<commit_before>/* Begin CVS Header
  $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/elementaryFluxModes/CEFMMethod.cpp,v $
  $Revision: 1.8 $
  $Name:  $
  $Author: shoops $
  $Date: 2009/09/16 16:15:35 $
  End CVS Header */

// Copyright (C) 2008 by <NAME>, Virginia Tech Intellectual
// Properties, Inc., EML Research, gGmbH, University of Heidelberg,
// and The University of Manchester.
// All rights reserved.

// Copyright (C) 2001-2007 by <NAME>, Virginia Tech Intellectual
// Properties, Inc. and EML Research, gGmbH.
// All rights reserved.

/**
 *  CEFMMethod class
 *  This class describes the interface to all optimization methods.
 *  The various method like RandomSearch or GA have to be derived from
 *  this class.
 *
 *  Created for Copasi by <NAME> 2002
 */

#include "copasi.h"

#include "CEFMTask.h"
#include "CEFMMethod.h"

#include "CEFMAlgorithm.h"
#include "CBitPatternTreeMethod.h"

#ifdef COPASI_SSA
# include "CSSAMethod.h"
#endif

CEFMMethod * CEFMMethod::createMethod(CCopasiMethod::SubType subType)
{
  CEFMMethod * pMethod = NULL;

  switch (subType)
    {
      case EFMAlgorithm:
        pMethod = new CEFMAlgorithm();
        break;

      case EFMBitPatternTreeAlgorithm:
        pMethod = new CBitPatternTreeMethod();
        break;

#ifdef COPASI_SSA
      case stoichiometricStabilityAnalysis:
        pMethod = new CSSAMethod();
        break;
#endif

      default:
        pMethod = new CEFMAlgorithm();
        break;
    }

  return pMethod;
}

// Default constructor
CEFMMethod::CEFMMethod():
    CCopasiMethod(CCopasiTask::fluxMode, CCopasiMethod::unset),
    mReorderedReactions()
{CONSTRUCTOR_TRACE;}

CEFMMethod::CEFMMethod(const CCopasiTask::Type & taskType,
                       const CEFMMethod::SubType & subType,
                       const CCopasiContainer * pParent):
    CCopasiMethod(taskType, subType, pParent),<commit_msg>Changed default method to be the new bit pattern tree algorithm.<commit_after>/* Begin CVS Header
  $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/elementaryFluxModes/CEFMMethod.cpp,v $
  $Revision: 1.9 $
  $Name:  $
  $Author: shoops $
  $Date: 2009/12/07 17:14:50 $
  End CVS Header */

// Copyright (C) 2008 by <NAME>, Virginia Tech Intellectual
// Properties, Inc., EML Research, gGmbH, University of Heidelberg,
// and The University of Manchester.
// All rights reserved.

// Copyright (C) 2001-2007 by <NAME>, Virginia Tech Intellectual
// Properties, Inc. and EML Research, gGmbH.
// All rights reserved.

/**
 *  CEFMMethod class
 *  This class describes the interface to all optimization methods.
 *  The various method like RandomSearch or GA have to be derived from
 *  this class.
 *
 *  Created for Copasi by <NAME> 2002
 */

#include "copasi.h"

#include "CEFMTask.h"
#include "CEFMMethod.h"

#include "CEFMAlgorithm.h"
#include "CBitPatternTreeMethod.h"

#ifdef COPASI_SSA
# include "CSSAMethod.h"
#endif

CEFMMethod * CEFMMethod::createMethod(CCopasiMethod::SubType subType)
{
  CEFMMethod * pMethod = NULL;

  switch (subType)
    {
      case EFMAlgorithm:
        pMethod = new CEFMAlgorithm();
        break;

      case EFMBitPatternTreeAlgorithm:
        pMethod = new CBitPatternTreeMethod();
        break;

#ifdef COPASI_SSA
      case stoichiometricStabilityAnalysis:
        pMethod = new CSSAMethod();
        break;
#endif

      default:
        pMethod = new CBitPatternTreeMethod();
        break;
    }

  return pMethod;
}

// Default constructor
CEFMMethod::CEFMMethod():
    CCopasiMethod(CCopasiTask::fluxMode, CCopasiMethod::unset),
    mReorderedReactions()
{CONSTRUCTOR_TRACE;}

CEFMMethod::CEFMMethod(const CCopasiTask::Type & taskType,
                       const CEFMMethod::SubType & subType,
                       const CCopasiContainer * pParent):
    CCopasiMethod(taskType, subType, pParent),
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