msequtilities.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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The End 
*/

// File version: 2003-07-01

/*
 * msequtilities contains a set of constants and arrays for scoring and setting the molecular
 * mass of a peptide sequence. Biemann notation is used for fragment ions.
 */

#include "stdafx.h"
#include "msequence.h"
#include "msequtilities.h"

/*
 * sets the default values for the necessary constants. see msequtilities.h for descriptions 
 */

msequtilities::msequtilities(masscalc::massType _t)
	: m_calc(_t)
{
	m_dCleaveCdefault = m_calc.calcMass("OH");
	m_dCleaveNdefault = m_calc.calcMass("H");
	m_dCleaveC = m_dCleaveCdefault;
	m_dCleaveN = m_dCleaveNdefault;
	const unsigned long lValue = 128;
	m_pfAaMass = new float[lValue];
	memset(m_pfAaMass,0,lValue*sizeof(float));
	m_pdAaMass = new double[lValue];
	memset(m_pdAaMass,0,lValue*sizeof(double));
	m_pdAaPrompt = new double[lValue];
	m_pdAaMod = new double[lValue];
	m_pdAaFullMod = new double[lValue];
	m_pfAScore = new float[lValue];
	m_pfBScore = new float[lValue];
	m_pfYScore = new float[lValue];
	m_pfXScore = new float[lValue];
	m_pfCScore = new float[lValue];
	m_pfZScore = new float[lValue];
	m_pfA18Score = new float[lValue];
	m_pfB18Score = new float[lValue];
	m_pfY18Score = new float[lValue];
	m_pfX18Score = new float[lValue];
	m_pfC18Score = new float[lValue];
	m_pfZ18Score = new float[lValue];
	m_pfA17Score = new float[lValue];
	m_pfB17Score = new float[lValue];
	m_pfY17Score = new float[lValue];
	m_pfX17Score = new float[lValue];
	m_pfC17Score = new float[lValue];
	m_pfZ17Score = new float[lValue];
	long a = 0;
	while(a < lValue)	{
		m_pdAaMod[a] = 0.0;
		m_pdAaPrompt[a] = 0.0;
		m_pdAaFullMod[a] = 0.0;
		m_pfXScore[a] = 1.0;
		m_pfYScore[a] = 1.0;
		m_pfAScore[a] = 1.0;
		m_pfBScore[a] = 1.0;
		m_pfCScore[a] = 1.0;
		m_pfZScore[a] = 1.0;
		m_pfX18Score[a] = 1.0;
		m_pfY18Score[a] = 1.0;
		m_pfA18Score[a] = 1.0;
		m_pfB18Score[a] = 1.0;
		m_pfC18Score[a] = 1.0;
		m_pfZ18Score[a] = 1.0;
		m_pfX17Score[a] = 1.0;
		m_pfY17Score[a] = 1.0;
		m_pfA17Score[a] = 1.0;
		m_pfB17Score[a] = 1.0;
		m_pfC17Score[a] = 1.0;
		m_pfZ17Score[a] = 1.0;
		a++;
	}
	set_aa();
	m_fNT = 0.0;
	m_fCT = 0.0;
	// Mass of a proton, i.e. +1 positive charge, hydrogen atom without its electron.
	// See http://antoine.frostburg.edu/chem/senese/101/atoms/index.shtml
	m_dProton = 1.007276;
	m_dWater = m_calc.calcMass("H2O");
	m_dAmmonia = m_calc.calcMass("NH3");
	m_dA = -m_calc.calcMass("CO")+m_calc.calcMass("H"); //MH: Add hydrogen mass to all A-ions
	m_dB = 0.0;
	m_dC = m_calc.calcMass("NH3");
	m_dY = m_calc.calcMass("H2O");;
	m_dX = m_calc.calcMass("CO2");
	// changed from m_dZ = m_dY - m_calc.calcMass("NH3") in 2006.02.01
	m_dZ = m_dY - m_calc.calcMass("NH2");
	m_bComplete = false;
	m_bPotential = false;
	m_vMotifs.clear();
	m_mapMotifs.clear();
	m_bPotentialMotif = false;
	m_bSequenceMods = false;
	m_mapMods.clear();
	m_bIsModified = false;

