/*
 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
"Package" refers to the collection of files distributed by the Copyright
  Holder, and derivatives of that collection of files created through
  textual modification.

"Standard Version" refers to such a Package if it has not been modified,
  or has been modified in accordance with the wishes of the Copyright
  Holder as specified below.

"Copyright Holder" is whoever is named in the copyright or copyrights
  for the package.

"You" is you, if you're thinking about copying or distributing this Package.

"Reasonable copying fee" is whatever you can justify on the basis of
  media cost, duplication charges, time of people involved, and so on.
  (You will not be required to justify it to the Copyright Holder, but
  only to the computing community at large as a market that must bear
  the fee.)

"Freely Available" means that no fee is charged for the item itself,
  though there may be fees involved in handling the item. It also means
  that recipients of the item may redistribute it under the same
  conditions they received it.

1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that
you duplicate all of the original copyright notices and associated
disclaimers.

2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder. A
Package modified in such a way shall still be considered the Standard
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3. You may otherwise modify your copy of this Package in any way, provided
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  Freely Available, such as by posting said modifications to Usenet
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  to include your modifications in the Standard Version of the Package.
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c.	rename any non-standard executables so the names do not conflict
  with standard executables, which must also be provided, and provide
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d.	make other distribution arrangements with the Copyright Holder.

4. You may distribute the programs of this Package in object code or
executable form, provided that you do at least ONE of the following:

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  where to get the Standard Version.
b.	accompany the distribution with the machine-readable source of the
  Package with your modifications.
c.	give non-standard executables non-standard names, and clearly
  document the differences in manual pages (or equivalent), together
  with instructions on where to get the Standard Version.
d.	make other distribution arrangements with the Copyright Holder.

5. You may charge a reasonable copying fee for any distribution of
this Package. You may charge any fee you choose for support of
this Package. You may not charge a fee for this Package itself.
However, you may distribute this Package in aggregate with other
(possibly commercial) programs as part of a larger (possibly
commercial) software distribution provided that you do not a
dvertise this Package as a product of your own. You may embed this
Package's interpreter within an executable of yours (by linking);
this shall be construed as a mere form of aggregation, provided that
the complete Standard Version of the interpreter is so embedded.

6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall
under the copyright of this Package, but belong to whomever generated
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Package. If such scripts or library files are aggregated with this
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neither be construed as a distribution of this Package nor shall it
fall under the restrictions of Paragraphs 3 and 4, provided that you
do not represent such an executable image as a Standard Version of
this Package.

7. C subroutines (or comparably compiled subroutines in other languages)
supplied by you and linked into this Package in order to emulate
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shall not be considered part of this Package, but are the equivalent
of input as in Paragraph 6, provided these subroutines do not change
the language in any way that would cause it to fail the regression
tests for the language.

8. Aggregation of this Package with a commercial distribution is always
permitted provided that the use of this Package is embedded; that is,
when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution. Such use shall not be
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9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.

10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.

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.
 */


#ifdef HEADER2017
#include "stdafx.h"
#include "msequence.h"
#include "msequtilities.h"
#endif


#ifdef HEADER2015
#include "../stdafx.h"
#include "../msequence.h"
#include "../msequtilities.h"
#endif


#ifdef HEADER2015P
#include "../stdafx.h"
#include "../msequence.h"
#include "../msequtilities.h"
#endif

