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

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

public final class ObjFunAnalysis<F extends Fluxome>
extends FbaProcess<F,FbaOptimizer.Results>
implements MonitoredProcess<FbaOptimizer.Results>

This class is used to perform objective function analyses.

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

Constructor Summary
ObjFunAnalysis(FbaOptimizer<F> computer)
          Constructs a new objective function process.
 
Method Summary
 F getFluxome()
          Returns the fluxome used in this process.
 OptSense getOptimizationSense()
          Returns the current optimization sense.
 ProgressMonitor getProgress()
          Returns a progress monitor for this process.
 void run(ResultsManager<FbaOptimizer.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(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

ObjFunAnalysis

public ObjFunAnalysis(FbaOptimizer<F> computer)
Constructs a new objective function process.

Parameters:
computer - the computer with which all results 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,FbaOptimizer.Results>
Returns:
the fluxome used in this process.

getOptimizationSense

public OptSense getOptimizationSense()
Returns the current optimization sense.

Returns:
the current optimization sense.

setOptimizationSense

public void setOptimizationSense(OptSense 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 process.

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

run

public void run(ResultsManager<FbaOptimizer.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<FbaOptimizer.Results>
Parameters:
resultsManager - the results manager to which the results will be added.