}
/*
 * clean up the arrays created using the new operator
 */

msequtilities::~msequtilities(void)
{
	if(m_pfAaMass != NULL)
		delete m_pfAaMass;
	if(m_pdAaMass != NULL)
		delete m_pdAaMass;
	if(m_pdAaMod != NULL)
		delete m_pdAaMod;
	if(m_pdAaPrompt != NULL)
		delete m_pdAaPrompt;
	if(m_pdAaFullMod != NULL)
		delete m_pdAaFullMod;
	if(m_pfAScore != NULL)
		delete m_pfAScore;
	if(m_pfBScore != NULL)
		delete m_pfBScore;
	if(m_pfYScore != NULL)
		delete m_pfYScore;
	if(m_pfXScore != NULL)
		delete m_pfXScore;
	if(m_pfCScore != NULL)
		delete m_pfCScore;
	if(m_pfZScore != NULL)
		delete m_pfZScore;
	if(m_pfA18Score != NULL)
		delete m_pfA18Score;
	if(m_pfB18Score != NULL)
		delete m_pfB18Score;
	if(m_pfY18Score != NULL)
		delete m_pfY18Score;
	if(m_pfX18Score != NULL)
		delete m_pfX18Score;
	if(m_pfC18Score != NULL)
		delete m_pfC18Score;
	if(m_pfZ18Score != NULL)
		delete m_pfZ18Score;
	if(m_pfA17Score != NULL)
		delete m_pfA17Score;
	if(m_pfB17Score != NULL)
		delete m_pfB17Score;
	if(m_pfY17Score != NULL)
		delete m_pfY17Score;
	if(m_pfX17Score != NULL)
		delete m_pfX17Score;
	if(m_pfC17Score != NULL)
		delete m_pfC17Score;
	if(m_pfZ17Score != NULL)
		delete m_pfZ17Score;
}

bool msequtilities::add_mod(const char _c,const size_t _v)
{
	m_mapMotifMods[_c] = _v;
	return true;
}

bool msequtilities::clear_motifs(const bool _b)	
{
	map<char,size_t>::iterator itValue = m_mapMotifMods.begin();
	while(itValue != m_mapMotifMods.end())	{
		m_pdAaMod[itValue->first+32] = 0.0;
		m_pdAaPrompt[itValue->first+32] = 0.0;
		itValue++;
	}
	if(_b)	{
		m_mapMotifMods.clear();
	}
	return true;
}

bool msequtilities::set_motifs(void)	
{
	map<char,size_t>::iterator itValue = m_mapMotifMods.begin();
	while(itValue != m_mapMotifMods.end())	{
		m_pdAaMod[itValue->first+32] = m_vMotifs[itValue->second].m_fMass;
		m_pdAaPrompt[itValue->first+32] = m_vMotifs[itValue->second].m_fMassPrompt;
		itValue++;
	}
	return true;
}

bool msequtilities::synthesis(const bool _b)
{
	if(_b)	{
		set_y('P',5.0);
		set_b('D',5.0);
		set_b('N',2.0);
		set_b('V',3.0);
		set_b('E',3.0);
		set_b('Q',2.0);
		set_b('I',3.0);
		set_b('L',3.0);
	}
	else	{
		char a = 0;
		while(a < 127)	{
			set_y(a,1.0);
			set_b(a,1.0);
			a++;
		}
	}
	return true;
}

/*
 * imports a list of complete residue modifications, using a string with the following format:
 * m1@r1,m2@r2,m3@r3, ...
 * where mX is the mass of the modification, in Daltons, and rX is the single letter code for the
 * modified residue. there is no limit to the length of the string (but there are only 20 amino acids)
 * NOTE: lower case index values are reserved for potential modifications and may not be used here
 */