#include <pappsomspp/core/pappsoexception.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_pfA18Score  = new float[lValue];
  m_pfB18Score  = new float[lValue];
  m_pfY18Score  = new float[lValue];
  m_pfX18Score  = new float[lValue];
  m_pfA17Score  = new float[lValue];
  m_pfB17Score  = new float[lValue];
  m_pfY17Score  = new float[lValue];
  m_pfX17Score  = new float[lValue];
  m_piAaDepth   = new int[lValue];
  m_piCtMod     = new int[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_pfX18Score[a]  = 1.0;
      m_pfY18Score[a]  = 1.0;
      m_pfA18Score[a]  = 1.0;
      m_pfB18Score[a]  = 1.0;
      m_pfX17Score[a]  = 1.0;
      m_pfY17Score[a]  = 1.0;
      m_pfA17Score[a]  = 1.0;
      m_pfB17Score[a]  = 1.0;
      m_piAaDepth[a]   = 10;
      m_piCtMod[a]     = 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_dHydrogen = 1.007825035;
  m_dWater    = m_calc.calcMass("H2O");
  m_dAmmonia  = m_calc.calcMass("NH3");
  m_dA        = -m_calc.calcMass("CO");
  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;
  m_bPrompt           = false;
  m_bPhosphoSerine    = false;
  m_bPhosphoThreonine = false;
  m_iSTYlimit         = 10;
  m_bForcedMods       = false;
}
/*
 * clean up the arrays created using the new operator
 */

msequtilities::~msequtilities(void)
{
  if(m_piAaDepth != NULL)
    {
      delete m_piAaDepth;
    }
  if(m_piCtMod != NULL)
    {
      delete m_piCtMod;
    }
  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_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_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;
}

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 = 0;
  while(tStart < 'z' + 1)
    {
      m_pdAaMod[tStart]    = 0.0;
      m_pdAaPrompt[tStart] = 0.0;
      m_piAaDepth[tStart]  = 10;
      m_piCtMod[tStart]    = 0;
      tStart++;
    }
  m_pdAaMod['['] = 0.0;
  m_pdAaMod[']'] = 0.0;
  if(m_bPotentialMotif)
    {
      return false;
    }
  m_bPotential = false;
  if(_s.empty())
    return false;
  m_bForcedMods = false;
  if(_s.find("-1@B") != _s.npos)
    {
      m_bForcedMods = true;
    }
  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';
  double fSum       = 0.0;
  char cValue[128];
  bool bIsCt = false;
  while(fValue != 0.0)
    {
      m_bPotential = true;
      bIsCt        = false;
      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];
      int iDepth = 10;
      if(cRes >= '0' && cRes <= '9')
        {
          size_t tIndex = 0;
          while(_s[tAt] >= '0' && _s[tAt] <= '9' && tIndex < 127)
            {
              cValue[tIndex] = _s[tAt];
              tIndex++;
              tAt++;
            }
          cValue[tIndex] = '\0';
          iDepth         = atoi(cValue);
          cRes           = _s[tAt];
        }
      if(cRes == ']')
        {
          if(isalpha(_s[tAt + 1]))
            {
              tAt++;
              cRes  = _s[tAt];
              bIsCt = true;
            }
          else
            {
              bIsCt = false;
            }
        }
      if(cRes >= 'A' && cRes <= 'Z')
        {
          cRes += 32;
        }
      if(iDepth)
        {
          m_pdAaMod[cRes]    = fValue;
          m_pdAaPrompt[cRes] = fPrompt;
          m_piAaDepth[cRes]  = iDepth;
        }
      if(bIsCt)
        {
          m_piCtMod[cRes] = 1;
        }
      else
        {
          m_piCtMod[cRes] = 0;
        }
      fSum += fPrompt;
      tStart = _s.find(',', tAt);
      if(tStart == _s.npos)
        break;
      tStart++;
      strValue = _s.substr(tStart, _s.size() - tStart);
      fValue   = atof(strValue.c_str());
    }
  if(fPrompt == 0.0)
    {
      m_bPrompt = false;
    }
  else
    {
      m_bPrompt = true;
    }
  m_bPhosphoThreonine = false;
  m_bPhosphoSerine    = false;
  m_bPhosphoTyrosine  = false;
  m_iSTYlimit         = 10;
  if(m_pdAaMod['n'] < 1.01 && m_piAaDepth['n'] == 10)
    {
      m_piAaDepth['n'] = 1;
    }
  if(m_pdAaMod['q'] < 1.01 && m_piAaDepth['q'] == 10)
    {
      m_piAaDepth['q'] = 1;
    }
  if(fabs(m_pdAaMod['t'] - 79.966331) < 0.1)
    {
      m_iSTYlimit         = 3;
      m_bPhosphoThreonine = true;
    }
  m_bPhosphoSerine = false;
  if(fabs(m_pdAaMod['s'] - 79.966331) < 0.1)
    {
      m_bPhosphoSerine = true;
      m_iSTYlimit      = 3;
    }
  m_bPhosphoTyrosine = false;
  if(fabs(m_pdAaMod['y'] - 79.966331) < 0.1)
    {
      m_bPhosphoTyrosine = true;
      m_iSTYlimit        = 3;
    }
  return true;
}

