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mscore_hrk.cpp
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mscore_hrk.cpp
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/*
* Portions are Copyright (c) 2003-2006 Fred Hutchinson Cancer Research Center
* Additional code Copyright (c) 2010-2011 Institute for Systems Biology
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#include "stdafx.h"
#include "msequence.h"
#include "mspectrum.h"
#include "msequtilities.h"
#include "xmlparameter.h"
#include "mscore_hrk.h"
// Factory instance, registers itself with the mscoremanager.
static mscorefactory_hrk factory;
mscorefactory_hrk::mscorefactory_hrk()
{
mscoremanager::register_factory("hrk-score", this);
}
mplugin* mscorefactory_hrk::create_plugin()
{
return new mscore_hrk();
}
mscore_hrk::mscore_hrk(void)
{
m_dScale = 0.05;
m_maxEnd = 0;
m_dIsotopeCorrection = 1.0;
}
mscore_hrk::~mscore_hrk(void)
{
}
bool mscore_hrk::clear()
{
m_vmiType.clear();
return true;
}
/*
* allows score object to issue warnings, or set variable based on xml.
*/
bool mscore_hrk::load_param(XmlParameter &_x)
{
if (!mscore::load_param(_x))
return false;
if (m_pSeqUtilFrag == &m_seqUtil)
m_dIsotopeCorrection = 1.0005; /* monoisotopic */
else
m_dIsotopeCorrection = 1.0011; /* average */
string strValue;
string strKey = "k-score, histogram scale";
if(_x.get(strKey,strValue)) {
m_dScale = atof(strValue.c_str());
}
return true;
}
/*
* called before spectrum conditioning to allow the score object to
* modify the spectrum in ways specific to the scoring algorithm.
* default implementation does nothing.
*/
bool mscore_hrk::precondition(mspectrum &_s)
{
if (_s.m_vMI.size() == 0)
return false;
if (!mscore::precondition(_s))
return false;
return true;
}
/*
* called before scoring inside the score() function to allow any
* necessary resetting of member variables.
*/
void mscore_hrk::prescore(const size_t _i)
{
mscore::prescore(_i);
// Initialize of clear the used intensity look-up.
if (m_miUsed.m_pfI == NULL)
m_miUsed.init(0, m_maxEnd);
else
m_miUsed.clear();
}
/*
* mconvert converts from mass and charge to integer ion value
* for mi vector.
*/
unsigned long mscore_hrk::mconvert(double _m, const long _c)
{
const double fZ = (double)_c;
double dMass = (fZ*m_pSeqUtilFrag->m_dProton + _m)/fZ;
return imass(dMass);
}
/*
* sfactor returns a factor applied to the final convolution score.
*/
double mscore_hrk::sfactor()
{
/*
* Multiply by log(length) to remove length dependence on dot product score
* Divide by 3.0 to scale score to 1000
*/
double dFactor = log((double)m_lSeqLength)*1.0 /
(3.0*sqrt((double)m_lSeqLength)); /* change iLenPeptide to tot # of fragment ions? */
dFactor *= 1000.0;
return dFactor;
}
/*
* report_score formats a hyper score for output.
*/
void mscore_hrk::report_score(char* buffer, float hyperscore)
{
sprintf(buffer, "%d",(int) (hyperscore + 0.5));
}
/*
* add_mi does the work necessary to set up an mspectrum object for modeling.
* - an entry in the m_State object is made for the parent ion M+H
* once an mspectrum has been added, the original mspectrum is no longer
* needed for modeling, as all of the work associated with a spectrum
* is only done once, prior to modeling sequences.
*/
bool mscore_hrk::add_mi(mspectrum &_s)
{
if (!mscore::add_mi(_s))
return false;
//MH - intercept function for high res data
if(m_lErrorType & mscore::T_FRAGMENT_PPM){
return add_mi_hr(_s);
} else if ( (m_lErrorType & mscore::T_FRAGMENT_DALTONS) && m_fErr<1.0){
//Must request smaller than 1 dalton bin to use high-res
return add_mi_hr(_s);
}
vmiType vType;
if (_s.m_vMI.size() == 0)
{
// Return value appears to be ignored, so just add empty type.
