

public void setReactionNames(java.util.Collection<java.lang.String> reactionNames)
Sets the names of reactions for which flux intervals are to be computed.

Parameters:
reactionNames - the names of reactions for which flux intervals are to be computed.

run

public 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.

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.

Specified by:
run in interface KernelProcess<java.util.Map<java.lang.String,Interval>>
Parameters:
resultsManager - the results manager to which the results will be added.