bool
msequtilities::modify_annotation(string &_s)
{
  string strValue = _s;
  if(!_s.empty() && *strValue.rbegin() != ',')
    {
      strValue += ",";
    }
  m_bForcedMods = false;
  if(strValue.find("-1@B") != strValue.npos)
    {
      m_bForcedMods = true;
    }
  strValue += m_strDefaultMaybe;
  if(strValue.empty())
    {
      return false;
    }
  size_t tStart     = 0;
  bool bIsCt        = false;
  const size_t tEnd = 'z' + 1;
  while(tStart < tEnd)
    {
      m_pdAaMod[tStart]    = 0.0;
      m_pdAaPrompt[tStart] = 0.0;
      m_piAaDepth[tStart]  = 10;
      m_piCtMod[tStart]    = 0;
      tStart++;
    }
  if(m_bPotentialMotif)
    {
      return false;
    }
  m_bPotential   = false;
  tStart         = 0;
  size_t tAt     = 0;
  size_t tColon  = 0;
  double fValue  = 0.0;
  double fPrompt = 0.0;
  string strV    = strValue;
  fValue         = atof(strV.c_str());
  char cRes      = '\0';
  char cValue[128];
  while(fValue != 0.0)
    {
      m_bPotential = true;
      tAt          = strV.find('@', tStart);
      bIsCt        = false;
      if(tAt == strV.npos)
        break;
      tColon  = strV.find(':', tStart);
      fPrompt = 0.0;
      if(tColon != strV.npos && tColon < tAt)
        {
          fPrompt = atof(strV.substr(tColon + 1, tAt - tColon).c_str());
        }
      tAt++;
      cRes       = strV[tAt];
      int iDepth = 10;
      if(cRes >= '0' && cRes <= '9')
        {
          size_t tIndex = 0;
          while(strV[tAt] >= '0' && strV[tAt] <= '9' && tIndex < 127)
            {
              cValue[tIndex] = strV[tAt];
              tIndex++;
              tAt++;
            }
          cValue[tIndex] = '\0';
          iDepth         = atoi(cValue);
          cRes           = strV[tAt];
        }
      if(cRes == ']')
        {
          if(isalpha(strV[tAt + 1]))
            {
              tAt++;
              cRes  = strV[tAt];
              bIsCt = true;
            }
          else
            {
              bIsCt = false;
            }
        }
      if(cRes >= 'A' && cRes <= 'Z')
        {
          cRes += 32;
        }
      if(iDepth)
        {
          m_pdAaMod[cRes]    = fValue;
          m_pdAaPrompt[cRes] = fPrompt;
          m_piAaDepth[cRes]  = iDepth;
        }
      if(bIsCt)
        {
          m_piCtMod[cRes] = 1;
        }
      else
        {
          m_piCtMod[cRes] = 0;
        }
      tStart = strV.find(',', tAt);
      if(tStart == strV.npos)
        break;
      tStart++;
      strValue = strV.substr(tStart, strV.size() - tStart);
      fValue   = atof(strValue.c_str());
    }
  m_bPhosphoThreonine = false;
  m_bPhosphoSerine    = false;
  m_bPhosphoTyrosine  = false;
  m_iSTYlimit         = 10;
  if(m_pdAaMod['n'] < 1.01 && m_piAaDepth['n'] == 10)
    {
      m_piAaDepth['n'] = 1;
    }
  if(m_pdAaMod['q'] < 1.01 && m_piAaDepth['q'] == 10)
    {
      m_piAaDepth['q'] = 1;
    }
  if(fabs(m_pdAaMod['t'] - 79.966331) < 0.1)
    {
      m_iSTYlimit         = 3;
      m_bPhosphoThreonine = true;
    }
  m_bPhosphoSerine = false;
  if(fabs(m_pdAaMod['s'] - 79.966331) < 0.1)
    {
      m_bPhosphoSerine = true;
      m_iSTYlimit      = 3;
    }
  m_bPhosphoTyrosine = false;
  if(fabs(m_pdAaMod['y'] - 79.966331) < 0.1)
    {
      m_bPhosphoTyrosine = true;
      m_iSTYlimit        = 3;
    }
  return true;
}


