p3mprocess.cpp

/*
 Copyright (C) 2003-2004 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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The End 
*/

// File version: 2004-02-01
// File version: 2004-03-01
// File version: 2004-03-01
// File version: 2004-07-12
// File version: 2004-10-05
// File version: 2004-11-01
// File version: 2005-01-01

/*
 * the process object coordinates the function of tandem. it contains the information
 * loaded from the input XML file in the m_xmlValues object and performance
 * information in the m_xmlPerformance object. The mass spectra to be analyzed are
 * in the m_vSpectra vector container. A set of input parameters are used to
 * initialize constants that are used in processing the mass spectra.
 * NOTE: see tandem.cpp for an example of how to use an mprocess class
 * NOTE: mprocess uses cout to report errors. This may not be appropriate for
 *       many applications. Feel free to change this to a more appropriate mechanism
 */

#include "stdafx.h"
#include <algorithm>
#include <set>
#include "msequence.h"
#include "msequencecollection.h"
#include "msequenceserver.h"
#include "msequtilities.h"
#include "mspectrum.h"
#include "loadmspectrum.h"
#include "xmlparameter.h"
#include "xmltaxonomy.h"
#include "mscore.h"
#include "mprocess.h"
#include "saxbiomlhandler.h"
#include "saxsaphandler.h"
#include "mbiomlreport.h"
#include "mrefine.h"

// #define TANDEM_EXACT 1

/*
 * global less than operators to be used in sort operations
 */
p3mprocess::p3mprocess(void)
{
	string strKey = "process, version";
	string strValue = "X! P3 ";
	strValue += VERSION;
	m_xmlPerformance.set(strKey,strValue);
}

p3mprocess::~p3mprocess(void)
{
}
/*
 * taxonomy uses the taxonomy information in the input XML file to load
 * the msequenceServer member object with file path names to the required
 * sequence list files (FASTA format only in the initial release). If these
 */
bool p3mprocess::taxonomy()
{
#ifdef X_P3
	string strValue;
	string strKey = "list path, taxonomy information";
	m_xmlValues.get(strKey,strValue);
	string strTaxonPath = strValue;
	strKey = "protein, taxon";
	m_xmlValues.get(strKey,strValue);
	long lReturn = m_svrSequences.u_load_file(strTaxonPath,strValue);
/*
 * return false if the load_file method fails
 */
	if(lReturn == 2)	{
		cout << "\nThe taxonomy parameter file \"" << strTaxonPath.c_str();
		cout << "\" did not contain the value \"" << strValue.c_str() << "\".\nCheck your settings and try again.\n";
		return false;
	}
	if(lReturn == 1)	{
		cout << "\nThe taxonomy parameter file \"" << strTaxonPath.c_str();
		cout << "\" could not be found.\nCheck your settings and try again.\n";
		return false;
	}
	return true;
#endif
	return true;
}
/*
 * merge_spectra takes an mspectrum vector from an external source and merges it
 * with the m_vSpectra vector. this method is used to combine information obtained
 * from other threads with this mprocess object
 */
bool p3mprocess::merge_spectra()
{
	string strKey = "refine, maximum valid expectation value";
	string strValue;
	m_xmlValues.get(strKey,strValue);
	double dMaxExpect = 0.01;
	if(strValue.size() > 0)	{
		dMaxExpect = atof(strValue.c_str());
	}
	size_t a = 0;
	size_t b = 0;
	size_t c = 0;
	{
		while(a < m_vSpectra.size())	{
			m_vSpectra[a].m_hHyper.model();
			m_vSpectra[a].m_hHyper.set_protein_factor(1.0);
			a++;
		}
		a = 0;
		double dExpect = 1.0;
		SEQMAP::iterator itValue;
		while(a < m_vSpectra.size())	{
			b = 0;
			dExpect = (double)m_vSpectra[a].m_hHyper.expect_protein(m_pScore->hconvert(m_vSpectra[a].m_fHyper));
			if(dExpect <= dMaxExpect)	{
				m_vSpectra[a].m_bActive = false;
				while(b < m_vSpectra[a].m_vseqBest.size())	{
					c = 0;
					while(c < m_vseqBest.size())	{
						if(m_vSpectra[a].m_vseqBest[b].m_tUid == m_vseqBest[c].m_tUid)	{
							break;
						}
						c++;
					}
					if(c == m_vseqBest.size())	{
						m_vseqBest.push_back(m_vSpectra[a].m_vseqBest[b]);
						itValue = m_mapSequences.find(m_vseqBest[c].m_tUid);
						m_vseqBest[c].m_strSeq = ((*itValue).second.c_str());
						m_vseqBest[c].m_vDomains.clear();
					}
					b++;
					if(m_bUseHomologManagement && b >= 5)	{
						break;
					}
				}
			}
			m_vSpectra[a].reset();
			a++;
		}
	}
	return true;
}

