mspectrumcondition.cpp

/*
 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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*/

// File version: 2003-07-01
// File version: 2005-01-01

/*
 * the mspectrumcondition object analyzes tandem mass spectra and alters them to
 * be suitable for searching. it loads a set of parameters from an XmlParameters
 * object and uses those values for the spectrum analysis. this object contains
 * more "get" and "set" type methods than most of the other objects in this
 * project: there was considerable experimentation necessary to refine the spectrum
 * analysis methods and these additional methods were used for these experiments.
  *
 * mspectrumcondition performs a series of operations on a spectrum list to make
 * compatible with the scoring methods. the spectrum can be normalized, adjacent
 * peaks removed, parent ion masses excluded, low mass parents excluded, highly
 * charged parents excluded, low mass fragments excluded, and low intensity
 * fragment ions excluded.
*/
#include "stdafx.h"
#include <algorithm>
#include "msequence.h"
#include "msequencecollection.h"
#include "msequenceserver.h"
#include "msequtilities.h"
#include "mspectrum.h"
#include "xmlparameter.h"
#include "mspectrumcondition.h"
#include "mscore.h"

bool lessThanMImz(const mi &_l,const mi &_r);

/*
 * global less than operator for mi classes: to be used in sort operations to achieve
 * list ordered from lowest to highest m/z
 */
bool lessThanMImz(const mi &_l,const mi &_r)
{
	return _l.m_fM < _r.m_fM;
}

/*
 * mspectrumcondition performs a series of operations on a spectrum list to make
 * compatible with the scoring methods. the spectrum can be normalized, adjacent
 * peaks removed, parent ion masses excluded, low mass parents excluded, highly
 * charged parents excluded, low mass fragments excluded, and low intensity
 * fragment ions excluded.
 */
mspectrumcondition::mspectrumcondition(void)
{
	m_bUseMaxPeaks = true;
	m_bUseDynamicRange = true;
	m_bUseMinMass = true;
	m_bUseParent = true;
	m_bUseLowestMass = true;
	m_bUseMinSize = true;
	m_bUseNoiseSuppression = true;
	m_bUseChargeSuppression = true;
	m_bCondition = true;
	m_bUseNeutralLoss = false;
	m_bUsePhosphoDetection = false;

	m_tMaxPeaks = 50;
	m_fDynamicRange = 100.0;
	m_fMinMass = 500.0;
	m_fMaxMass = 6000.0;
	m_fLowestMass = 150.0;
	m_fParentLower = 2.0;
	m_fParentUpper = 2.0;
	m_lMinSize = 5;
	m_fNeutralLoss = 0.0;
	m_fNeutralLossWidth = 0.0;
	m_fFactor = 1.0;
	m_fMaxZ = 4.0;
}

mspectrumcondition::~mspectrumcondition(void)
{
}
/*
 * condition is the method called by mprocess to condition a particular mspectrum object.
 * by checking the appropriate flags, the various properties of a spectrum can be altered,
 * and the spectrum rejected if it does not pass the appropriate tests. 
 * NOTE: the order of operations is important here: do not change it unless you feel you
 *       fully understand why things were done in this order.
 */