bool msequtilities::modify_all(string &_s)
{
	size_t tStart = 'A';
	while(tStart < 'Z'+1)	{
		m_pdAaFullMod[tStart] = 0.0;
		tStart++;
	}
	tStart = 'a';
	while(tStart < 'z'+1)	{
		m_pdAaFullMod[tStart] = 0.0;
		tStart++;
	}
	m_pdAaFullMod[']'] = 0.0;
	m_pdAaFullMod['['] = 0.0;
	tStart = 0;
	if(_s.empty())
		return false;
	size_t tAt = 0;
	double fValue;
	string strValue = _s.substr(tStart,_s.size()-tStart);
	fValue = atof(strValue.c_str());
	while(fValue != 0.0)	{
		m_bComplete = true;
		tAt = _s.find('@',tStart);
		if(tAt == _s.npos)
			break;
		tAt++;
		if(isalpha(_s[tAt]))	{
			m_pdAaFullMod[_s[tAt]] = fValue;
			m_pdAaFullMod[_s[tAt]+32] = fValue;
		}
		else	{
			m_pdAaFullMod[_s[tAt]] = fValue;
		}
		tStart = _s.find(',',tAt);
		if(tStart == _s.npos)
			break;
		tStart++;
		strValue = _s.substr(tStart,_s.size()-tStart);
		fValue = atof(strValue.c_str());
	}
	return true;
}
/*
 * imports a list of potential residue modifications, using a string with the following format:
 * m1@r1,m2@r2,m3@r3, ...
 * where mX is the mass of the modification, in Daltons, and rX is the single letter code for the
 * modified residue. there is no limit to the length of the string (but there are only 20 amino acids)
 * NOTE: lower case index values are reserved for potential modifications
 */

bool msequtilities::modify_maybe(string &_s)
{
	size_t tStart = 'a';
	while(tStart < 'z'+1)	{
		m_pdAaMod[tStart] = 0.0;
		m_pdAaPrompt[tStart] = 0.0;
		tStart++;
	}
	m_pdAaMod['['] = 0.0;
	m_pdAaMod[']'] = 0.0;

	m_bPotential = false;
	if(_s.empty())
		return false;
	tStart = 0;
	size_t tAt = 0;
	size_t tColon = 0;
	double fValue = 0.0;
	double fPrompt = 0.0;
	string strValue = _s.substr(tStart,_s.size()-tStart);
	m_strDefaultMaybe = strValue;
	fValue = atof(strValue.c_str());
	char cRes = '\0';
	while(fValue != 0.0)	{
		m_bPotential = true;
		tAt = _s.find('@',tStart);
		if(tAt == _s.npos)
			break;
		tColon = _s.find(':',tStart);
		fPrompt = 0.0;
		if(tColon != _s.npos && tColon < tAt)	{
			fPrompt = atof(_s.substr(tColon+1,tAt - tColon).c_str());
		}
		tAt++;
		cRes = _s[tAt];
		if(cRes >= 'A' && cRes <= 'Z')	{
			cRes += 32;
		}
		m_pdAaMod[cRes] = fValue;
		m_pdAaPrompt[cRes] = fPrompt;
		tStart = _s.find(',',tAt);
		if(tStart == _s.npos)
			break;
		tStart++;
		strValue = _s.substr(tStart,_s.size()-tStart);
		fValue = atof(strValue.c_str());
	}
	return true;
}

bool msequtilities::modify_annotation(string &_s)
{
	size_t tStart = 'a';
	const size_t tEnd = 'z'+1;
	while(tStart < tEnd)	{
		m_pdAaMod[tStart] = 0.0;
		m_pdAaPrompt[tStart] = 0.0;
		tStart++;
	}
	m_pdAaMod['['] = 0.0;
	m_pdAaMod[']'] = 0.0;

	m_bPotential = false;
	tStart = 0;
	size_t tAt = 0;
	size_t tColon = 0;
	double fValue = 0.0;
	double fPrompt = 0.0;
	string strValue = _s;
	if(!_s.empty())	{
		strValue += ",";
	}
	strValue += m_strDefaultMaybe;
	if(strValue.empty())	{
		return false;
	}
	string strV = strValue;
	fValue = atof(strV.c_str());
	char cRes = '\0';
	while(fValue != 0.0)	{
		m_bPotential = true;
		tAt = strValue.find('@',tStart);
		if(tAt == strValue.npos)
			break;
		tColon = strValue.find(':',tStart);
		fPrompt = 0.0;
		if(tColon != strValue.npos && tColon < tAt)	{
			fPrompt = atof(strValue.substr(tColon+1,tAt - tColon).c_str());
		}
		tAt++;
		cRes = strValue[tAt];
		if(cRes >= 'A' && cRes <= 'Z')	{
			cRes += 32;
		}
		m_pdAaMod[cRes] = fValue;
		m_pdAaPrompt[cRes] = fPrompt;
		tStart = strValue.find(',',tAt);
		if(tStart == strValue.npos)
			break;
		tStart++;
		strV = strValue.substr(tStart,_s.size()-tStart);
		fValue = atof(strV.c_str());
	}
	return true;
}


