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

java.lang.Object
  extended by sbrt.kernel.fba.proc.FbaProcess<F,FbaOptimizer.Results>
      extended by sbrt.kernel.fba.proc.FbaOptProcess<F>
Type Parameters:
F - the fluxome type.
All Implemented Interfaces:
KernelProcess<FbaOptimizer.Results>

public final class FbaOptProcess<F extends Fluxome>
extends FbaProcess<F,FbaOptimizer.Results>

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

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

Constructor Summary
FbaOptProcess(FbaOptimizer<F> computer)
          Constructs a new FBA optimization process.
 
Method Summary
 F getFluxome()
          Returns the fluxome used in this process.
 LinearComb<java.lang.String> getObjectiveFunction()
          Returns the current objective function.
 OptSense getOptimizationSense()
          Returns the current optimization sense.
 void run(ResultsManager<FbaOptimizer.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(OptSense 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

FbaOptProcess

public FbaOptProcess(FbaOptimizer<F> computer)
Constructs a new FBA optimization process.

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

getFluxome

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

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

getObjectiveFunction

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

Returns:
the current objective function.

getOptimizationSense

public OptSense 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(OptSense sense)
Sets the optimization sense to the provided value.

Parameters:
sense - an optimization sense.

run

public void run(ResultsManager<FbaOptimizer.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.