CLNAMethod.h

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// Begin CVS Header
//   $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/lna/CLNAMethod.h,v $
//   $Revision: 1.1 $
//   $Name:  $
//   $Author: jpahle $
//   $Date: 2011/05/24 17:33:44 $
// End CVS Header

// Copyright (C) 2011 by Pedro Mendes, Virginia Tech Intellectual
// Properties, Inc., University of Heidelberg, and The University
// of Manchester.
// All rights reserved.

#ifndef COPASI_CLNAMethod_H__
#define COPASI_CLNAMethod_H__

#include <vector>
#include "utilities/CMatrix.h"
#include "utilities/CCopasiMethod.h"
#include "utilities/CAnnotatedMatrix.h"
#include "steadystate/CSteadyStateMethod.h"

#define LNA_OK 0
#define LNA_NOT_OK 1

class CModel;

class CLNAMethod: public CCopasiMethod
{
public:
  enum EVStatus
  {
    allNeg = 0,
    nonNegEigenvaluesExist
  };

private:

  CModel * mpModel;

  /**
   * LNA Matrices
   */
  CMatrix<C_FLOAT64> mBMatrixReduced;
  CArrayAnnotation* mBMatrixReducedAnn;

  CMatrix<C_FLOAT64> mCovarianceMatrixReduced;
  CArrayAnnotation* mCovarianceMatrixReducedAnn;

  CMatrix<C_FLOAT64> mCovarianceMatrix;
  CArrayAnnotation* mCovarianceMatrixAnn;

  // Jacobian matrix of the reduced system
  CMatrix<C_FLOAT64> mJacobianReduced;

  // Link matrix that links the dependent and the reduced system
  CMatrix<C_FLOAT64> mL;

  C_FLOAT64 mSteadyStateResolution;

  CSteadyStateMethod::ReturnCode mSSStatus;

  CLNAMethod::EVStatus mEVStatus;

  void initObjects();

public:
  /**
   * Create a LNA method.
   * Note: the returned object has to be released after use with delete
   */
  static CLNAMethod * createMethod(CCopasiMethod::SubType subType = CCopasiMethod::linearNoiseApproximation);


  /**
   * Default constructor
   * @param const CCopasiContainer * pParent (Default: NULL)
   */
  CLNAMethod(const CCopasiContainer * pParent = NULL);

  /**
   * Copy constructor
   * @param const CLNAMethod & src
   * @param const CCopasiContainer * pParent (Default: NULL)
   */
  CLNAMethod(const CLNAMethod & src,
             const CCopasiContainer * pParent = NULL);

  /**
   * Deconstructor
   */
  virtual ~CLNAMethod();

  /**
   * This methods must be called to elevate subgroups to
   * derived objects. The default implementation does nothing.
   * @return bool success
   */
  virtual bool elevateChildren();

  const CMatrix<C_FLOAT64> & getBMatrixReduced() const
  {return mBMatrixReduced;}

  const CArrayAnnotation* getBMatrixReducedAnn() const
  {return mBMatrixReducedAnn;}

  const CMatrix<C_FLOAT64> & getCovarianceMatrix() const
  {return mCovarianceMatrix;}

  const CArrayAnnotation* getCovarianceMatrixAnn() const
  {return mCovarianceMatrixAnn;}

  const CMatrix<C_FLOAT64> & getCovarianceMatrixReduced() const
  {return mCovarianceMatrixReduced;}

  const CArrayAnnotation* getCovarianceMatrixReducedAnn() const
  {return mCovarianceMatrixReducedAnn;}

  // remove the following, or change scaled versions to
  // fano factors, coefficient of variations etc.
  const CArrayAnnotation* getScaledBMatrixReducedAnn() const
  {return mBMatrixReducedAnn;}

  const CArrayAnnotation* getUnscaledBMatrixReducedAnn() const
  {return mBMatrixReducedAnn;}

  const CArrayAnnotation* getScaledCovarianceMatrixAnn() const
  {return mCovarianceMatrixAnn;}

  const CArrayAnnotation* getScaledCovarianceMatrixReducedAnn() const
  {return mCovarianceMatrixReducedAnn;}

  const CArrayAnnotation* getUnscaledCovarianceMatrixAnn() const
  {return mCovarianceMatrixAnn;}

  const CArrayAnnotation* getUnscaledCovarianceMatrixReducedAnn() const
  {return mCovarianceMatrixReducedAnn;}


  int calculateCovarianceMatrixReduced();

  void calculateCovarianceMatrixFull();

  /**
   * Resizes all result matrices and updates the corresponding
   * array annotations.
   * This needs to be called before output initialization (in case
   * the output references parts of the matrix) from the task
   * initialization, but it also needs to be called before
   * selecting elements of the matrices in the object selection
   * dialog.
   * The model needs to be set before calling this.
   */
  virtual void resizeAllMatrices();

  /**
   * Set the Model
   */
  void setModel(CModel* model);

  /**
   * Get the Model
   */
  const CModel* getModel() const;

  /**
   * the LNA entry point
   */
  int CalculateLNA();

  /**
   *
   */
  virtual bool process();

  /**
   * Read some parameters from configuration file
   */
  C_INT32 load(CReadConfig & configBuffer);

  void setSteadyStateStatus(CSteadyStateMethod::ReturnCode SSStatus);

  void setEigenValueStatus(CLNAMethod::EVStatus status);

  const CSteadyStateMethod::ReturnCode & getSteadyStateStatus() const
  {return mSSStatus;}

  const CLNAMethod::EVStatus & getEigenValueStatus() const
  {return mEVStatus;}

  void setSteadyStateResolution(C_FLOAT64 factor);

  /**
  * Check if the method is suitable for this problem
  * @return bool suitability of the method
  */
  virtual bool isValidProblem(const CCopasiProblem * pProblem);

private:
  /**
   * Intialize the method parameter
   */
  void initializeParameter();
};
#endif // COPASI_CLNAMethod_H__