CLNATask.h

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// Begin CVS Header
//   $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/lna/CLNATask.h,v $
//   $Revision: 1.1 $
//   $Name:  $
//   $Author: jpahle $
//   $Date: 2011/05/24 17:33:45 $
// 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.

/**
 * CLNATask class.
 *
 * This class implements a linear noise approximation analysis task which is comprised
 * of a problem and a method.
 *
 * Created for Copasi by Juergen Pahle 2010
 */

#ifndef COPASI_CLNATask_H__
#define COPASI_CLNATask_H__

#include <iostream>

#include "utilities/CCopasiTask.h"
#include "utilities/CMatrix.h"
#include "utilities/CReadConfig.h"
#include "steadystate/CSteadyStateMethod.h"
#include "steadystate/CSteadyStateProblem.h"
#include "steadystate/CEigen.h"

class CLNAProblem;
class CState;

class CLNATask : public CCopasiTask
{
  //Attributes
private:

  //Operations
public:

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

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

  /**
   * Destructor
   */
  virtual ~CLNATask();

  /**
   * Create a method of the specified type to solve the task.
   * It is the duty of the caller to release the CCopasiMethod.
   * @param const CCopasiMethod::SubType & type
   * @return CCopasiMethod *
   */
  virtual CCopasiMethod * createMethod(const int & type) const;

  /**
   * Resizes result matrices and updates array annotations for a specific task.
   * This is used when we need to know about the data structures of a task result
   * without actually performing the task, e.g. when selecting objects for output.
   * For now we assume that this functionality is also performed when
   * initialize() is called.
   */
  virtual bool updateMatrices();

  /**
   * Initialize the task. If an ostream is given this ostream is used
   * instead of the target specified in the report. This allows nested
   * tasks to share the same output device.
   * @param const OutputFlag & of
   * @param COutputHandler * pOutputHandler
   * @param std::ostream * pOstream (default: NULL)
   * @return bool success
   */
  virtual bool initialize(const OutputFlag & of,
                          COutputHandler * pOutputHandler,
                          std::ostream * pOstream);

  /**
   * Process the task with or without initializing to the initial state.
   * @param const bool & useInitialValues
   * @return bool success
   */
  virtual bool process(const bool & useInitialValues);

  /**
   * Perform neccessary cleanup procedures
   */
  virtual bool restore();

  /**
   * Loads parameters for this solver with data coming from a
   * CReadConfig object. (CReadConfig object reads an input stream)
   * @param configbuffer reference to a CReadConfig object.
   */
  void load(CReadConfig & configBuffer);

  // Friend functions
  friend std::ostream &operator<<(std::ostream &os,
                                  const CLNATask &A);

  /**
   * This functionality is expected from the problem but has to be implemented
   * here for the moment. This is called from the corresponding method of the problem
   */
  void printResult(std::ostream * ostream) const;

private:
  /**
   * cleanup()
   */
  void cleanup();
};

#endif // COPASI_CLNATask_H__