m_vmiType.push_back(vType);
return true;
}
int iWindowCount = 10;
float fMaxI = 0;
float fTotI = 0;
miLookup tempLookup;
vector<mi>::iterator itMI = _s.m_vMI.begin();
vector<mi>::iterator itEnd = _s.m_vMI.end();
int startMass = imass(itMI->m_fM);
int endMass = imass(itEnd[-1].m_fM);
// Screen peeks on upper end.
int endMassMax = (int)(((_s.m_dMH + (_s.m_fZ - 1) * m_seqUtil.m_dProton) / _s.m_fZ) * 2.0 + 0.5) + iWindowCount;
while (itMI != itEnd && endMass >= endMassMax) {
itEnd--;
endMass = imass(itEnd[-1].m_fM);
}
if (itMI == itEnd) // No peaks left.
{
// Return value appears to be ignored, so just add empty type.
m_vmiType.push_back(vType);
return true;
}
tempLookup.init(max(0, startMass - 50), endMass + 50);
if (tempLookup.m_end > m_maxEnd)
m_maxEnd = tempLookup.m_end;
int peakCount = 0;
while (itMI != itEnd) {
int iM = imass(itMI->m_fM);
float fI = sqrt(itMI->m_fI);
fTotI += fI;
if (fMaxI < fI)
fMaxI = fI;
if (tempLookup[iM] < fI)
{
if (tempLookup[iM] == 0.0)
peakCount++;
tempLookup[iM] = fI;
}
itMI++;
}
float fMinCutoff = (float) (0.05 * fMaxI);
int range = (int) min(endMassMax, iWindowCount + endMass) - startMass;
if (range > 3000)
iWindowCount=10;
else if (range > 2500)
iWindowCount=9;
else if (range > 2000)
iWindowCount=8;
else if (range > 1500)
iWindowCount=7;
else if (range > 1000)
iWindowCount=6;
else
iWindowCount=5;
int iWindowSize = range / iWindowCount;
/*
* Process input spectrum for dot product - split windows
*/
for (int i = 0; i < iWindowCount; i++) {
float fMaxWindowI = 0.0;
int iStart = startMass + i*iWindowSize;
/*
* Get maximum intensity within window
*/
for (int ii = iStart; ii < iStart + iWindowSize; ii++) {
float fI = tempLookup[ii];
if (fI > fMaxWindowI)
fMaxWindowI = fI;
}
if (fMaxWindowI > 0.0 && fMaxWindowI > fMinCutoff) {
double dFactor= 1.0 / fMaxWindowI;
/*
* Normalize within window
*/
for (int ii = iStart; ii < iStart + iWindowSize; ii++) {
double dI = tempLookup.get(ii);
tempLookup[ii] = (float) (dI * fMaxI * dFactor);
}
}
}
/*
* Reduce intensity and make unit vector by dividing
* every point by sqrt(sum(x^2))
*/
double dSpectrumArea = 0.0;
for (int i = startMass; i <= endMass; i++) {
double d = tempLookup.get(i);
if (d > 0.0)
dSpectrumArea += d * d;
}
dSpectrumArea = sqrt(dSpectrumArea);
for (int i = startMass; i <= endMass; i++) {
float f = tempLookup.get(i);
if (f > 0.0)
tempLookup[i] = (float) (f / dSpectrumArea);
}
/*
* Perform mix-range modification to input spectrum
*/
miLookup tempRangeLookup;
tempRangeLookup.init(tempLookup.m_start, tempLookup.m_end);
for (int i = tempLookup.m_start; i < tempLookup.m_end; i++) {
double sum = 0.0;
for (int ii = i - 50 ; ii <= i + 50 ; ii++)
sum += tempLookup.get(ii);
tempRangeLookup[i] = (float) (sum / 101.0);
}
MIType uType;
for (int i = tempLookup.m_start; i < tempLookup.m_end; i++) {
tempLookup[i] -= tempRangeLookup[i];
if (tempLookup[i] > 0) {
uType.m_lM = i;
uType.m_fI = tempLookup[i];
vType.push_back(uType);
}
}
m_vmiType.push_back(vType);
return true;
}
/*
* dot is the fundamental logic for scoring a peptide with a mass spectrum.
* the mass spectrum is determined by the value of m_lId, which is its index
* number in the m_vsmapMI vector. the sequence is represented by the values
* that are currently held in m_plSeq (integer masses).
