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CHardklor2.cpp
1523 lines (1272 loc) · 40.8 KB
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CHardklor2.cpp
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/*
Copyright 2007-2016, Michael R. Hoopmann, Institute for Systems Biology
Michael J. MacCoss, University of Washington
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 "CHardklor2.h"
using namespace std;
using namespace MSToolkit;
CHardklor2::CHardklor2(CAveragine *a, CMercury8 *m, CModelLibrary *lib){
averagine=a;
mercury=m;
models=lib;
bEcho=true;
bMem=false;
PT=NULL;
}
CHardklor2::~CHardklor2(){
averagine=NULL;
mercury=NULL;
models=NULL;
if(PT!=NULL) {
PT=NULL;
}
}
hkMem& CHardklor2::operator[](const int& index){
return vResults[index];
}
void CHardklor2::Echo(bool b){
bEcho=b;
}
int CHardklor2::GoHardklor(CHardklorSetting sett, Spectrum* s){
//Member variables
MSReader r;
Spectrum curSpec,c;
vector<int> v;
FILE* fout=NULL;
int TotalScans;
int manyPep, zeroPep, lowSigPep;
int iPercent;
int minutes, seconds;
int i;
vector<pepHit> vPeps;
//initialize variables
cs=sett;
loadTime=0;
analysisTime=0;
TotalScans=0;
manyPep=0;
zeroPep=0;
lowSigPep=0;
iPercent=0;
getTimerFrequency(timerFrequency);
vResults.clear();
//For noise reduction
CNoiseReduction nr(&r,cs);
//Signature
//if(bEcho) cout << "\n\nHardklor, v2.06, Mike Hoopmann, Mike MacCoss\nCopyright 2007-2012\nUniversity of Washington\n" << endl;
//Set the periodic table
if(PT==NULL) PT=averagine->getPT();
//Ouput file info to user
if(bEcho){
if(s==NULL) cout << "Reading from file: " << cs.inFile << endl;
if(!bMem) cout << "Writing to file: " << cs.outFile << endl;
}
if(cs.fileFormat==dunno) {
cout << "Unknown file format or bad extension." << endl;
return -1;
}
if (!bMem) fout = fopen(cs.outFile, "wt");
//read a spectrum
getExactTime(startTime);
//Read in the initial spectrum
r.setFilter(cs.mzXMLFilter);
r.setRawFilter(cs.rawFilter);
if(s!=NULL){
curSpec=*s;
} else {
if(cs.boxcar==0){
if (cs.scan.iLower > 0) {
int scn = cs.scan.iLower;
r.readFile(&cs.inFile[0], curSpec, scn);
while (curSpec.getScanNumber() == 0) {
scn++;
if (cs.scan.iUpper > 0) {
if (scn > cs.scan.iUpper) break;
} else {
if (scn > r.getLastScan()) break;
}
r.readFile(NULL, curSpec, scn);
}
} else r.readFile(&cs.inFile[0], curSpec);
} else {
if(cs.boxcarFilter==0){
if(!nr.DeNoiseD(curSpec)) curSpec.setScanNumber(0);
//if(!nr.DeNoise(curSpec)) curSpec.setScanNumber(0);
//do something about this...
} else {
if(!nr.DeNoiseC(curSpec)) curSpec.setScanNumber(0);
}
}
}
getExactTime(stopTime);
tmpTime1=toMicroSec(stopTime);
tmpTime2=toMicroSec(startTime);
loadTime+=(tmpTime1-tmpTime2);
//Check that file was read
if(curSpec.getScanNumber()==0) {
if(s!=NULL) {
cout << "Spectrum is invalid." << endl;
return -2;
}
if(cs.scan.iLower>0) cout << cs.inFile << " is invalid, or requested scan number is of incorrect format." << endl;
else cout << cs.inFile << " is invalid, or contains no spectrum." << endl;
return -2;
}
//Write scan information to output file.
if(!bMem){
if (cs.reducedOutput) WriteScanLine(curSpec, fout, 2);
else if (cs.xml) WriteScanLine(curSpec, fout, 1);
else WriteScanLine(curSpec, fout, 0);
} else {
currentScanNumber = curSpec.getScanNumber();
}
//Output progress indicator
if(bEcho) cout << iPercent;
//While there is still data to read in the file.
while(true){
getExactTime(startTime);
TotalScans++;
//Smooth if requested
if(cs.smooth>0) SG_Smooth(curSpec,cs.smooth,4);
//Centroid if needed; notice that this copy wastes a bit of time.
//TODO: make this more efficient
if(cs.boxcar==0 && !cs.centroid) Centroid(curSpec,c);
else c=curSpec;
//There is a bug when using noise reduction that results in out of order m/z values
//TODO: fix noise reduction so sorting isn't needed
if(c.size()>0) c.sortMZ();
//Analyze
QuickHardklor(c,vPeps);
//export results
for(i=0;i<(int)vPeps.size();i++){
if(!bMem){
if(cs.reducedOutput) WritePepLine(vPeps[i],c,fout,2);
else if(cs.xml) WritePepLine(vPeps[i],c,fout,1);
else WritePepLine(vPeps[i],c,fout,0);
} else {
ResultToMem(vPeps[i],c);
}
}
//Update progress
if(bEcho){
if (r.getPercent() > iPercent){
if(iPercent<10) cout << "\b";
else cout << "\b\b";
cout.flush();
iPercent=r.getPercent();
cout << iPercent;
cout.flush();
}
}
getExactTime(stopTime);
tmpTime1=toMicroSec(stopTime);
tmpTime2=toMicroSec(startTime);
analysisTime+=tmpTime1-tmpTime2;
if(s!=NULL) break;
//Check if any user limits were made and met
if( (cs.scan.iUpper == cs.scan.iLower) && (cs.scan.iLower != 0) ){
break;
} else if( (cs.scan.iLower < cs.scan.iUpper) && (curSpec.getScanNumber() >= cs.scan.iUpper) ){
break;
}
//Read next spectrum from file.