bool p3mprocess::merge_spectra(vector<mspectrum> &_s)
{
	string strKey = "refine, maximum valid expectation value";
	string strValue;
	m_xmlValues.get(strKey,strValue);
	double dMaxExpect = 0.01;
	if(strValue.size() > 0)	{
		dMaxExpect = atof(strValue.c_str());
	}
	size_t a = 0;
	size_t b = 0;
	size_t c = 0;
	{
		while(a < _s.size())	{
			_s[a].m_hHyper.model();
			_s[a].m_hHyper.set_protein_factor(1.0);
			a++;
			if(m_bUseHomologManagement && _s[a].m_vseqBest.size() > 5)	{
				_s[a].m_vseqBest.erase(_s[a].m_vseqBest.begin()+5,_s[a].m_vseqBest.end());
			}
		}
		a = 0;
		double dExpect = 1.0;
		SEQMAP::iterator itValue;
		while(a < _s.size())	{
			b = 0;
			dExpect = (double)_s[a].m_hHyper.expect_protein(_s[a].m_fHyper);
			if(dExpect <= dMaxExpect)	{
				while(b < _s[a].m_vseqBest.size())	{
					c = 0;
					while(c < m_vseqBest.size())	{
						if(_s[a].m_vseqBest[b].m_tUid == m_vseqBest[c].m_tUid)	{
							break;
						}
						c++;
					}
					if(c == m_vseqBest.size())	{
						m_vseqBest.push_back(_s[a].m_vseqBest[b]);
						itValue = m_mapSequences.find(m_vseqBest[c].m_tUid);
						m_vseqBest[c].m_strSeq = ((*itValue).second.c_str());
						m_vseqBest[c].m_vDomains.clear();
					}
					b++;
				}
			}
			_s[a].reset();
			a++;
		}
	}
	return true;
}
/*
 * merge_map adds new values to the existing m_mapSequences map.
*/
bool p3mprocess::merge_map(SEQMAP &_s,DESMAP &_d)
{
	SEQMAP::iterator itValue = _s.begin();
	SEQMAP::iterator itEnd = _s.end();
	while(itValue != itEnd)	{
		if(m_mapSequences.find(itValue->first) == m_mapSequences.end())	{
			m_mapSequences.insert(*itValue);
		}
		itValue++;
	}
	DESMAP::iterator itV = _d.begin();
	DESMAP::iterator itE = _d.end();
	while(itV != itE)	{
		if(m_mapDesc.find(itV->first) == m_mapDesc.end())	{
			m_mapDesc.insert(*itV);
		}
		itV++;
	}
	return true;
}

/*
 * merge_map adds new values to the existing m_mapSequences map.
*/
bool p3mprocess::merge_map(SEQMAP &_s)
{
	return mprocess::merge_map(_s);
}

bool p3mprocess::load_sequences()
{
#ifdef X_P3
	vector<msequence> vSeq;
	string strValue;
	string strKey = "list path, taxonomy information";
	m_xmlValues.get(strKey,strValue);
	string strTaxonPath = strValue;
	strKey = "protein, taxon";
	m_xmlValues.get(strKey,strValue);
	long lReturn = m_svrSequences.load_file(strTaxonPath,strValue);
/*
 * return false if the load_file method fails
 */
	if(lReturn == 2)	{
		cout << "\nThe taxonomy parameter file \"" << strTaxonPath.c_str();
		cout << "\" did not contain the value \"" << strValue.c_str() << "\".\nCheck your settings and try again.\n";
		return false;
	}
	if(lReturn == 1)	{
		cout << "\nThe taxonomy parameter file \"" << strTaxonPath.c_str();
		cout << "\" could not be found.\nCheck your settings and try again.\n";
		return false;
	}
	m_svrSequences.u_maps(m_mapDesc,vSeq);
	size_t a = 0;
	DESMAP mapDes;
	m_mapSequences.clear();
	while(a < vSeq.size())	{
		mapDes[vSeq[a].m_strDes] = a;
		m_mapSequences[vSeq[a].m_tUid] = vSeq[a].m_strSeq;
		a++;
	}
	a = 0;
	while(a < m_vseqBest.size())	{
		m_vseqBest[a] = vSeq[mapDes[m_vseqBest[a].m_strDes]];
		a++;
	}
	strKey = "refine, sequence path";
	// Check for input sequences for refinement to be loaded from a bioml file
	// Loading done for each thread
	m_xmlValues.get(strKey,strValue);
	if(strValue.size() > 0)	{
		SAXBiomlHandler saxFile;
		saxFile.setFileName(strValue.c_str());
		saxFile.parse();
		a = 0;
		while(a < saxFile.m_vseqBest.size())	{
			if(m_mapSequences.find(saxFile.m_vseqBest[a].m_tUid) == m_mapSequences.end())	{
				m_vseqBest.push_back(saxFile.m_vseqBest[a]);
				m_mapSequences.insert(SEQMAP::value_type(saxFile.m_vseqBest[a].m_tUid,saxFile.m_vseqBest[a].m_strSeq));
			}
			a++;
		}
	}
#endif
	return true;
}