bool mspectrumcondition::condition(mspectrum &_s, mscore &_score)
{
/*
 * first do simple spectrum screening.
 */
	if(m_bUsePhosphoDetection)	{
		if(!find_loss(_s,98.0,3.0))	{
			return false;
		}
	}
	_s.m_vMINeutral.clear();
	sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMImz);
	if(_s.m_vdStats.size() == 0)	{
		vector<mi>::iterator itMI = _s.m_vMI.begin();
		vector<mi>::iterator itEnd = _s.m_vMI.end();
		double dSum = 0.0;
		double dMax = 0.0;
		while(itMI != itEnd)	{
			if(dMax < itMI->m_fI)	{
				dMax = itMI->m_fI;
			}
			dSum += itMI->m_fI;
			itMI++;
		}
		_s.m_vdStats.push_back(dSum);
		_s.m_vdStats.push_back(dMax);
		_s.m_vdStats.push_back(m_fFactor);
	}
	/*
	 * check the parent charge against maximum charge allowed
	*/
	if(m_bUseChargeSuppression)	{
	if(_s.m_fZ > m_fMaxZ)	{
		return false;
	}
	}
/*
	 * check the parent ion mass against the minimum mass allowed (about 600.0 is usually safe)
 */
	if(m_bUseMinMass)	{
		if(_s.m_dMH < m_fMinMass)
		return false;
	}
/*
	 * check the parent ion mass against the maximum mass allowed
 */
	if (m_bUseMaxMass)	{
		if(_s.m_dMH > m_fMaxMass)
			return false;
	}
		/*
	* reject the spectrum if there aren't enough peaks even before conditioning.
		*/
	if(m_bUseMinSize)	{
		if((long)_s.m_vMI.size() < m_lMinSize)
				return false;
		}
    /*
    * give the score object a chance to perform score specific modifications
    * or veto this spectrum.
    */
	if(!_score.precondition(_s)) {
				return false;
			}

	/*
	* if conditioning is turned off, then simply accept the spectrum.
	*/
	if(!m_bCondition)	{
		return true;
		}

	size_t tSize = _s.m_vMI.size();
	size_t a = 0;
	float fMaxI = 0;
/*
 * this method doesn't really remove isotopes: it cleans up multiple intensities within one Dalton
 * of each other.
 */
//	sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMImz);
	remove_isotopes(_s);
/*
 * remove ions near the parent ion m/z
 */
	if(m_bUseParent)	{
		remove_parent(_s);
	}
/*
 * remove low mass immonium ions prior to normalization
 */
	if(m_bUseLowestMass)	{
		remove_low_masses(_s);
	}
/*
 * normalize the spectrum 
 */
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	vector<mi>::iterator itEnd = _s.m_vMI.end();
	double dSum = 0.0;
	double dMax = 0.0;
	while(itMI != itEnd)	{
		if(dMax < itMI->m_fI)	{
			dMax = itMI->m_fI;
		}
		dSum += itMI->m_fI;
		itMI++;
	}
	_s.m_vdStats.clear();
	_s.m_vdStats.push_back(dSum);
	_s.m_vdStats.push_back(dMax);
	_s.m_vdStats.push_back(m_fFactor);
	if(m_bUseDynamicRange)	{
		dynamic_range(_s);
	}
	if(m_bUseNeutralLoss)	{
		remove_neutral(_s);
	}
/*
* reject the spectrum if there aren't enough peaks 
*/
	if(m_bUseMinSize)	{
		if((long)_s.m_vMI.size() < m_lMinSize)
			return false;
	}
/*
 * check to see if the spectrum has the characteristics of noise 
 */
	if(m_bUseNoiseSuppression)	{
		if(is_noise(_s))	{
			return false;
		}
	}
/*
* retrieve the N most intense peaks
*/
	clean_isotopes(_s);
	if(m_bUseMaxPeaks)	{
		sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMI);
		remove_small(_s);
	}
	sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMImz);
	itMI = _s.m_vMI.begin();
	itEnd = _s.m_vMI.end();
	dSum = 0.0;
	dMax = 0.0;
	while(itMI != itEnd)	{
		if(dMax < itMI->m_fI)	{
			dMax = itMI->m_fI;
		}
		dSum += itMI->m_fI;
		itMI++;
	}
	_s.m_vdStats[0] = dSum*m_fFactor;
	_s.m_vdStats[1] = dMax*m_fFactor;
	_s.m_vdStats[2] = m_fFactor;
	return true;
}
/*
 * check_neutral looks for the loss of water or ammonia in a spectrum. this
 * method is not used in this implementation: it is for further experimentation
 */
bool mspectrumcondition::find_loss(mspectrum &_s,const float _d,const float _t)
{
	sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMI);
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	vector<mi>::iterator itEnd = _s.m_vMI.end();
	vector<mi>::iterator itLast = itMI;
	unsigned long a = 0;
	float fPlus = (float)(_s.m_dMH*0.001)/_s.m_fZ;
	float fD = (float)(1.00727 + (_s.m_dMH - 1.00727 - _d)/_s.m_fZ);
	while(a < 2 && itMI != itEnd)	{
		if(fabs(itMI->m_fM - fD) < fPlus)	{
			return true;
		}
		itMI++;
		a++;
	}
	return false;
}

