msemistate.h

/*
 Copyright (C) 2003 Ronald C Beavis, all rights reserved
 X! tandem 
 This software is a component of the X! proteomics software
 development project

Use of this software governed by the Artistic license, as reproduced here:

The Artistic License for all X! software, binaries and documentation

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*/

#ifndef MSEMISTATE_H
#define MSEMISTATE_H

// File version: 2005-12-01
/*
  modified December 2010 by Insilicos LLC to support object serialization for 
  Hadoop and MPI use
*/
/*
 * msemistate is a specialty class used to store information necessary for the state machine that
 * mprocess uses to perform semi-enzymatic cleavages
 */

class mpyrostate
{
public:
	mpyrostate(void)	{
		m_bPotential = false;
		m_bPyro = false;
		m_dModMass = 0.0;
		m_cRes = '\0';
	}
	virtual ~mpyrostate(void)	{
	}
	bool m_bPotential;
	bool m_bPyro;
	double m_dModMass;
	char m_cRes;
};

class msemistate
{
public:
      msemistate(void) { 
	    m_lLastCleave = -1;
		m_lStart = 0;
		m_lEnd = 0;
		m_lStartI = 0;
		m_lEndI = 0;
		m_bStart = true;
		m_lLimit = 5;
		m_bActive = false;
      }
      virtual ~msemistate(void) {
      }

	  bool activate(const bool _b)	{
		  m_bActive = _b;
		  return m_bActive;
	  }

	  bool is_active()	{
		  return m_bActive;
	  }

	  long limit(const long _l)	{
		  if(_l >= 0)	{
			  m_lLimit = _l;
		  }
		  return m_lLimit;
	  }

	  bool reset(const long _s,const long _e,const long _c)	{
		  if(!m_bActive)	{
			  return false;
		  }
		  m_lLastCleave = _c;
		  m_lStartI = _s;
		  m_lEndI =_e;
		  m_lStart = _s;
		  m_lEnd = _e;
		  m_lEnd--;
		  m_bStart = true;
		  return true;
	  }

	  bool next(long &_s,long &_e)	{
		  if(!m_bActive)	{
			  return false;
		  }
		  if(m_bStart)	{
			  _s = m_lStart;
			  _e = m_lEnd;
			  m_lEnd--;
			  if(m_lEnd == m_lLastCleave || m_lEnd - m_lStart < m_lLimit)	{
				  m_bStart = false;
				  m_lEnd = m_lEndI;
				  m_lStart++;
			  }
			  return true;
		  }
		  else	{
			  if((m_lLastCleave != -1 && m_lStart > m_lLastCleave) || m_lEnd - m_lStart < m_lLimit)	{
				  _s = m_lStartI;
				  _e = m_lEndI;
				  return false;
			  }
			  _s = m_lStart;
			  _e = m_lEnd;
			  m_lStart++;
			  return true;
		  }
		  return false;
	  }

//private:  for serialization access bpratt
	  bool m_bActive;
	  long m_lStart;
	  long m_lEnd;
	  long m_lStartI;
	  long m_lEndI;
	  bool m_bStart;
	  long m_lLimit;
	  long m_lLastCleave;
};

#endif