*/
double mscore_hrk::dot(unsigned long *_v)
{
//MH - intercept function for high res data
if(m_lErrorType & mscore::T_FRAGMENT_PPM){
return (dot_hr(_v));
} else if ( (m_lErrorType & mscore::T_FRAGMENT_DALTONS) && m_fErr<1.0){
//Must request smaller than 1 dalton bin to use high-res
return (dot_hr(_v));
}
unsigned long lCount = 0;
double dScore = 0.0;
float fTmp;
vector<MIType>::iterator itType = m_vmiType[m_lId].begin();
vector<MIType>::const_iterator itEnd = m_vmiType[m_lId].end();
vector<MIType>::const_iterator itBegin = itType;
vector<MIType>::iterator itGreater;
for (int a = 0; m_plSeq[a] != 0; a++) {
int iIon = (int) m_plSeq[a];
// Search for first peak in spectrum greater than or equal
// that in current sequence. Because there are usually a
// lot more spectrum peaks than sequence peaks, jumping ahead
// has significant performance benefits.
const int step = 5;
while (step < itEnd - itType && itType[step].m_lM < m_plSeq[a]) {
itType += step;
}
while(itType != itEnd && itType->m_lM < m_plSeq[a]) {
itType++;
}
itGreater = itType;
if (itType != itEnd && iIon == itType->m_lM) {
fTmp = itType->m_fI;
if (m_miUsed.get(iIon) < fTmp) {
dScore += fTmp - m_miUsed.get(iIon);
m_miUsed[iIon] = fTmp;
lCount++;
}
itGreater = itType + 1;
}
if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
fTmp = ((float)0.5)*itType[-1].m_fI;
if (m_miUsed.get(iIon-1) < fTmp) {
dScore += fTmp - m_miUsed.get(iIon-1);
m_miUsed[iIon-1] = fTmp;
}
}
if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
fTmp = ((float)0.5)*itGreater->m_fI;
if (m_miUsed.get(iIon+1) < fTmp) {
dScore += fTmp - m_miUsed.get(iIon+1);
m_miUsed[iIon+1] = fTmp;
}
}
}
*_v = lCount;
return (dScore);
}
/* MH
* add_mi_hr is similar to add_mi for seting up an mspectrum object for modeling.
* It is designed for hi res data, and does not use integer binning. A paired
* dot_hr function has been created to perform dot products from these models.
* - an entry in the m_State object is made for the parent ion M+H
* once an mspectrum has been added, the original mspectrum is no longer
* needed for modeling, as all of the work associated with a spectrum
* is only done once, prior to modeling sequences.
*/
bool mscore_hrk::add_mi_hr(mspectrum &_s)
{
vmiType vType;
if (_s.m_vMI.size() == 0)
{
// Return value appears to be ignored, so just add empty type.
m_vmiType.push_back(vType);
return true;
}
int iWindowCount = 10;
int iMaxI = 0;
int iTotI = 0;
MIType uType;
vector<MIType> tempLookup;
vector<mi>::iterator itMI = _s.m_vMI.begin();
vector<mi>::iterator itEnd = _s.m_vMI.end();
int startMass = imass(itMI->m_fM);
int endMass = imass(itEnd[-1].m_fM);
// Screen peeks on upper end.
int endMassMax = (int)(((_s.m_dMH + (_s.m_fZ - 1) * m_seqUtil.m_dProton) / _s.m_fZ) * 2.0 + 0.5) + iWindowCount;
while (itMI != itEnd && endMass >= endMassMax) {
itEnd--;
endMass = imass(itEnd[-1].m_fM);
}
if (itMI == itEnd) // No peaks left.
{
// Return value appears to be ignored, so just add empty type.
m_vmiType.push_back(vType);
return true;
}
int peakCount = 0;
while (itMI != itEnd) {
//note that these are reversed. Intensity is stored as an integer
//because it can be inaccurate. Mass is stored as a float for
//accuracy.