/*
 * check_neutral looks for the loss of water or ammonia in a spectrum. this
 * method is not used in this implementation: it is for further experimentation
 */
bool mspectrumcondition::check_neutral(mspectrum &_s)
{
	sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMI);
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	vector<mi>::iterator itEnd = _s.m_vMI.end();
	vector<mi>::iterator itLast = itMI;
	unsigned long a = 0;
	unsigned long lCount = 0;
	float fM = 0.0;
	while(a < 10)	{
		itMI = itLast;
		while(itMI != itEnd && itMI->m_fM < 300.0)	{
			itMI++;
		}
		if(itMI == itEnd)
			break;
		fM = (float)(itMI->m_fM - 18.0);
		itMI++;
		itLast = itMI;
		while(itMI < itEnd)	{
			if(fabs(fM - itMI->m_fM) < 2.5)	{
				lCount++;
				break;
			}
			itMI++;
		}
		a++;
	}
	if(lCount < 1)
		return false;
	return true;
}
/*
 * remove isotopes removes multiple entries within 0.95 Da of each other, retaining
 * the highest value. this is necessary because of the behavior of some peak 
 * finding routines in commercial software
 */

bool mspectrumcondition::remove_isotopes(mspectrum &_s)
{
       if(_s.m_vMI.size() < 2)
                return true;

        vector<mi>::iterator itMI_ecriture = _s.m_vMI.begin();
        vector<mi>::iterator itMI_lecture = _s.m_vMI.begin() + 1;
        vector<mi>::const_iterator itMI_fin = _s.m_vMI.end();
		vector<mi> miTemp;
		float fEcriture = itMI_ecriture->m_fM;
        while( itMI_lecture != itMI_fin )
        {
                if( ( itMI_lecture->m_fM - fEcriture) >= 0.95 || itMI_lecture->m_fM < 200.0)
                {
						miTemp.push_back(*itMI_ecriture);
                        itMI_ecriture = itMI_lecture;
						fEcriture = itMI_ecriture->m_fM;
                }
                else if( itMI_lecture->m_fI > itMI_ecriture->m_fI )
                {
                        *itMI_ecriture = *itMI_lecture;
                }
                itMI_lecture++;
        }
		miTemp.push_back(*itMI_ecriture);
		_s.m_vMI = miTemp;
        return true;
}

/*
 * clean_isotopes removes peaks that are probably C13 isotopes
 */
bool mspectrumcondition::clean_isotopes(mspectrum &_s)
{

       if( _s.m_vMI.size() < 2 )
                return true;

        vector<mi>::iterator itMI_ecriture = _s.m_vMI.begin();
        vector<mi>::iterator itMI_lecture = _s.m_vMI.begin() + 1;
        vector<mi>::const_iterator itMI_fin = _s.m_vMI.end();
 		vector<mi> miTemp;
 		float fEcriture = itMI_ecriture->m_fM;
        while( itMI_lecture != itMI_fin )
        {
                if( ( itMI_lecture->m_fM - fEcriture) >= 1.5  || itMI_lecture->m_fM < 200.0)
                {
						miTemp.push_back(*itMI_ecriture);
                        itMI_ecriture = itMI_lecture;
						fEcriture = itMI_ecriture->m_fM;
                }
                else if( itMI_lecture->m_fI > itMI_ecriture->m_fI )
                {
                        *itMI_ecriture = *itMI_lecture;
                }
                itMI_lecture++;
        }
		miTemp.push_back(*itMI_ecriture);
		_s.m_vMI = miTemp;
        return true;