bool msequtilities::motif_set(const msequence &_s)
{
	m_mapMods.clear();
	m_mapMods = _s.m_mapMods;
	if(!m_mapMods.empty())	{
		m_bSequenceMods = true;
	}
	else	{
		m_bSequenceMods = false;
	}
	if(m_vMotifs.empty())	{
		return false;
	}
	m_mapMotifs.clear();
	char *pString = new char[_s.m_strSeq.size()+1];
	strcpy(pString,_s.m_strSeq.c_str());
	char *pValue = pString;
	size_t a = 0;
	size_t b = 0;
	size_t tPos;
	const size_t tMotifs = m_vMotifs.size();
	while(*pValue != '\0')	{
		a = 0;
		while(a < tMotifs)	{
			if(m_vMotifs[a].check(pValue,tPos))	{
				m_mapMotifs[pValue-pString+tPos] = a;
			}
			a++;
		}
		pValue++;
	}
	delete pString;
	return true;
}

bool msequtilities::modify_motif(const string &_s)
{
	m_vMotifs.clear();
	m_bPotentialMotif = false;
	if(_s.empty())	{
		return false;
	}
	size_t tStart = 0;
	size_t tAt = 0;
	float fValue;
	string strValue = _s.substr(tStart,_s.size()-tStart);
	fValue = (float)atof(strValue.c_str());
	char *pOut = new char[1024];
	mmotif motValue;
	while(fValue != 0.0)	{
		tAt = _s.find('@',tStart);
		if(tAt == _s.npos)
			break;
		tAt = tStart;
		tStart = _s.find(',',tAt);
		if(tStart == _s.npos)	{
			strValue = _s.substr(tAt,tStart-tAt);
			strcpy(pOut,strValue.c_str());
			motValue.initialize();
			if(motValue.set(pOut))	{
				m_vMotifs.push_back(motValue);
			}
			break;
		}
		else	{
			strValue = _s.substr(tAt,_s.size()-tAt);
			strcpy(pOut,strValue.c_str());
			motValue.initialize();
			if(motValue.set(pOut))	{
				m_vMotifs.push_back(motValue);
			}
		}
		tStart++;
		strValue = _s.substr(tStart,_s.size()-tStart);
		fValue = (float)atof(strValue.c_str());
	}
	if(!m_vMotifs.empty())	{
		m_bPotential = true;
		m_bPotentialMotif = true;
	}
	return true;
}

/*
 * sets the mass of the c-terminal residue modification for a protein
 */
bool msequtilities::modify_c(const float _f)
{
	m_fCT = _f;
	return true;
}
/*
 * sets the mass of the n-terminal residue modification for a protein
 */
bool msequtilities::modify_n(const float _f)
{
	m_fNT = _f;
	return true;
}
/*
 * initializes the mass of amino acid residues (less water)
 *     chemical formulas found at http://haven.isb-sib.ch/tools/isotopident/htdocs/aa-list.html
 */
bool msequtilities::set_aa()
{
	float *pValue = m_pfAaMass;
	if(pValue == NULL)
		return false;
	double *pdValue = m_pdAaMass;
	if(pdValue == NULL)
		return false;

	if (m_calc.getMassType() == masscalc::monoisotopic)	{
		pdValue['a'] = pdValue['A'] = m_calc.calcMass("C3H5ON");
		pValue['a'] = pValue['A'] = (float)pdValue['A'];

		pdValue['b'] = pdValue['B'] = m_calc.calcMass("C4H6O2N2");	// Same as N
		pValue['b'] = pValue['B'] = (float)pdValue['B'];

