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

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

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

This class is used to analyze the plasticity of fluxes.

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

Nested Class Summary
static class FluxPlasticityProcess.Results
          This class is used to represent the results of a flux plasticity process.
 
Constructor Summary
FluxPlasticityProcess(F fluxome)
          Constructs a new flux plasticity process.
 
Method Summary
 F getFluxome()
          Returns the fluxome used in this flux plasticity process.
 ProgressMonitor getProgress()
          Returns a progress monitor for this process.
 void run(ResultsManager<FluxPlasticityProcess.Results> resultsManager)
          Iterates thru the flux interval source set via setFluxRangeSource(Iterable), computes the flux plasticity measures, and adds the results of each to the provided results manager.
 void setFluxIntervalSource(java.lang.Iterable<java.util.Map<java.lang.String,Interval>> intervalSource)
          Sets the flux interval source.
 void setZeroCutoff(double zeroCutoff)
          Sets the zero cutoff 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

FluxPlasticityProcess

public FluxPlasticityProcess(F fluxome)
Constructs a new flux plasticity process.

Parameters:
fluxome - the fluxome for which flux plasticities will be determined.
Method Detail

getFluxome

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

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

getProgress

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

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

setFluxIntervalSource

public void setFluxIntervalSource(java.lang.Iterable<java.util.Map<java.lang.String,Interval>> intervalSource)
Sets the flux interval source. These are the flux intervals for which flux plasticities will be measured.

Parameters:
intervalSource - a source of flux ranges, or constraints.

setZeroCutoff

public void setZeroCutoff(double zeroCutoff)
Sets the zero cutoff to the provided value. The zero cutoff is the value used to decide which computed values are close enough to zero to be considered equal to zero. This value is an upper bound and should itself be close to zero, like 1E-6 for example.

Parameters:
zeroCutoff - the zero cutoff.

run

public void run(ResultsManager<FluxPlasticityProcess.Results> resultsManager)
Iterates thru the flux interval source set via setFluxRangeSource(Iterable), computes the flux plasticity measures, and adds the results of each to the provided results manager.

Specified by:
run in interface KernelProcess<FluxPlasticityProcess.Results>
Parameters:
resultsManager - the results manager to which each set of results is added.