}
/*
 * is_noise attempts to determine if the spectrum is simply noise. if the spectrum
 * does not have any peaks within a window near the parent ion mass, it is considered
 * noise.
 */

bool mspectrumcondition::is_noise(mspectrum &_s)
{
	if(!m_bUseNoiseSuppression)
		return false;
	size_t a = 0;
	size_t tSize = _s.m_vMI.size();
	float fZ = _s.m_fZ;
	float fMax = (float)(_s.m_dMH/fZ);
	if(fZ == 1)	{
		fMax = (float)(_s.m_dMH - 600.0);
	}
	if(fZ == 2)	{
		fMax = (float)(_s.m_dMH - 600.0);
	}
	while(a < tSize)	{
		if(_s.m_vMI[a].m_fM > fMax)
			return false;
		a++;
	}
	return true;
}
/*
 * load makes internal copies of the relavent parameters found in the XmlParameter object
 */
bool mspectrumcondition::load(XmlParameter &_x)
{
	string strKey;
	string strValue;
	strKey = "spectrum, dynamic range";
	m_bUseDynamicRange = _x.get(strKey,strValue);
	if(m_bUseDynamicRange)	{
		m_fDynamicRange = (float)atof(strValue.c_str());
	}
	strKey = "spectrum, total peaks";
	m_bUseMaxPeaks = _x.get(strKey,strValue);
	if(m_bUseMaxPeaks)	{
		m_tMaxPeaks = atoi(strValue.c_str());
	}
	strKey = "spectrum, minimum peaks";
	m_bUseMinSize = _x.get(strKey,strValue);
	if(m_bUseMinSize)	{
		m_lMinSize = atoi(strValue.c_str());
	}
	strKey = "spectrum, minimum parent m+h";
	m_bUseMinMass = _x.get(strKey,strValue);
	if(m_bUseMinMass)	{
		m_fMinMass = (float)atof(strValue.c_str());
	}
	strKey = "spectrum, maximum parent m+h";
	m_bUseMaxMass = _x.get(strKey,strValue);
	if(m_bUseMaxMass)	{
		m_fMaxMass = (float)atof(strValue.c_str());
	}
	strKey = "spectrum, minimum fragment mz";
	m_bUseLowestMass = _x.get(strKey,strValue);
	if(m_bUseLowestMass)	{
		m_fLowestMass = (float)atof(strValue.c_str());
	}
	strKey = "spectrum, use conditioning";
	bool bCondition = _x.get(strKey,strValue);
	if(bCondition)	{
		if(strValue == "yes")	{
			m_bCondition = true;
		}
		else if(strValue == "no")	{
			m_bCondition = false;
		}
		else	{
			m_bCondition = true;
		}
	}
	strKey = "spectrum, use noise suppression";
	bool bUseNoiseSuppression = _x.get(strKey,strValue);
	if(bUseNoiseSuppression)	{
		if(strValue == "yes")	{
			m_bUseNoiseSuppression = true;
		}
		else if(strValue == "no")	{
			m_bUseNoiseSuppression = false;
		}
		else	{
			m_bUseNoiseSuppression = true;
		}
	}
	strKey = "spectrum, use neutral loss window";
	bool bUseNeutralLoss = _x.get(strKey,strValue);
	if(bUseNeutralLoss)	{
		if(strValue == "yes")	{
			m_bUseNeutralLoss = true;
		}
		else if(strValue == "no")	{
			m_bUseNeutralLoss = false;
		}
		else	{
			m_bUseNeutralLoss = false;
		}
	}
	if(m_bUseNeutralLoss)	{
		strKey = "spectrum, neutral loss window";
		if(_x.get(strKey,strValue))	{
			m_fNeutralLossWidth = (float)atof(strValue.c_str());
		}
		strKey = "spectrum, neutral loss mass";
		if(_x.get(strKey,strValue))	{
			m_fNeutralLoss = (float)atof(strValue.c_str());
		}
	}
	strKey = "spectrum, maximum parent charge";
	if(_x.get(strKey,strValue))	{
		m_fMaxZ = (float)atof(strValue.c_str());
		if(m_fMaxZ < 1.0)	{
			m_fMaxZ = 4.0;
		}
	}
	return true;
}
/*