		pdValue['c'] = pdValue['C'] = m_calc.calcMass("C3H5ONS");
		pValue['c'] = pValue['C'] = (float)pdValue['C'];
		
		pdValue['d'] = pdValue['D'] = m_calc.calcMass("C4H5O3N");
		pValue['d'] = pValue['D'] = (float)pdValue['D'];
		
		pdValue['e'] = pdValue['E'] = m_calc.calcMass("C5H7O3N");
		pValue['e'] = pValue['E'] = (float)pdValue['E'];
		
		pdValue['f'] = pdValue['F'] = m_calc.calcMass("C9H9ON");
		pValue['f'] = pValue['F'] = (float)pdValue['F'];
		
		pdValue['g'] = pdValue['G'] = m_calc.calcMass("C2H3ON");
		pValue['g'] = pValue['G'] = (float)pdValue['G'];
		
		pdValue['h'] = pdValue['H'] = m_calc.calcMass("C6H7ON3");
		pValue['h'] = pValue['H'] = (float)pdValue['H'];
		
		pdValue['i'] = pdValue['I'] = m_calc.calcMass("C6H11ON");
		pValue['i'] = pValue['I'] = (float)pdValue['I'];
		
		pdValue['j'] = pdValue['J'] = 0.0;
		pValue['j'] = pValue['J'] = (float)pdValue['J'];
		
		pdValue['k'] = pdValue['K'] = m_calc.calcMass("C6H12ON2");
		pValue['k'] = pValue['K'] = (float)pdValue['K'];
		
		pdValue['l'] = pdValue['L'] = m_calc.calcMass("C6H11ON");
		pValue['l'] = pValue['L'] = (float)pdValue['L'];
		
		pdValue['m'] = pdValue['M'] = m_calc.calcMass("C5H9ONS");
		pValue['m'] = pValue['M'] = (float)pdValue['M'];
		
		pdValue['n'] = pdValue['N'] = m_calc.calcMass("C4H6O2N2");
		pValue['n'] = pValue['N'] = (float)pdValue['N'];
		
		pdValue['o'] = pdValue['O'] = m_calc.calcMass("C4H6O2N2");	// Same as N
		pValue['o'] = pValue['O'] = (float)pdValue['O'];
		
		pdValue['p'] = pdValue['P'] = m_calc.calcMass("C5H7ON");
		pValue['p'] = pValue['P'] = (float)pdValue['P'];
		
		pdValue['q'] = pdValue['Q'] = m_calc.calcMass("C5H8O2N2");
		pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
		
		pdValue['r'] = pdValue['R'] = m_calc.calcMass("C6H12ON4");
		pValue['r'] = pValue['R'] = (float)pdValue['R'];
		
		pdValue['s'] = pdValue['S'] = m_calc.calcMass("C3H5O2N");
		pValue['s'] = pValue['S'] = (float)pdValue['S'];
		
		pdValue['t'] = pdValue['T'] = m_calc.calcMass("C4H7O2N");
		pValue['t'] = pValue['T'] = (float)pdValue['T'];
		
		pdValue['u'] = pdValue['U'] = 150.953640;	// Why?
		pValue['u'] = pValue['U'] = (float)pdValue['U'];
		
		pdValue['v'] = pdValue['V'] = m_calc.calcMass("C5H9ON");
		pValue['v'] = pValue['V'] = (float)pdValue['V'];
		
		pdValue['w'] = pdValue['W'] = m_calc.calcMass("C11H10ON2");
		pValue['w'] = pValue['W'] = (float)pdValue['W'];
		
		pdValue['x'] = pdValue['X'] = 111.060000;	// Why?
		pValue['x'] = pValue['X'] = (float)pdValue['X'];
		
		pdValue['y'] = pdValue['Y'] = m_calc.calcMass("C9H9O2N");
		pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
		
		pdValue['z'] = pdValue['Z'] = m_calc.calcMass("C5H8O2N2");	// Same as Q
		pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
	}
	else {
		/*
		 * unfortunately, the average masses for amino acids do not
		 * seem to be straight sums of the average masses for the atoms
		 * they contain.
		 *
		 * instead of using the mass calculator, these numbers are taken
		 * as constants from the web page referenced above.
		 */
		pdValue['a'] = pdValue['A'] = 71.0788;
		pValue['a'] = pValue['A'] = (float)pdValue['A'];

