sbrt.kernel.fba.proc
Class FbaOptimizationProcess

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

public final class FbaOptimizationProcess
extends FbaProcess<FbaOptComputer.Results>

This class is used to perform basic Flux Balance Analysis optimization.

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

Constructor Summary
FbaOptimizationProcess(FbaOptComputer computer)
          Constructs a new FBA optimization experiment.
 
Method Summary
 Fluxome getFluxome()
          Returns the fluxome used in this experiment.
 LinearComb<java.lang.String> getObjectiveFunction()
          Returns the current objective function.
 OptimizationSense getOptimizationSense()
          Returns the current optimization sense.
 void run(ResultsManager<FbaOptComputer.Results> resultsManager)
          Computes the optimal value of the current objective function and adds the results to the provided results manager via its ResultsManager.addData(Object) method.
 void setObjectiveFunction(LinearComb<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 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

FbaOptimizationProcess

public FbaOptimizationProcess(FbaOptComputer computer)
Constructs a new FBA optimization experiment.

Parameters:
computer - the computer with which all optimizations will be performed.
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.

getObjectiveFunction

public LinearComb<java.lang.String> getObjectiveFunction()
Returns the current objective function.

Returns:
the current objective function.

getOptimizationSense

public OptimizationSense getOptimizationSense()
Returns the current optimization sense.

Returns:
the current optimization sense.

setObjectiveFunction

public void setObjectiveFunction(LinearComb<java.lang.String> objective)
Sets the objective function to the provided mathematical expression.

Parameters:
objective - a mathematical expression of reaction names.

setOptimizationSense

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

Parameters:
sense - an optimization sense.

run

public void run(ResultsManager<FbaOptComputer.Results> resultsManager)
Computes the optimal value of the current objective function and adds the results to the provided results manager via its ResultsManager.addData(Object) method.

Parameters:
resultsManager - the results manager to which the computed results will be added.