 * use the dynamic range parameter to set the maximum intensity value for the spectrum.
 * then remove all peaks with a normalized intensity < 1
 */
bool mspectrumcondition::dynamic_range(mspectrum &_s)
{
	if (!m_bUseDynamicRange) {
		return false;
	}
	size_t tSize = _s.m_vMI.size();
	float fI = 1.0;
	if(tSize > 0)	{
		fI = _s.m_vMI[0].m_fI;
	}
	size_t a = 0;
	while(a < tSize)	{
		if(_s.m_vMI[a].m_fI > fI)	{
			fI = _s.m_vMI[a].m_fI;
		}
		a++;
	}
	m_fFactor = fI/m_fDynamicRange;
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	while(itMI != _s.m_vMI.end())	{
		itMI->m_fI /= m_fFactor;
		if(itMI->m_fI < 1.0)	{
			itMI = _s.m_vMI.erase(itMI);
		}
		else	{
			itMI++;
		}
	}
	return true;
}
/*
 * limit the total number of peaks used
 */
bool mspectrumcondition::remove_small(mspectrum &_s)
{
	if(!m_bUseMaxPeaks)	{
		return false;
	}
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	// The test line was changed in 2006.09.01 to correct a problem
	// created by VC++ 2005. This new version uses a strict bounds checking
	// style for STL iterators, that cause a run time error if an iterator
	// longer than .end() is produced by incrementing the iterator. The previous
	// test was 
	//
	//				if(itMI+m_tMaxPeaks < _s.m_vMI.end())
	//
	// which caused the error when the statement was false.
	if(m_tMaxPeaks < _s.m_vMI.size())	{
		_s.m_vMI.erase(itMI+m_tMaxPeaks,_s.m_vMI.end());
	}
	return true;
}
/*
 * set up m/z regions to ignore: those immediately below the m/z of the parent ion
 * which will contain uninformative neutral loss ions, and those immediately above
 * the parent ion m/z, which will contain the parent ion and its isotope pattern
 */
bool mspectrumcondition::remove_parent(mspectrum &_s)
{
	if(!m_bUseParent)
		return false;
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	float fParentMz = (float)(1.00727+(_s.m_dMH - 1.00727)/_s.m_fZ);
	while(itMI != _s.m_vMI.end())	{
		if(fParentMz - itMI->m_fM >= 0.0 && fParentMz - itMI->m_fM < m_fParentLower/_s.m_fZ)	{
			itMI = _s.m_vMI.erase(itMI);
		}
		else if(itMI->m_fM - fParentMz > 0.0 && itMI->m_fM - fParentMz < m_fParentUpper/_s.m_fZ)	{
			itMI = _s.m_vMI.erase(itMI);
		}
		else	{
			itMI++;
		}
	}
	return true;
}
/*
 * remove_low_masses deletes peaks with m/z values below the m_fLowestMass member value
 */
bool mspectrumcondition::remove_low_masses(mspectrum &_s)
{
	if(!m_bUseLowestMass)
		return false;
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	while(itMI != _s.m_vMI.end())	{
		if(itMI->m_fM > m_fLowestMass)	{
			break;
		}
		itMI++;
	}
	_s.m_vMI.erase(_s.m_vMI.begin(),itMI);
	return true;
}
/*
 * remove_neutral
 */
bool mspectrumcondition::remove_neutral(mspectrum &_s)
{
	if(!m_bUseNeutralLoss)
		return false;
	vector<mi>::iterator itMI = _s.m_vMI.begin();
	while(itMI != _s.m_vMI.end())	{
		if(fabs((_s.m_dMH - itMI->m_fM) - m_fNeutralLoss) <= m_fNeutralLossWidth)	{
			_s.m_vMINeutral.push_back(*itMI);
			itMI = _s.m_vMI.erase(itMI);
		}
		else	{
			itMI++;
		}
	}
	return true;
}
/*
 * get_noise_suppression gets the current value of the m_bUseNoiseSuppression member