		pdValue['b'] = pdValue['B'] = 114.1038;	// Same as N
		pValue['b'] = pValue['B'] = (float)pdValue['B'];

		pdValue['c'] = pdValue['C'] = 103.1388;
		pValue['c'] = pValue['C'] = (float)pdValue['C'];
		
		pdValue['d'] = pdValue['D'] = 115.0886;
		pValue['d'] = pValue['D'] = (float)pdValue['D'];
		
		pdValue['e'] = pdValue['E'] = 129.1155;
		pValue['e'] = pValue['E'] = (float)pdValue['E'];
		
		pdValue['f'] = pdValue['F'] = 147.1766;
		pValue['f'] = pValue['F'] = (float)pdValue['F'];
		
		pdValue['g'] = pdValue['G'] = 57.0519;
		pValue['g'] = pValue['G'] = (float)pdValue['G'];
		
		pdValue['h'] = pdValue['H'] = 137.1411;
		pValue['h'] = pValue['H'] = (float)pdValue['H'];
		
		pdValue['i'] = pdValue['I'] = 113.1594;
		pValue['i'] = pValue['I'] = (float)pdValue['I'];
		
		pdValue['j'] = pdValue['J'] = 0.0;
		pValue['j'] = pValue['J'] = (float)pdValue['J'];
		
		pdValue['k'] = pdValue['K'] = 128.1741;
		pValue['k'] = pValue['K'] = (float)pdValue['K'];
		
		pdValue['l'] = pdValue['L'] = 113.1594;
		pValue['l'] = pValue['L'] = (float)pdValue['L'];
		
		pdValue['m'] = pdValue['M'] = 131.1926;
		pValue['m'] = pValue['M'] = (float)pdValue['M'];
		
		pdValue['n'] = pdValue['N'] = 114.1038;
		pValue['n'] = pValue['N'] = (float)pdValue['N'];
		
		pdValue['o'] = pdValue['O'] = 114.1038;	// Same as N
		pValue['o'] = pValue['O'] = (float)pdValue['O'];
		
		pdValue['p'] = pdValue['P'] = 97.1167;
		pValue['p'] = pValue['P'] = (float)pdValue['P'];
		
		pdValue['q'] = pdValue['Q'] = 128.1307;
		pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
		
		pdValue['r'] = pdValue['R'] = 156.1875;
		pValue['r'] = pValue['R'] = (float)pdValue['R'];
		
		pdValue['s'] = pdValue['S'] = 87.0782;
		pValue['s'] = pValue['S'] = (float)pdValue['S'];
		
		pdValue['t'] = pdValue['T'] = 101.1051;
		pValue['t'] = pValue['T'] = (float)pdValue['T'];
		
		pdValue['u'] = pdValue['U'] = 0.0;	// Why?
		pValue['u'] = pValue['U'] = (float)pdValue['U'];
		
		pdValue['v'] = pdValue['V'] = 99.1326;
		pValue['v'] = pValue['V'] = (float)pdValue['V'];
		
		pdValue['w'] = pdValue['W'] = 186.2132;
		pValue['w'] = pValue['W'] = (float)pdValue['W'];
		
		pdValue['x'] = pdValue['X'] = 113.1594;	// Why?
		pValue['x'] = pValue['X'] = (float)pdValue['X'];
		
		pdValue['y'] = pdValue['Y'] = 163.1760;
		pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
		
		pdValue['z'] = pdValue['Z'] = 128.1307;	// Same as Q
		pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
	}

