mcleave.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:

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*/

#ifndef MCLEAVE_H
#define MCLEAVE_H

// File version: 2006-03-10
/*
 * mcleave is a specialty class meant to store information about protein cleavage specificity
 * and rapidly test a peptide sequence to see if it is cleavable.
 * NOTE: mcleave.h does not have a corresponding .cpp file
 */
class mcleave_single
{
public:
	mcleave_single(void)	{
		strcpy(m_pNCleave,"KR");
		strcpy(m_pCCleave,"P");
		m_bN = true;
		m_bC = false;
		m_bNX = false;
		m_bCX = false;
		m_lType = 0;
	}
	virtual ~mcleave_single(void) { }

	char m_pNCleave[32]; // residues that are valid cleavage sites (or invalid if m_bN = false)
	char m_pCCleave[32]; // residues that are valid cleavage sites (or invalid if m_bC = false)
	bool m_bN; // if true, all residues in m_pNCleave can be N-temrinal to a cleavable bond
	bool m_bC; // if true, all residues in m_pNCleave can be C-temrinal to a cleavable bond
	bool m_bCX;
	bool m_bNX;
	unsigned long m_lType;
	mcleave_single& operator=(const mcleave_single &rhs)	{
		strcpy(m_pNCleave,rhs.m_pNCleave);
		strcpy(m_pCCleave,rhs.m_pCCleave);
		m_bN = rhs.m_bN;
		m_bC = rhs.m_bC;
		m_bNX = rhs.m_bNX;
		m_bCX = rhs.m_bCX;
		m_lType = rhs.m_lType;
		return *this;
	}
	/*
 * load takes a string containing cleavage information and parses it
 * these strings take the format:
 * A|B, where A or B are expressions of the form [xyz] or {xyz}. if square brackets, only the single letter
 * abbreviations in the brackets are valid at that position for a cleavage, and if french brackets, those
 * single letter abbreviations are the only non-valid residues at that position. For example, trypsin 
 * can be represented by [KR]|{P}, i.e. cleave C-terminal to a K or R residue, except when followed by
 * a P. The expression [X]|[X] means cleave at all residues.
 * NOTE: use of upper case characters is required for amino acid abbreviations
 */
	bool load(string &_s)	{
		if(_s == "[X]|[X]")	{
			m_lType = 0x01;
			return true;
		}
		else if(_s == "[KR]|{P}" || _s == "[RK]|{P}")	{
			m_lType = 0x02;
			return true;
		}
		m_lType = 0x04;
		size_t a = 0;
		size_t b = 0;
		if(_s[a] == '[')	{
			m_bN = true;
			a++;
			b = 0;
			while(a < _s.size() && _s[a] != ']')	{
				m_pNCleave[b] = _s[a];
				a++;
				b++;
			}
			m_pNCleave[b] = '\0';
			a = _s.find('|');
			if(a == _s.npos)
				return false;
			a++;
			if(_s[a] == '{')	{
				m_bC = false;
				a++;
				b = 0;
				while(a < _s.size() && _s[a] != '}')	{
					m_pCCleave[b] = _s[a];
					a++;
					b++;
				}
				m_pCCleave[b] = '\0';
			}
			else if(_s[a] == '[')	{
				m_bC = true;
				a++;
				b = 0;
				while(a < _s.size() && _s[a] != ']')	{
					m_pCCleave[b] = _s[a];
					a++;
					b++;
				}
				m_pCCleave[b] = '\0';
			}
		}
		else if(_s[a] == '{')	{
			m_bN = false;
			a++;
			b = 0;
			while(a < _s.size() && _s[a] != '}')	{
				m_pNCleave[b] = _s[a];
				a++;
				b++;
			}
			m_pNCleave[b] = '\0';
			a = _s.find('|');
			if(a == _s.npos)
				return false;
			a++;
			if(_s[a] == '{')	{
				m_bC = false;
				a++;
				b = 0;
				while(a < _s.size() && _s[a] != '}')	{
					m_pCCleave[b] = _s[a];
					a++;
					b++;
				}
				m_pCCleave[b] = '\0';
			}
			else if(_s[a] == '[')	{
				m_bC = true;
				a++;
				b = 0;
				while(a < _s.size() && _s[a] != ']')	{
					m_pCCleave[b] = _s[a];
					a++;
					b++;
				}
				m_pCCleave[b] = '\0';
			}
		}
		if(m_pNCleave[0] == 'X')	{
			m_bNX = true;
		}
		if(m_pCCleave[0] == 'X')	{
			m_bCX = true;
		}
		return true;
	}
/*
 * test takes the abbreviations for the residue N-terminal to a potentially cleaved bond
 * and the residue C-terminal to the bond and checks to see if the bond can be cleaved
 * according to the rules stored in the load method. load must always be called at least once
 * prior to using test, or the results may be unpredictable
 */
	bool test(const char _n,const char _c)	{
		if(m_lType & 0x01)
			return true;
		if(m_lType & 0x02)	{
			if(_n == 'K' || _n == 'R')	{
				if(_c != 'P')	{
					return true;
				}
			}
			return false;
		}
		bool bReturn = false;
		bool bN = false;
		bool bC = false;
		if(m_bNX)	{
			bN = true;
		}
		else	{
			if(strchr(m_pNCleave,_n))
				bN = true;
		}
		if(m_bN)	{
			bReturn = bN;
		}
		else	{
			bReturn = !bN;
		}
		if(!bReturn)
			return false;
		if(m_bCX)	{
			bC = true;
		}
		else	{
			if(strchr(m_pCCleave,_c))
				bC = true;
		}
		if(m_bC && bC)	{
			return true;
		}
		else if(!m_bC && !bC)	{
			return true;
		}
		return false;
	}
};

