sbrt.kernel.fba.proc
Class ObjectiveFunctionAnalysis

java.lang.Object
  extended by sbrt.kernel.fba.proc.FbaProcess<FbaOptComputer.Results>
      extended by sbrt.kernel.fba.proc.ObjectiveFunctionAnalysis
All Implemented Interfaces:
KernelProcess<FbaOptComputer.Results>, MonitoredProcess<FbaOptComputer.Results>

public final class ObjectiveFunctionAnalysis
extends FbaProcess<FbaOptComputer.Results>
implements MonitoredProcess<FbaOptComputer.Results>

This class is used to perform objective function experiments.

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

Constructor Summary
ObjectiveFunctionAnalysis(FbaOptComputer computer)
          Constructs a new objective function experiment.
 
Method Summary
 Fluxome getFluxome()
          Returns the fluxome used in this experiment.
 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 setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
          Sets the objective function input source.
 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

ObjectiveFunctionAnalysis

public ObjectiveFunctionAnalysis(FbaOptComputer computer)
Constructs a new objective function experiment.

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

getFluxome

public Fluxome getFluxome()
Returns the fluxome used in this experiment.

Specified by:
getFluxome in class FbaProcess<FbaOptComputer.Results>
Returns:
the fluxome used in this experiment.

getOptimizationSense

public OptimizationSense getOptimizationSense()
Returns the current optimization sense.

Returns:
the current optimization sense.

setOptimizationSense

public void setOptimizationSense(OptimizationSense sense)
Sets the optimization sense to the provided value.

Parameters:
sense - an optimization sense.

setObjectiveFunctionSource

public void setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
Sets the objective function input source.

Parameters:
objectiveSource - a source of objective functions whose optimal values are to be computed.

getProgress

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

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

run

public 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.

An objective function is retrieved from the objective source, its optimal value is computed, and the results are added to the provided results manager. This is repeated until the end of the objective source is reached.

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