	return true;
}
/*
 * sets the score for a particular a ion
 */
bool msequtilities::set_a(const char _c,const float _f)
{
	m_pfAScore[_c] = _f;
	m_pfA18Score[_c] = _f;
	m_pfA17Score[_c] = _f;
	return true;
}
/*
 * sets the score for a particular b ion
 */
bool msequtilities::set_b(const char _c,const float _f)
{
	m_pfBScore[_c] = _f;
	m_pfB18Score[_c] = _f;
	m_pfB17Score[_c] = _f;
	return true;
}
/*
 * sets the score for a particular x ion
 */
bool msequtilities::set_x(const char _c,const float _f)
{
	m_pfXScore[_c] = _f;
	m_pfX18Score[_c] = _f;
	m_pfX17Score[_c] = _f;
	return true;
}
/*
 * sets the score for a particular y ion
 */
bool msequtilities::set_y(const char _c,const float _f)
{
	m_pfYScore[_c] = _f;
	m_pfY18Score[_c] = _f;
	m_pfY17Score[_c] = _f;
	return true;
}

/*
 * sets the score for a particular c ion
 */
bool msequtilities::set_c(const char _c,const float _f)
{
	m_pfCScore[_c] = _f;
	m_pfC18Score[_c] = _f;
	m_pfC17Score[_c] = _f;
	return true;
}
/*
 * sets the score for a particular z ion
 */
bool msequtilities::set_z(const char _c,const float _f)
{
	m_pfZScore[_c] = _f;
	m_pfZ18Score[_c] = _f;
	m_pfZ17Score[_c] = _f;
	return true;
}

bool msequtilities::set_aa_file(string &_p)
{
	m_bIsModified = false;
	ifstream ifIn;
	ifIn.open(_p.c_str());
	if(ifIn.fail())	{
		return false;
	}
	vector<string> vstrValues;
	string strValue;
	char *pLine = new char[1024];
	while(ifIn.good() && !ifIn.eof())	{
		ifIn.getline(pLine,1023);
		strValue = pLine;
		vstrValues.push_back(strValue);
	}
	ifIn.close();
	size_t a = 0;
	size_t tStart;
	size_t tEnd;
	double dMass = 0.0;
	char cAa = '\0';
	const size_t tLength = vstrValues.size();
	string strType;
	string strLine;
	while(a < tLength)	{
		cAa = '\0';
		strType = " ";
		dMass = -1.0;
		strLine = vstrValues[a];
		if(strLine.find("<aa ") != strLine.npos)	{
			tStart = strLine.find("mass=\"");
			if(tStart != strLine.npos)	{
				tStart = strLine.find("\"",tStart);
				tStart++;
				dMass = atof(strLine.substr(tStart,strLine.size() - tStart).c_str());
			}
			tStart = strLine.find("type=\"");
			if(tStart != strLine.npos)	{
				tStart = strLine.find("\"",tStart);
				tStart++;
				cAa = strLine[tStart];
			}
			if(cAa != '\0' && dMass >= 0.0)	{
				if(cAa > 'Z')	{
					cAa -= 32;
				}
				if(isalpha(cAa))	{
					m_bIsModified = true;
					m_pdAaMass[cAa+32] = m_pdAaMass[cAa] = dMass;
					m_pfAaMass[cAa+32] = m_pfAaMass[cAa] = (float)dMass;
				}
			}
		}
		if(strLine.find("<molecule ") != strLine.npos)	{
			tStart = strLine.find("mass=\"");
			if(tStart != strLine.npos)	{
				tStart = strLine.find("\"",tStart);
				tStart++;
				dMass = atof(strLine.substr(tStart,strLine.size() - tStart).c_str());
			}
			tStart = strLine.find("type=\"");
			if(tStart != strLine.npos)	{
				tStart = strLine.find("\"",tStart);
				tStart++;
				tEnd = strLine.find("\"",tStart);
				if(tEnd != strLine.npos)	{
					strType = strLine.substr(tStart,tEnd - tStart);
				}
			}
			if(dMass >= 0.0 && strType != " ")	{
				if(strType == "NH3")	{
					m_bIsModified = true;
					m_dAmmonia = dMass;
				}
				if(strType == "H2O")	{
					m_bIsModified = true;
					m_dWater = dMass;
				}
			}
		}
		a++;
	}
	m_dC = m_dAmmonia;
	m_dY = m_dWater;
	return true;
}

bool msequtilities::is_modified()
{
	return m_bIsModified;
}

bool msequtilities::set_modified(const bool _b)
{
	m_bIsModified = _b;
	return m_bIsModified;
}