class mcleave
{
public:
	mcleave(void)	{
		m_lType = 0;
		m_vCleaves.clear();
		m_itStart = m_vCleaves.begin();
		m_itEnd = m_vCleaves.end();
	}
	virtual ~mcleave(void) { }

	vector<mcleave_single> m_vCleaves;
	vector<mcleave_single>::iterator m_itStart;
	vector<mcleave_single>::iterator m_itEnd;
	vector<mcleave_single>::iterator m_itValue;
	unsigned long m_lType;
	/*
 * load takes a string containing cleavage information and parses it
 * these strings take the format:
 * A|B, where A or B are expressions of the form [xyz] or {xyz}. if square brackets, only the single letter
 * abbreviations in the brackets are valid at that position for a cleavage, and if french brackets, those
 * single letter abbreviations are the only non-valid residues at that position. For example, trypsin 
 * can be represented by [KR]|{P}, i.e. cleave C-terminal to a K or R residue, except when followed by
 * a P. The expression [X]|[X] means cleave at all residues.
 * NOTE: use of upper case characters is required for amino acid abbreviations
 */
	bool load(string &_s)	{
		m_lType = 0x04;
		size_t a = 0;
		size_t tEnd = _s.size();
		string strTemp;
		mcleave_single clvTemp;
		m_vCleaves.clear();
		while(a < tEnd)	{
			if(_s[a] == ',')	{
				if(clvTemp.load(strTemp))	{
					m_vCleaves.push_back(clvTemp);
				}
				strTemp.erase(0,strTemp.size());
			}
			else if(strchr("ABCDEFGHIJKLMNOPQRSTUVWXYZ[]{}|",_s[a]))	{
				strTemp += _s[a];
			}
			else if(_s[a] >= 'a' && _s[a] <= 'z')	{
				strTemp += (char)(_s[a]-32);
			}
			a++;
		}
		if(!strTemp.empty())	{
			if(clvTemp.load(strTemp))	{
				m_vCleaves.push_back(clvTemp);
			}
		}
		m_itStart = m_vCleaves.begin();
		m_itEnd = m_vCleaves.end();
		if(m_vCleaves.size() == 1)	{
			m_lType = m_vCleaves[0].m_lType;
		}
		return !m_vCleaves.empty();
	}
/*
 * test takes the abbreviations for the residue N-terminal to a potentially cleaved bond
 * and the residue C-terminal to the bond and checks to see if the bond can be cleaved
 * according to the rules stored in the load method. load must always be called at least once
 * prior to using test, or the results may be unpredictable
 */
	bool test(const char _n,const char _c)	{
		if(m_lType & 0x01)
			return true;
		if(m_lType & 0x02)	{
			if(_n == 'K' || _n == 'R')	{
				if(_c != 'P')	{
					return true;
				}
			}
			return false;
		}
		m_itValue = m_itStart;
		while(m_itValue != m_itEnd)	{
			if(m_itValue->test(_n,_c))	{
				return true;
			}
			m_itValue++;
		}
		return false;
	}
};
#endif //ifdef MCLEAVE_H