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

java.lang.Object
  extended by sbrt.kernel.fba.proc.FbaProcess<F,java.util.Map<java.lang.String,Interval>>
      extended by sbrt.kernel.fba.proc.FluxIntervalProcess<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 FluxIntervalProcess<F extends Fluxome>
extends FbaProcess<F,java.util.Map<java.lang.String,Interval>>
implements MonitoredProcess<java.util.Map<java.lang.String,Interval>>

This class is used to perform flux interval computations.

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

Constructor Summary
FluxIntervalProcess(FluxIntervalComputer<F> computer)
          Constructs a new flux interval process.
 
Method Summary
 F getFluxome()
          Returns the fluxome used in this proces.
 ProgressMonitor getProgress()
          Returns a progress monitor for this process.
 void run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
          Computes the flux intervals of the reactions with the current names and adds them to the provided results manager.
 void setReactionNames(java.util.Set<java.lang.String> reactionNames)
          Sets the names of reactions for which flux ranges are to be computed.
 
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

FluxIntervalProcess

public FluxIntervalProcess(FluxIntervalComputer<F> computer)
Constructs a new flux interval process.

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

setReactionNames

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

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

getFluxome

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

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.

run

public void run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
Computes the flux intervals of the reactions with the current names and adds them to the provided results manager.

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