bool p3mprocess::clean_sequences(void)
{
	map<size_t,long> mapValue;
	map<size_t,long>::iterator itMap;
	size_t a = 0;
	size_t b = 0;
	size_t tLength = m_vSpectra.size();
	size_t tBest = 0;
	while(a < tLength)	{
		b = 0;
		tBest = m_vSpectra[a].m_vseqBest.size();
		while(b < tBest)	{
			mapValue[m_vSpectra[a].m_vseqBest[b].m_tUid] = 1;
			b++;
		}
		a++;
	}
	SEQMAP::iterator itValue = m_mapSequences.begin();
	while(itValue != m_mapSequences.end())	{
		itMap = mapValue.find((*itValue).first);
		if(itMap == mapValue.end())	{
			m_mapSequences.erase(itValue);
			itValue = m_mapSequences.begin();
		}
		else	{
			itValue++;
		}
	}
	DESMAP::iterator itV = m_mapDesc.begin();
	while(itV != m_mapDesc.end())	{
		itMap = mapValue.find((*itV).second);
		if(itMap == mapValue.end())	{
			m_mapDesc.erase(itV);
			itV = m_mapDesc.begin();
		}
		else	{
			itV++;
		}
	}
	return true;
}

/*
 * create_score takes an msequence object and a start and an end sequence position
 * and saves that msequence, its mdomain and scoring in the spectrum that has just
 * been scored. equivalent msequence objects (based on their hyper score)
 * are stored sequentially in a vector in the mspectrum object
 */
bool p3mprocess::create_score(const msequence &_s,const size_t _v,const size_t _w,const long _m,bool _p)
{
	long lIonCount = 0;
	float fScore = -1.0;
	float fHyper = -1.0;
	size_t a = 0;
	size_t b = 0;
	size_t c = 0;
	bool bOk = false;
	bool bDom = false;
	long lCount = 0;
	bool bIonCheck = false;
	bool bMassCheck = false;
/*
 * score each mspectrum identified as a candidate in the m_pScore->m_State object
 */
	while(lCount < m_pScore->m_State.m_lEqualsS)	{
		a = m_pScore->m_State.m_plEqualsS[lCount];
		lCount++;
		lIonCount = 0;
		fScore = 1.0;
		fHyper = 1.0;
		m_pScore->m_lMaxCharge = (long)(m_vSpectra[a].m_fZ+0.1);
/*
 * in versions prior to 2004.03.01, spectra with m_bActive == false were
 * rejected at this point, to save time & because of a problem with
 * multiple recording of the same sequence. starting with 2004.03.01,
 * the later problem has been corrected, and because of point mutation
 * analysis, it has become important to reexamine all sequences.
 */
		fScore = m_pScore->score(a);
		fHyper = m_pScore->m_fHyper;
/*
 * If the convolution score is greater than 2.0, record information in the ion-type histograms
 */
		if(fScore > 2.0)	{
			m_tPeptideScoredCount++;
			lIonCount = m_pScore->m_plCount[mscore::S_B] + m_pScore->m_plCount[mscore::S_Y];
			lIonCount += m_pScore->m_plCount[mscore::S_C] + m_pScore->m_plCount[mscore::S_Z];
			lIonCount += m_pScore->m_plCount[mscore::S_A] + m_pScore->m_plCount[mscore::S_X];
			m_vSpectra[a].m_hHyper.add(m_pScore->hconvert(fHyper));
			m_vSpectra[a].m_hConvolute.add(m_pScore->hconvert(fScore));
			m_vSpectra[a].m_chBCount.add(m_pScore->m_plCount[mscore::S_A] + 
								m_pScore->m_plCount[mscore::S_B] + 
								m_pScore->m_plCount[mscore::S_C]);
			m_vSpectra[a].m_chYCount.add(m_pScore->m_plCount[mscore::S_X] + 
								m_pScore->m_plCount[mscore::S_Y] + 
								m_pScore->m_plCount[mscore::S_Z]);
