/*
 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

Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some 
semblance of artistic control over the development of the package, 
while giving the users of the package the right to use and distribute 
the Package in a more-or-less customary fashion, plus the right to 
make reasonable modifications. 

Definitions
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	Holder, and derivatives of that collection of files created through 
	textual modification. 

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	or has been modified in accordance with the wishes of the Copyright 
	Holder as specified below. 

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	for the package. 

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The End 
*/

// 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 "saxsaphandler.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_bUseChargeSuppression = true;
	m_bCondition = true;
	m_bUseNeutralLoss = false;
	m_bUsePhosphoDetection = false;

	m_tMaxPeaks = 50;
	m_fDynamicRange = 100.0;
	m_fMinMass = 500.0;
	m_fLowestMass = 150.0;
	m_fParentLower = 2.0;
	m_fParentUpper = 2.0;
	m_lMinSize = 5;
	m_lMaxCharge = 3;
	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)
{
/*
 * bail out if conditioning has been turned off
 */
	if(m_bUsePhosphoDetection)	{
		if(!find_loss(_s,98.0,3.0))	{
			return false;
		}
	}
	if(m_bUseAllowedNeutralLosses)	{
		size_t m = 0;
		size_t tSize = m_vdNeutralLosses.size();
		bool bOK = false;
		while(m < tSize && !bOK)	{
			bOK = find_loss(_s,(float)m_vdNeutralLosses[m],(float)0.5,(float)0.05);
			m++;
		}
		if(!bOK)	{
			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);
	}
	if(_s.m_fZ > m_fMaxZ)	{
		return false;
	}
	if(!m_bCondition)	{
		return true;
	}
/*
 * give the score object a chance to perform score specific modifications
 * or veto this spectrum.
 */
	if(!_score.precondition(_s)) {
		return false;
	}
	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;
	}
/*
* 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,const float _p)
{
	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();
	float fMax = itMI->m_fI;
	while(itMI != itEnd)	{
		if(itMI->m_fI > fMax)	{
			fMax = itMI->m_fI;
		}
		itMI++;
	}
	fMax *= _p;
	itMI = _s.m_vMI.begin();
	float fD = (float)(1.007276 + ((_s.m_dMH - 1.007276 - _d)/_s.m_fZ));
	while(itMI != itEnd)	{
		if(fabs(itMI->m_fM - fD) <= _t && itMI->m_fI >= fMax)	{
			return true;
		}
		itMI++;
	}
	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;

}
/*
 * 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, 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 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, allowed neutral losses";
	m_bUseAllowedNeutralLosses = _x.get(strKey,strValue);
	if(m_bUseAllowedNeutralLosses)	{
		m_vdNeutralLosses.clear();
		string strV;
		size_t tLength = strValue.size();
		size_t a = 0;
		while(a < tLength)	{
			if(!isspace(strValue[a]))	{
				strV += strValue[a];
			}
			a++;
		}
		tLength = strV.size();
		if(tLength > 0)	{
			a = 0;
			size_t b = strV.find(',',a);
			double dValue = 0.0;
			while(b != strV.npos)	{
				dValue = atof(strV.substr(a,b-a).c_str());
				if(dValue != 0.0)	{
					m_vdNeutralLosses.push_back(dValue);
				}
				a = b + 1;
				b = strV.find(',',a);
			}
			dValue = atof(strV.substr(a,tLength-a).c_str());
			if(dValue != 0.0)	{
				m_vdNeutralLosses.push_back(dValue);
			}
			if(m_vdNeutralLosses.empty())	{
				m_bUseAllowedNeutralLosses = false;
			}
		}
		else	{
				m_bUseAllowedNeutralLosses = false;
		}
	}
	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;
}
/*
 * 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_charge sets the current value of the m_lMaxCharge member
 */
bool mspectrumcondition::set_max_charge(const long _m)
{
	m_lMaxCharge = _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_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;
}

