mpmods.cpp

/*
 Copyright (C) 2005 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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*/

// File version: 2005-09-01

#include "stdafx.h"
#include <sys/timeb.h>
#include <ctime>
#include "mpmods.h"
#include "mprocess.h"
#include "mscore.h"

mpmods::mpmods(){
	m_pProcess=NULL;
}
mpmods::~mpmods(){
}

bool mpmods::set_mprocess(mprocess *_p){
	if(m_pProcess != NULL)
		delete m_pProcess;
	m_pProcess = _p;
	return true;
}

/*
 * process potential modifications using a minimum of at least 5 missed cleavages
 */
bool mpmods::refine()
{
	vector<mspectrum> vspRollback;
	string strKey;
	string strValue;
	size_t tActiveNow = 0;
	size_t a = 0;
	size_t tPips = 0;

/*
 *  set the maximum expectation value
 */
	strKey = "refine, maximum valid expectation value";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	if(strValue.size() > 0)	{
		m_dMaxExpect = atof(strValue.c_str());
	}
	strKey = "refine, use annotations";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	m_pProcess->m_bAnnotation = true;
	if(strValue == "no")	{
		m_pProcess->m_bAnnotation = false;
	}
/*
 * set up the modification masses and cleavage specs
 */
	strKey = "refine, tic percent";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	double dTicPercent = atof(strValue.c_str());
	if(dTicPercent == 0)	{
		dTicPercent = 20.0;
	}
	size_t tTicMax = (size_t)((double)m_pProcess->m_vseqBest.size()*dTicPercent/100.0);
	if(tTicMax < 1)	{
		tTicMax = 1;
	}
	strKey = "scoring, maximum missed cleavage sites";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	m_pProcess->m_tMissedCleaves = atoi(strValue.c_str());
	if(m_pProcess->m_tMissedCleaves < 5)	{
		m_pProcess->m_tMissedCleaves = 5;
	}
	strKey = "refine, cleavage semi";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	if(strValue == "yes")	{
		m_pProcess->m_semiState.activate(true);
	}
	else	{
		m_pProcess->m_semiState.activate(false);
	}
	if(m_pProcess->m_lThread == 0 || m_pProcess->m_lThread == 0xFFFFFFFF)	{
		cout << "\tpartial cleavage ";
		cout.flush();
	}

	strKey = "refine, potential modification mass";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	m_pProcess->m_pScore->m_seqUtil.modify_maybe(strValue);
	strKey = "refine, potential modification motif";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	m_pProcess->m_pScore->m_seqUtil.modify_motif(strValue);
	m_pProcess->m_strLastMods.clear();
/*
 * score the spectra against each sequence
 */
	a = 0;
	while(a < m_pProcess->m_vseqBest.size())	{
		m_pProcess->score(m_pProcess->m_vseqBest[a]);
		tPips++;
		if(tPips == tTicMax)	{
			if(m_pProcess->m_lThread == 0 || m_pProcess->m_lThread == 0xFFFFFFFF)	{
				cout << ".";
				cout.flush();
				m_pProcess->m_prcLog.log(".");
			}
			tPips = 0;
		}
		a++;
	}