			if(m_bCrcCheck && _p && m_vSpectra[a].m_hHyper.m_ulCount < 400)	{
				m_bPermute = true;
			}
			else if(m_vSpectra[a].m_dMH > 3000.0 && m_vSpectra[a].m_hHyper.m_ulCount < 400)	{
				m_bPermuteHigh = true;
			}
		}
		bIonCheck = false;
		if(lIonCount > m_lIonCount)	{
			if( (m_pScore->m_plCount[mscore::S_A] || m_pScore->m_plCount[mscore::S_B] || m_pScore->m_plCount[mscore::S_C]) && 
				(m_pScore->m_plCount[mscore::S_X] || m_pScore->m_plCount[mscore::S_Y] || m_pScore->m_plCount[mscore::S_Z]))	{
				bIonCheck = true;
			}
		}
		bMassCheck = m_errValues.check(m_vSpectra[a].m_dMH,m_pScore->seq_mh());
		if(!_p)	{
			bMassCheck = false;
		}
/*
 * if the same score has been recorded for another peptide in the same msequence object,
 * add a domain to that object, but do not update the entire object
 */
		if(bMassCheck && bIonCheck && fHyper == m_vSpectra[a].m_fHyper && m_vSpectra[a].m_tCurrentSequence == _s.m_tUid)	{
			vector<maa> vAa;
			mdomain domValue;
			domValue.m_vAa.clear();
			double dDelta = 0.0;
			if(m_pScore->get_aa(vAa,_v,dDelta))	{
				b = 0;
				while(b < vAa.size())	{
					domValue.m_vAa.push_back(vAa[b]);
					b++;
				}
			}
			if(fabs(dDelta) > 2.5)	{
				domValue.m_fScore = fScore;
				domValue.m_fHyper = fHyper;
				domValue.m_dMH = m_pScore->seq_mh();
				// m_fDelta was changed to m_dDelta in 2006.02.01
				domValue.m_dDelta = m_vSpectra[a].m_dMH - m_pScore->seq_mh();
				domValue.m_lE = _w;
				domValue.m_lS = _v;
				domValue.m_lMissedCleaves = _m;
				domValue.m_bUn = m_bUn;
				unsigned long lType = 1;
				unsigned long sType = 1;
				while(lType < m_pScore->m_lType+1)	{
					domValue.m_mapScore[lType] = m_pScore->m_pfScore[sType];
					domValue.m_mapCount[lType] = m_pScore->m_plCount[sType];
					lType *= 2;
					sType++;
				}
				b = 0;
				bOk = true;
				while(bOk && b < m_vSpectra[a].m_vseqBest.back().m_vDomains.size())	{
					if(domValue == m_vSpectra[a].m_vseqBest.back().m_vDomains[b]){	
						bOk = false;
					}
					b++;
				}
				if(bOk)	{
					m_vSpectra[a].m_vseqBest.back().m_vDomains.push_back(domValue);
				}
			}
		}
/*
 * if the same hyper score has been recorded for a different msequence object, retain that
 * object and add the new msequence to the back of the m_vseqBest vector
 */
		else if(bMassCheck && bIonCheck && fHyper == m_vSpectra[a].m_fHyper)	{			
			vector<maa> vAa;
			msequence seqValue;
			mdomain domValue;
			domValue.m_vAa.clear();
			double dDelta = 0.0;
			if(m_pScore->get_aa(vAa,_v,dDelta))	{
				b = 0;
				while(b < vAa.size())	{
					domValue.m_vAa.push_back(vAa[b]);
					b++;
				}
			}
			if(fabs(dDelta) > 2.5)	{
				domValue.m_fScore = fScore;
				domValue.m_fHyper = fHyper;
				domValue.m_dMH = m_pScore->seq_mh();
				// m_fDelta was changed to m_dDelta in 2006.02.01
				domValue.m_dDelta = m_vSpectra[a].m_dMH - m_pScore->seq_mh();
				domValue.m_lE = _w;
				domValue.m_lS = _v;
				domValue.m_lMissedCleaves = _m;
				domValue.m_bUn = m_bUn;
				unsigned long lType = 1;
				unsigned long sType = 1;
				while(lType < m_pScore->m_lType+1)	{