bool
msequtilities::motif_set(const msequence &_s)
{
  m_mapMotifs.clear();
  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;
    }
  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;
              if(*pValue == 'G')
                {
                  cout << *pValue << "\n";
                  cout.flush();
                }
            }
          a++;
        }
      pValue++;
    }
  delete pString;
  if(m_mapMotifs.size())
    {
      return true;
    }
  return false;
}

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;
  size_t tComma = 0;
  float fValue;
  string strValue = _s.substr(tStart, _s.size() - tStart);
  fValue          = (float)atof(strValue.c_str());
  char *pOut      = new char[1024];
  while(fValue != 0.0)
    {
      tAt = _s.find('@', tStart);
      if(tAt == _s.npos)
        break;
      tComma = _s.find(',', tAt);
      if(tComma == _s.npos)
        {
          strValue = _s.substr(tStart, tComma - tStart);
          strcpy(pOut, strValue.c_str());
          mmotif motValue;
          motValue.initialize();
          if(motValue.set(pOut))
            {
              m_vMotifs.push_back(motValue);
            }
          break;
        }
      else
        {
          strValue = _s.substr(tStart, tComma - tStart);
          strcpy(pOut, strValue.c_str());
          mmotif motValue;
          motValue.initialize();
          if(motValue.set(pOut))
            {
              m_vMotifs.push_back(motValue);
            }
        }
      tStart   = tComma + 1;
      strValue = _s.substr(tStart, _s.size() - tStart);
      fValue   = (float)atof(strValue.c_str());
    }
  if(!m_vMotifs.empty())
    {
      m_bPotential      = true;
      m_bPotentialMotif = true;
      tStart            = 0;
      while(tStart < 'z' + 1)
        {
          m_pdAaMod[tStart]    = 0.0;
          m_pdAaPrompt[tStart] = 0.0;
          m_piAaDepth[tStart]  = 10;
          m_piCtMod[tStart]    = 0;
          tStart++;
        }
      m_pdAaMod['['] = 0.0;
      m_pdAaMod[']'] = 0.0;
    }
  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"); // This value is not used: see Note 1 at
                                     // the end of this method
      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("C12H21N3O3"); // pyrolysine
      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'] =
        m_calc.calcMass("C3H5ONSe"); // selenocysteine
      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'] =
        0.0; // X is interpreted as an internal cleavage site/stop codon. It is
             // the equivalent of "*".
      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"); // This value is not used: see Note 1 at
                                     // the end of this method.
      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; // This value is not used: see Note 1 at the end of this
                  // method.
      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'] = 237.31; // pyrolysine
      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'] = 103.1388 - 32.066 + 78.96; // selenocysteine
      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'] =
        0.0; // X is interpreted as an internal cleavage site/stop codon. It is
             // the equivalent of "*".
      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; // This value is not used: see Note 1 at the end of this
                  // method
      pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
    }
  /*
    Note 1: the single letter codes B and Z, which are ambiguity codes for D/N
    and E/Q respectively, are not used. When the amino acid sequence is read,
    any B or Z is replaced so that B => N and Z => Q. It is assumed that
    whenever this assignment is incorrect, the correct sequece will be caught by
    checking for deamidation in the normal course of the search, i.e., N => D
    and Q => E.
  */
  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;
}

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;
}