 */
bool mspectrumcondition::get_noise_suppression(void)
{
	return m_bUseNoiseSuppression;
}
/*
 * set_max_peaks sets the current value of the m_tMaxPeaks member
 */
bool mspectrumcondition::set_max_peaks(const long _p)
{
	m_tMaxPeaks = _p;
	return true;
}
/*
 * set_min_size sets the current value of the m_lMinSize member
 */
bool mspectrumcondition::set_min_size(const long _p)
{
	m_lMinSize = _p;
	return true;
}
/*
 * set_dynamic_range sets the current value of the m_fDynamicRange member
 */
bool mspectrumcondition::set_dynamic_range(const float _p)
{
	m_fDynamicRange = _p;
	return true;
}
/*
 * set_parent_exclusion sets the current value of the m_fParentLower & m_fParentUpper members
 */
bool mspectrumcondition::set_parent_exclusion(const float _l,const float _u)
{
	m_fParentLower = _l;
	m_fParentUpper = _u;
	return true;
}
/*
 * set_min_mass sets the current value of the m_fMinMass member
 */
bool mspectrumcondition::set_min_mass(const float _m)
{
	m_fMinMass = _m;
	return true;
}
/*
 * set_max_mass sets the current value of the m_fMaxMass member
 */
bool mspectrumcondition::set_max_mass(const float _m)
{
	m_fMaxMass = _m;
	return true;
}
/*
 * set_lowest_mass sets the current value of the m_fLowestMass member
 */
bool mspectrumcondition::set_lowest_mass(const float _m)
{
	m_fLowestMass = _m;
	return true;
}
/*
 * use_condition sets the current value of the m_bCondition member
 */
bool mspectrumcondition::use_condition(const bool _f)
{
	m_bCondition = _f;
	return m_bCondition;
}
/*
 * use_min_size sets the current value of the m_bUseMinSize member
 */
bool mspectrumcondition::use_min_size(const bool _f)
{
	m_bUseMinSize = _f;
	return m_bUseMinSize;
}
/*
 * use_max_peaks sets the current value of the m_bUseMaxPeaks member
 */
bool mspectrumcondition::use_max_peaks(const bool _f)
{
	m_bUseMaxPeaks = _f;
	return m_bUseMaxPeaks;
}
/*
 * use_charge_suppression sets the current value of the m_bUseChargeSuppression member
 */
bool mspectrumcondition::use_charge_suppression(const bool _f)
{
	m_bUseChargeSuppression = _f;
	return m_bUseChargeSuppression;
}
/*
 * use_dynamic_range sets the current value of the m_bUseDynamicRange member
 */
bool mspectrumcondition::use_dynamic_range(const bool _f)
{
	m_bUseDynamicRange = _f;
	return m_bUseDynamicRange;
}
/*
 * use_noise_suppression sets the current value of the m_bUseNoiseSuppression member
 */
bool mspectrumcondition::use_noise_suppression(const bool _f)
{
	m_bUseNoiseSuppression = _f;
	return m_bUseNoiseSuppression;
}
/*
 * use_lowest_mass sets the current value of the m_bUseLowestMass member
 */
bool mspectrumcondition::use_lowest_mass(const bool _f)
{
	m_bUseLowestMass = _f;
	return m_bUseLowestMass;
}
/*
 * use_min_mass sets the current value of the m_bUseMinMass member
 */
bool mspectrumcondition::use_min_mass(const bool _f)
{
	m_bUseMinMass = _f;
	return m_bUseMinMass;
}
/*
 * use_parent_exclusion sets the current value of the m_bUseParent member
 */
bool mspectrumcondition::use_parent_exclusion(const bool _f)
{
	m_bUseParent = _f;
	return m_bUseParent;
}