/*
 * use additional modifications if present, creating a rollback vector each time
 */
	long lPMCount = 1;
	char pValue[8];
	sprintf(pValue," %i",lPMCount);
	strKey = "refine, potential modification mass";
	strKey += pValue;
	string strMods;
	m_pProcess->m_xmlValues.get(strKey,strMods);
	strKey = "refine, potential modification motif";
	strKey += pValue;
	string strMotifs;
	m_pProcess->m_xmlValues.get(strKey,strMotifs);
	m_pProcess->m_strLastMods.clear();
	while(strMods.find('@') != strMods.npos || strMotifs.find('@') != strMotifs.npos)	{
		if(m_pProcess->m_lThread == 0 || m_pProcess->m_lThread == 0xFFFFFFFF)	{
			cout << " done.\n";
			m_pProcess->m_prcLog.log("done");
			cout << "\tpartial cleavage " << lPMCount << " ";
			cout.flush();
		}
		m_pProcess->m_pScore->m_seqUtil.modify_maybe(strMods);
		m_pProcess->m_pScore->m_seqUtil.modify_motif(strMotifs);
		if(m_pProcess->m_tMissedCleaves < 5)	{
			m_pProcess->m_tMissedCleaves = 5;
		}
		a = 0;
		tPips = 0;
		while(a < m_pProcess->m_vseqBest.size())	{
			m_pProcess->score(m_pProcess->m_vseqBest[a]);
			tPips++;
			if(tPips == tTicMax)	{
				if(m_pProcess->m_lThread == 0 || m_pProcess->m_lThread == 0xFFFFFFFF)	{
					cout << ".";
					m_pProcess->m_prcLog.log(".");
					cout.flush();
				}
				tPips = 0;
			}
			a++;
		}
		lPMCount++;
		sprintf(pValue," %i",lPMCount);
		strKey = "refine, potential modification mass";
		strKey += pValue;
		m_pProcess->m_xmlValues.get(strKey,strMods);
		strKey = "refine, potential modification motif";
		strKey += pValue;
		m_pProcess->m_xmlValues.get(strKey,strMotifs);
		m_pProcess->m_strLastMods.clear();
	}
/*
 * update active state of spectra
 */
	m_pProcess->load_best_vector();
	a = 0;
	while(a < m_pProcess->m_vSpectra.size())	{
		if(!m_pProcess->m_vSpectra[a].m_bActive)
			tActiveNow++;
		a++;
	}
	if(tActiveNow >= m_pProcess->m_tActive)	{
		m_pProcess->m_tRefinePartial = tActiveNow - m_pProcess->m_tActive;
	}
	m_pProcess->m_tActive = tActiveNow;

/*
 *  clear the potential modifications, if required
 */
	strKey = "refine, use potential modifications for full refinement";
	m_pProcess->m_xmlValues.get(strKey,strValue);
	if(strValue != "yes")	{
		strKey = "residue, potential modification mass";
		m_pProcess->m_xmlValues.get(strKey,strValue);
		m_pProcess->m_pScore->m_seqUtil.modify_maybe(strValue);
		strKey = "residue, potential modification motif";
		m_pProcess->m_xmlValues.get(strKey,strValue);
		m_pProcess->m_pScore->m_seqUtil.modify_motif(strValue);
	}

	if(m_pProcess->m_lThread == 0 || m_pProcess->m_lThread == 0xFFFFFFFF)	{
		cout << " done.\n";
		cout.flush();
	}
	m_pProcess->m_bAnnotation = false;
	m_pProcess->m_strLastMods.clear();
	m_pProcess->m_semiState.activate(false);
	return true;
}

/*
 * mpmodsmanager contains static short-cuts for dealing with mpmods
 * plug-ins.
 */
const char* mpmodsmanager::TYPE = "refinement, potential modifications algorithm";

/*
 * create_mpmods creates the correct mpmods object for the given set of XML
 * parameters.
 */
mpmods* mpmodsmanager::create_mpmods(XmlParameter &_x)
{
	string strValue;
	string strKey = TYPE;
	if (!_x.get(strKey,strValue))
		strValue = "tandem";
	return (mpmods*) mpluginmanager::get().create_plugin(TYPE, strValue.data());
}

/*
 * register_factory registers a factory with the mpluginmanager for
 * creating mpmods derived objects.
 */
void mpmodsmanager::register_factory(const char* _spec, mpluginfactory* _f)
{
	mpluginmanager::get().register_factory(TYPE, _spec, _f);
}


// Factory instance, registers itself with the mpmodsmanager.
static mpmodsfactory_tandem factory;
	
mpmodsfactory_tandem::mpmodsfactory_tandem()
{
	mpmodsmanager::register_factory("tandem", this);
}

mplugin* mpmodsfactory_tandem::create_plugin()
{
	return new mpmods();
}