uType.m_lM = (int)(sqrt(itMI->m_fI)+0.5);
uType.m_fI = itMI->m_fM;
tempLookup.push_back(uType);
if(iMaxI < (int)uType.m_lM) iMaxI = (int)uType.m_lM;
itMI++;
}
float fMinCutoff = 0.05f * (float)iMaxI;
int range = (int) min(endMassMax, iWindowCount + endMass) - startMass;
if (range > 3000)
iWindowCount=10;
else if (range > 2500)
iWindowCount=9;
else if (range > 2000)
iWindowCount=8;
else if (range > 1500)
iWindowCount=7;
else if (range > 1000)
iWindowCount=6;
else
iWindowCount=5;
int iWindowSize = range / iWindowCount;
/*
* Process input spectrum for dot product - split windows
*/
int i=0;
int ii;
int iStart=0;
while(iStart<(int)tempLookup.size()){
float fMaxWindowI = 0.0;
float fWindowEnd = (float)startMass+i*iWindowSize;
for(ii=iStart; ii<(int)tempLookup.size() && tempLookup[ii].m_fI<fWindowEnd; ii++){
float fI = (float)tempLookup[ii].m_lM;
if (fI > fMaxWindowI) fMaxWindowI = fI;
}
if (fMaxWindowI > 0.0 && fMaxWindowI > fMinCutoff) {
//Normalize within window
for (ii = iStart; ii<(int)tempLookup.size() && tempLookup[ii].m_fI<fWindowEnd; ii++) {
double dI = (double)tempLookup[ii].m_lM;
tempLookup[ii].m_lM = (int) (dI * iMaxI / fMaxWindowI);
}
}
iStart=ii;
i++;
}
/*
* Reduce intensity and make unit vector by dividing
* every point by sqrt(sum(x^2))
*/
double dSpectrumArea = 0.0;
for (i = 0; i < (int)tempLookup.size(); i++) {
double d = (double) tempLookup[i].m_lM;
if (d > 0.0) dSpectrumArea += d * d;
}
dSpectrumArea = sqrt(dSpectrumArea);
for (i = 0; i < (int)tempLookup.size(); i++) {
float f = (float)tempLookup[i].m_lM*1000.0f;
if (f > 0.0) tempLookup[i].m_lM = (int) (f / dSpectrumArea);
}
/*
* Perform mix-range modification to input spectrum
*/
vector<int> tempRangeLookup;
for (i = 0; i < (int)tempLookup.size(); i++) {
double sum = 0;
for (int ii = 0; tempLookup[ii].m_fI <= tempLookup[i].m_fI+50.0 ; ii++){
if(tempLookup[ii].m_fI < tempLookup[i].m_fI-50.0) continue;
sum += (double)tempLookup[ii].m_lM;
if(ii==tempLookup.size()-1) break;
}
tempRangeLookup.push_back((int)(sum / 101.0));
}
for (i = 0; i < (int)tempLookup.size(); i++) {
if( (int)tempLookup[i].m_lM > tempRangeLookup[i]) {
tempLookup[i].m_lM -= tempRangeLookup[i];
uType.m_lM = tempLookup[i].m_lM;
uType.m_fI = tempLookup[i].m_fI;
vType.push_back(uType);
}
if(i+1>m_maxEnd) m_maxEnd=i+1;
}
m_vmiType.push_back(vType);
return true;
}
/* MH:
* dot_hr is the same as dot, but modified for sparse arrays and high mass accuracy.
* the mass spectrum is determined by the value of m_lId, which is its index
* number in the m_vsmapMI vector. the sequence is represented by the values
* that are currently held in m_pfSeq (float masses).
*/
double mscore_hrk::dot_hr(unsigned long *_v)
{
unsigned long lCount = 0;
double dScore = 0.0;
int iTmp;
float fPpm;
float fPpmUser;
float fPpmUser2x;
//Treat tolerances different depending on PPM or Daltons
if(m_lErrorType & T_FRAGMENT_PPM) fPpmUser = (float)(m_fErr*1e6/200.0); //convert back to true ppm parameter
else fPpmUser = m_fErr;
//Check out twice as far for half the score - this is equivalent to checking the next bin
fPpmUser2x = (float)(fPpmUser*2.0);
int i=1;
int iBin;
//perform a single pass through each array.