					domValue.m_mapScore[lType] = m_pScore->m_pfScore[sType];
					domValue.m_mapCount[lType] = m_pScore->m_plCount[sType];
					lType *= 2;
					sType++;
				}
				seqValue = _s;
				seqValue.m_strSeq = " ";
				m_mapSequences.insert(SEQMAP::value_type(_s.m_tUid,_s.m_strSeq));
				m_mapDesc.insert(DESMAP::value_type(_s.m_strDes,_s.m_tUid));
				seqValue.m_vDomains.clear();
				seqValue.m_vDomains.push_back(domValue);
				seqValue.format_description();
				bOk = true;
				b = 0;
				while(bOk && b < m_vSpectra[a].m_vseqBest.size())	{
					if(m_vSpectra[a].m_vseqBest[b].m_tUid == _s.m_tUid)	{
						c = 0;
						bDom = true;
						while(bDom && c < m_vSpectra[a].m_vseqBest[b].m_vDomains.size())	{
							if(m_vSpectra[a].m_vseqBest[b].m_vDomains[c] == domValue)	{
								bDom = false;
								bOk = false;
							}
							c++;
						}
						if(bDom)	{
							m_vSpectra[a].m_vseqBest[b].m_vDomains.push_back(domValue);
							bOk = false;
						}
					}
					b++;
				}
				if(bOk)	{
					m_vSpectra[a].m_tCurrentSequence = _s.m_tUid;
					seqValue.m_iRound = m_iCurrentRound;
					m_vSpectra[a].m_vseqBest.push_back(seqValue);
				}
			}
		}
/*
 * if the hyper score is the best found so far for the mspectrum, delete the old msequence
 * objects and record this one.
 */
		else if(bMassCheck && bIonCheck && fHyper > m_vSpectra[a].m_fHyper && lIonCount > m_lIonCount)	{
			vector<maa> vAa;
			msequence seqValue;
			mdomain domValue;
			domValue.m_vAa.clear();
			double dDelta = 0.0;
			if(m_pScore->get_aa(vAa,_v,dDelta))	{
				b = 0;
				while(b < vAa.size())	{
					domValue.m_vAa.push_back(vAa[b]);
					b++;
				}
			}
			if(fabs(dDelta) > 2.5)	{
				m_vSpectra[a].m_fScoreNext = m_vSpectra[a].m_fScore;
				m_vSpectra[a].m_fHyperNext = m_vSpectra[a].m_fHyper;
				m_vSpectra[a].m_fScore = fScore;
				m_vSpectra[a].m_fHyper = fHyper;
				domValue.m_fScore = fScore;
				domValue.m_fHyper = fHyper;
				domValue.m_lE = _w;
				domValue.m_lS = _v;
				domValue.m_lMissedCleaves = _m;
				domValue.m_dMH = m_pScore->seq_mh();
				// m_fDelta was changed to m_dDelta in 2006.02.01
				domValue.m_dDelta = m_vSpectra[a].m_dMH - m_pScore->seq_mh();
				domValue.m_bUn = m_bUn;
				unsigned long lType = 1;
				unsigned long sType = 1;
				while(lType < m_pScore->m_lType+1)	{
					domValue.m_mapScore[lType] = m_pScore->m_pfScore[sType];
					domValue.m_mapCount[lType] = m_pScore->m_plCount[sType];
					lType *= 2;
					sType++;
				}
				seqValue = _s;
				seqValue.m_strSeq = " ";
				m_mapSequences.insert(SEQMAP::value_type(_s.m_tUid,_s.m_strSeq));
				m_mapDesc.insert(DESMAP::value_type(_s.m_strDes,_s.m_tUid));
				seqValue.m_vDomains.clear();
				seqValue.m_vDomains.push_back(domValue);
				seqValue.format_description();
				m_vSpectra[a].m_tCurrentSequence = _s.m_tUid;
				seqValue.m_iRound = m_iCurrentRound;
				m_vSpectra[a].m_vseqBest.clear();
				m_vSpectra[a].m_vseqBest.push_back(seqValue);
			}
		}
		else if (_p && bIonCheck && fHyper > m_vSpectra[a].m_fHyperNext)
		{
			m_vSpectra[a].m_fScoreNext = fScore;
			m_vSpectra[a].m_fHyperNext = fHyper;
		}
	}
	return true;
}