mmotif.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 MMOTIF_H
#define MMOTIF_H

// File version: 2004-06-01
// File version: 2005-01-01
/*
  modified December 2010 by Insilicos LLC to support object serialization for 
  Hadoop and MPI use
*/
/*
 * mmotif is a specialty class meant to store information about protein sequence motifs.
 * NOTE: mmotif.h does not have a corresponding .cpp file
 */

class mmotifres
{
public:

	mmotifres(void)
	{
		m_bRes = false;
		m_bPos = true;
		m_bIsX = false;
		strcpy(m_pMotif,"");
	}

	virtual ~mmotifres(void)
	{
	}
	char m_pMotif[32];
	bool m_bRes;
	bool m_bPos;
	bool m_bIsX;

	bool set(const char *_p)	{
		if(_p == NULL)	{
			return false;
		}
		if(strlen(_p) == 0)	{
			return false;
		}
		strcpy(m_pMotif,"");
		m_bIsX = false;
		m_bRes = true;
		m_bPos = true;
		if(strchr(_p,'!') == NULL)	{
			m_bRes = false;
		}
		if(strchr(_p,'X') != NULL)	{
			m_bIsX = true;
			m_bPos = true;
			strcpy(m_pMotif,"X");
			return true;
		}
		char *pValue = new char[strlen(_p)+1];
		strcpy(pValue,_p);
		char *pStart = pValue;
		char *pEnd = pStart;
		size_t a = 0;
		if(strchr(pValue,'[') != NULL)	{
			pStart = strchr(pValue,'[');
			pStart++;
			while(*pStart != ']' && *pStart != '\0')	{
				if(isalpha(*pStart))	{
					m_pMotif[a] = *pStart;
				}
				pStart++;
				a++;
			}
			m_pMotif[a] = '0';
			m_bPos = true;
			return true;
		}
		else if(strchr(pValue,'{') != NULL)	{
			pStart = strchr(pValue,'{');
			pStart++;
			while(*pStart != ']' && *pStart != '\0')	{
				if(isalpha(*pStart))	{
					m_pMotif[a] = *pStart;
				}
				pStart++;
				a++;
			}
			m_pMotif[a] = '0';
			m_bPos = false;
			return true;
		}
		else	{
			pStart = pValue;
			while(*pStart != '0')	{
				if(isalpha(*pStart))	{
					m_pMotif[a] = *pStart;
					a++;
					break;
				}
				pStart++;
			}
			m_pMotif[a] = '\0';
			m_bPos = true;
		}
		return false;
	}

	bool check(const char _c)	{
		if(m_bIsX)	{
			return true;
		}
		if(m_bPos)	{
			if(strchr(m_pMotif,_c) != NULL)	{
				return true;
			}
			return false;
		}
		if(strchr(m_pMotif,_c) == NULL)	{
			return true;
		}
		return false;
	}
	mmotifres& operator=(const mmotifres &rhs)	{
		strcpy(m_pMotif,rhs.m_pMotif);
		m_bRes = rhs.m_bRes;
		m_bPos = rhs.m_bPos;
		m_bIsX = rhs.m_bIsX;
		return *this;
	}
#ifdef HAVE_MULTINODE_TANDEM  // support for Hadoop and/or MPI?
	template<class Archive> 
	void serialize(Archive &ar,  const unsigned int version)
	{
		ar & m_pMotif;
		ar & m_bRes;
		ar & m_bPos;
		ar & m_bIsX;
	}
#endif
};

class mmotif
{
public:

	mmotif(void)
	{
		m_fMass = 0.0;
		m_fMassPrompt = 0;
		m_tPos = 0;
	}

	virtual ~mmotif(void)
	{
	}
	vector<mmotifres> m_vresMotifs;
	float m_fMass;
	float m_fMassPrompt;
	size_t m_tPos;
	bool set(const char *_p)	{
		if(_p == NULL)	{
			return false;
		}
		if(strlen(_p) == 0)	{
			return false;
		}
		const char *pStart = (char *)strchr(_p,'@');
		const char *pColon = (char *)strchr(_p,':');
		if(pStart == NULL)	{
			return false;
		}
		m_fMassPrompt = 0.0;
		if(pColon != NULL && pColon < pStart)	{
			m_fMassPrompt = (float)atof(pColon+1);
		}
		m_fMass = (float)(atof(_p));
		pStart++;
		size_t a = 0;
		size_t b = 0;
		size_t tEnd = strlen(pStart);
		char *pOut = new char[256];
		mmotifres motRes;
		m_vresMotifs.clear();
		while(a < tEnd)	{
			if(pStart[a] == '[')	{
				a++;
				b = 0;
				pOut[b] = '[';
				b++;
				while(pStart[a] != '\0' && pStart[a] != ']')	{
					pOut[b] = pStart[a];
					b++;
					a++;
				}
				pOut[b] = ']';
				b++;
				pOut[b] = '\0';
				motRes.set(pOut);
				if(motRes.m_bRes)	{
					m_tPos = m_vresMotifs.size();
				}
				m_vresMotifs.push_back(motRes);
			}
			else if(pStart[a] == '{')	{
				a++;
				b = 0;
				pOut[b] = '{';
				b++;
				while(pStart[a] != '\0' && pStart[a] != '}')	{
					pOut[b] = pStart[a];
					b++;
					a++;
				}
				pOut[b] = '}';
				b++;
				pOut[b] = '\0';
				motRes.set(pOut);
				if(motRes.m_bRes)	{
					m_tPos = m_vresMotifs.size();
				}
				m_vresMotifs.push_back(motRes);
			}
			else if(pStart[a] == '(')	{
				a++;
				unsigned long c = (unsigned long)atoi(pStart+a);
				if(c > 0)
					c--;
				while(pStart[a] != '\0' && pStart[a] != ')')	{
					a++;
				}
				if(!m_vresMotifs.empty())	{
					b = 0;
					while(b < c)	{
						m_vresMotifs.push_back(motRes);
						b++;
					}
				}
			}
			else if(isalpha(pStart[a]))	{
				b = 0;
				pOut[b] = pStart[a];
				b++;
				if(pStart[a+1] == '!')	{
					pOut[b] = pStart[a+1];
					b++;
				}
				pOut[b] = '\0';
				motRes.set(pOut);
				if(motRes.m_bRes)	{
					m_tPos = m_vresMotifs.size();
				}
				m_vresMotifs.push_back(motRes);
			}
			a++;
		}
		delete pOut;
		return true;
	}

	bool check(const char *_p,size_t &_o)	{
		size_t a = 0;
		const size_t tSize = m_vresMotifs.size();
		while(*(_p+a) != '\0' && a < tSize)	{
			if(!m_vresMotifs[a].check(*(_p+a)))	{
				return false;
			}
			a++;
		}
		if(a != tSize)	{
			return false;
		}
		_o = m_tPos;
		return true;
	}

	bool initialize()	{
		m_vresMotifs.clear();
		m_fMass = 0.0;
		m_tPos = 0;
		return true;
	}

	mmotif& operator=(const mmotif &rhs)	{
		m_fMass = rhs.m_fMass;
		m_tPos = rhs.m_tPos;
		m_vresMotifs.clear();
		size_t a = 0;
		while(a < rhs.m_vresMotifs.size())	{
			m_vresMotifs.push_back(rhs.m_vresMotifs[a]);
			a++;
		}
		return *this;
	}
#ifdef HAVE_MULTINODE_TANDEM  // support for Hadoop and/or MPI?
	template<class Archive>
	void serialize(Archive &ar,  const unsigned int version)
	{
		ar & m_vresMotifs;
		ar & m_fMass;
		ar & m_tPos;
	}
#endif
};
#endif