//check every point in m_pfSeq, but don't revisit positions in m_vmiType
for (int a = 0; m_pfSeq[a] != 0; a++) {
float fIon = (float) m_pfSeq[a];
while(fIon > m_vmiType[m_lId][i].m_fI){
i++;
if(i==m_vmiType[m_lId].size()){
i--;
break;
}
}
if(fIon > m_vmiType[m_lId][i].m_fI+1.0) break;
//Use different calculation based on unit type
if( (m_vmiType[m_lId][i].m_fI-fIon) < (fIon-m_vmiType[m_lId][i-1].m_fI) ){
if(m_lErrorType & T_FRAGMENT_PPM) fPpm = (float)(-(fIon-m_vmiType[m_lId][i].m_fI)/m_vmiType[m_lId][i].m_fI*1e6);
else fPpm = m_vmiType[m_lId][i].m_fI - fIon;
iBin=i;
} else {
if(m_lErrorType & T_FRAGMENT_PPM) fPpm = (float)((fIon-m_vmiType[m_lId][i-1].m_fI)/m_vmiType[m_lId][i-1].m_fI*1e6);
else fPpm = fIon - m_vmiType[m_lId][i-1].m_fI;
iBin=i-1;
}
//Check within tolerance
if(fPpm<fPpmUser){
iTmp = m_vmiType[m_lId][iBin].m_lM;
if ((int)m_miUsed.get(iBin) < iTmp) {
dScore += (double)(iTmp - (int)m_miUsed.get(iBin));
m_miUsed[iBin] = (float)iTmp;
lCount++;
}
continue;
}
//Check at twice the tolerance
if(fPpm<fPpmUser2x){
iTmp = m_vmiType[m_lId][iBin].m_lM / 2;
if ((int)m_miUsed.get(iBin) < iTmp) {
dScore += (double)(iTmp - (int)m_miUsed.get(iBin));
m_miUsed[iBin] = (float)iTmp;
}
}
}
dScore/=1000.0; //this returns dScore to something like its original incarnation.
*_v = lCount;
return (dScore);
}
/*
* MH: The add_N functions are overloaded to support calculation of high res
* mass fragments in the context of the scoring algorithm. m_pfSeq holds
* the accurate mass fragments.
*/
bool mscore_hrk::add_A(const unsigned long _t,const long _c)
{
unsigned long a = 0;
//get the conversion factor between a straight sequence mass and an a-ion
double dValue = m_pSeqUtilFrag->m_dA;
//deal with protein N-terminus
if(m_bIsN) dValue += m_pSeqUtilFrag->m_fNT;
//deal with non-hydrolytic cleavage
dValue += (m_pSeqUtilFrag->m_dCleaveN - m_pSeqUtilFrag->m_dCleaveNdefault);
if(m_Term.m_lN) dValue += m_pSeqUtilFrag->m_pdAaMod['['];
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
unsigned long lValue = 0;
//calculate the conversion factor between an m/z value and its integer value
//as referenced in m_vsmapMI
char cValue = '\0';
float *pfScore = m_pSeqUtilFrag->m_pfAScore;
unsigned long lCount = 0;
//from N- to C-terminus, calcuate fragment ion m/z values and store the results
//look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a < m_lSeqLength) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
//m_pfSeq[lCount] = dValue/(double)_c+m_pSeqUtilFrag->m_dProton;
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
a++;
}
//set the next integer mass value to 0: this marks the end of the array
m_plSeq[lCount] = 0;
m_pfSeq[lCount] = 0.0;
return true;
}
bool mscore_hrk::add_B(const unsigned long _t,const long _c)
{
unsigned long a = 0;
//get the conversion factor between a straight sequence mass and a b-ion
double dValue = m_pSeqUtilFrag->m_dB;
//deal with protein N-terminus
if(m_bIsN) dValue += m_pSeqUtilFrag->m_fNT;
//deal with non-hydrolytic cleavage
dValue += (m_pSeqUtilFrag->m_dCleaveN - m_pSeqUtilFrag->m_dCleaveNdefault);
if(m_Term.m_lN) dValue += m_pSeqUtilFrag->m_pdAaMod['['];
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
unsigned long lValue = 0;
//calculate the conversion factor between an m/z value and its integer value
//as referenced in m_vsmapMI
char cValue = '\0';
long lCount = 0;
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
//from N- to C-terminus, calcuate fragment ion m/z values and store the results
//look up appropriate scores from m_pSeqUtilFrag->m_pfBScore
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a < m_lSeqLength-1) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
a++;
}
m_plSeq[lCount] = 0;
m_pfSeq[lCount] = 0.0;
return true;
}
bool mscore_hrk::add_C(const unsigned long _t,const long _c)
{
unsigned long a = 0;
//get the conversion factor between a straight sequence mass and a b-ion
double dValue = m_pSeqUtilFrag->m_dC;
//deal with protein N-terminus
if(m_bIsN) dValue += m_pSeqUtilFrag->m_fNT;
//deal with non-hydrolytic cleavage
dValue += (m_pSeqUtilFrag->m_dCleaveN - m_pSeqUtilFrag->m_dCleaveNdefault);
if(m_Term.m_lN) dValue += m_pSeqUtilFrag->m_pdAaMod['['];
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
unsigned long lValue = 0;
//calculate the conversion factor between an m/z value and its integer value
//as referenced in m_vsmapMI
char cValue = '\0';
long lCount = 0;
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
//from N- to C-terminus, calcuate fragment ion m/z values and store the results
//look up appropriate scores from m_pSeqUtilFrag->m_pfBScore
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a < m_lSeqLength-2) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
a++;
}
m_plSeq[lCount] = 0;
m_pfSeq[lCount] = 0.0;
return true;
}
bool mscore_hrk::add_X(const unsigned long _t,const long _c)
{
long a = m_lSeqLength - 1;
//get the conversion factor between a straight sequence mass and an x-ion
double dValue = m_pSeqUtilFrag->m_dX;
//deal with non-hydrolytic cleavage
dValue += (m_pSeqUtilFrag->m_dCleaveC - m_pSeqUtilFrag->m_dCleaveCdefault);
if(m_Term.m_lC) dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
//deal with protein C-teminus
if(m_bIsC) dValue += m_pSeqUtilFrag->m_fCT;
unsigned long lValue = 0;
//calculate the conversion factor between an m/z value and its integer value
//as referenced in m_vsmapMI
char cValue = '\0';
unsigned long lCount = 0;
float fSub = 0.0;
float *pfScore = m_pSeqUtilFrag->m_pfXScore;
//from C- to N-terminus, calcuate fragment ion m/z values and store the results
//look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a > 0) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
a--;
}
//set the next integer mass value to 0: this marks the end of the array
m_plSeq[lCount] = 0;
m_pfSeq[lCount] = 0.0;
return true;
}
bool mscore_hrk::add_Y(const unsigned long _t,const long _c)
{
long a = m_lSeqLength - 1;
//get the conversion factor between a straight sequence mass and a y-ion
double dValue = m_pSeqUtilFrag->m_dY;
unsigned long lValue = 0;
//deal with non-hydrolytic cleavage
dValue += (m_pSeqUtilFrag->m_dCleaveC - m_pSeqUtilFrag->m_dCleaveCdefault);
if(m_Term.m_lC) dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
//deal with protein C-teminus
if(m_bIsC) dValue += m_pSeqUtilFrag->m_fCT;
char cValue = '\0';
unsigned long lCount = 0;
float fSub = 0.0;
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
//from C- to N-terminus, calcuate fragment ion m/z values and store the results
//look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a > 0) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
if(_t == 0) {
if(a < 5) {
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
}
} else {
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
}
a--;
}
//set the next integer mass value to 0: this marks the end of the array
m_plSeq[lCount] = 0;
m_pfSeq[lCount] = 0.0;
return true;
}
bool mscore_hrk::add_Z(const unsigned long _t,const long _c)
{
long a = m_lSeqLength - 1;
//get the conversion factor between a straight sequence mass and a y-ion
double dValue = m_pSeqUtilFrag->m_dZ;
unsigned long lValue = 0;
//deal with non-hydrolytic cleavage
dValue += (m_pSeqUtilFrag->m_dCleaveC - m_pSeqUtilFrag->m_dCleaveCdefault);
if(m_Term.m_lC) dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
//deal with protein C-teminus
if(m_bIsC) dValue += m_pSeqUtilFrag->m_fCT;
char cValue = '\0';
unsigned long lCount = 0;
float fSub = 0.0;
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
//from C- to N-terminus, calcuate fragment ion m/z values and store the results
//look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a > 0) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
//MH: tandem uses m_pfSeq differently than K-score.
m_pfSeq[lCount] = (float)((dValue+_c*m_pSeqUtilFrag->m_dProton)/(double)_c);
lCount++;
a--;
}
//set the next integer mass value to 0: this marks the end of the array
m_plSeq[lCount] = 0;
m_pfSeq[lCount] = 0;
return true;
}