getExactTime(startTime);
if(cs.boxcar==0) {
r.readFile(NULL,curSpec);
} else {
if(cs.boxcarFilter==0){
//possible to not filter?
nr.DeNoiseD(curSpec);
} else {
//case 5: nr.DeNoise(curSpec); break; //this is for filtering without boxcar
nr.DeNoiseC(curSpec);
}
}
getExactTime(stopTime);
tmpTime1=toMicroSec(stopTime);
tmpTime2=toMicroSec(startTime);
loadTime+=(tmpTime1-tmpTime2);
if(curSpec.getScanNumber()!=0){
//Write scan information to output file.
if(cs.reducedOutput){
WriteScanLine(curSpec,fout,2);
} else if(cs.xml) {
fprintf(fout,"</Spectrum>\n");
WriteScanLine(curSpec,fout,1);
} else {
WriteScanLine(curSpec,fout,0);
}
} else {
break;
}
}
if(!bMem) fclose(fout);
if(bEcho) {
cout << "\n" << endl;
cout << " Total number of scans analyzed: " << TotalScans << endl;
i=(int)timeToSec(loadTime,timerFrequency);
minutes = (int)(i/60);
seconds = i - (60*minutes);
cout << "\nFile access time: " << minutes << " minutes, " << seconds << " seconds." << endl;
i=(int)timeToSec(analysisTime,timerFrequency);
minutes = (int)(i/60);
seconds = i - (60*minutes);
cout << "Analysis Time: " << minutes << " minutes, " << seconds << " seconds." << endl;
if (minutes==0 && seconds==0){
cout << "IMPOSSIBLE!!!" << endl;
} else if(minutes <=2){
cout << "HOLY FRIJOLE!!" << endl;
} else if(minutes<=5) {
cout << "Like lightning!" << endl;
} else if(minutes<=10){
cout << "That's pretty damn fast!" << endl;
} else if(minutes<=20){
cout << "Monkeys calculate faster than that!" << endl;
} else if(minutes<=30){
cout << "You should have taken a lunch break." << endl;
} else if(minutes<=40){
cout << "Oi! Too freakin' slow!!" << endl;
} else {
cout << "You might be able to eek out some better performance by adjusting your parameters." << endl;
}
}
return 1;
}
int CHardklor2::BinarySearch(Spectrum& s, double mz, bool floor){
int mid=s.size()/2;
int upper=s.size();
int lower=0;
if(mz>=s[s.size()-1].mz) return s.size()-1;
if(mz<=s[0].mz) return 0;
while(s[mid].mz!=mz){
if(lower>=upper) break;
if(s[mid].mz>mz){
upper=mid-1;
mid=(lower+upper)/2;
} else {
lower=mid+1;
mid=(lower+upper)/2;
}
}
if(floor && s[mid].mz>mz && mid>0) return mid-1;
else if(!floor && s[mid].mz<mz && mid<s.size()) return mid+1;
else return mid;
}
//Calculates the resolution (FWHM) of a peak
double CHardklor2::CalcFWHM(double mz,double res,int iType){
double deltaM;
switch(iType){
case 0: //Orbitrap
deltaM = mz * sqrt(mz) / (20*res); //sqare root of 400
break;
case 1: //TOF
deltaM = mz / res;
break;
case 2: //QIT
deltaM = res / 5000.0;
break;
case 3: //FTICR
default:
deltaM = mz * mz / (400*res);
break;
}
return deltaM;
}
//First derivative method, returns base peak intensity of the set
void CHardklor2::Centroid(Spectrum& s, Spectrum& out){
int i,j;
float maxIntensity;
int bestPeak;
bool bLastPos;
int nextBest;
double FWHM;
Peak_T centroid;
out.clear();
//Get boundaries of the spectrum. centroids must be within boundaries.
double minMZ, maxMZ;
if(s.size()>0){
minMZ = s[0].mz;
maxMZ = s[s.size()-1].mz;
}
bLastPos=false;
for(i=0;i<s.size()-1;i++){
if(s[i].intensity<s[i+1].intensity) {
bLastPos=true;
continue;
} else {
if(bLastPos){
bLastPos=false;
//find max and add peak
maxIntensity=0;
for(j=i;j<i+1;j++){
if (s[j].intensity>maxIntensity){
maxIntensity=s[j].intensity;
bestPeak = j;
}
}
//Best estimate of Gaussian centroid
//Get 2nd highest point of peak
if(bestPeak==s.size()){
nextBest=bestPeak-1;
} else if(s[bestPeak-1].intensity > s[bestPeak+1].intensity){
nextBest=bestPeak-1;
} else {
nextBest=bestPeak+1;
}
//Get FWHM
FWHM = CalcFWHM(s[bestPeak].mz,cs.res400,cs.msType);
//Calc centroid MZ (in three lines for easy reading)
centroid.mz = (FWHM*FWHM*log(s[bestPeak].intensity/s[nextBest].intensity));
centroid.mz /= (GAUSSCONST*(s[bestPeak].mz-s[nextBest].mz));
centroid.mz += ((s[bestPeak].mz+s[nextBest].mz)/2);
//Calc centroid intensity
centroid.intensity=(float)(s[bestPeak].intensity/exp(-pow((s[bestPeak].mz-centroid.mz)/FWHM,2)*GAUSSCONST));
//some peaks are funny shaped and have bad gaussian fit.
//if error is more than 10%, keep existing intensity
if( fabs((s[bestPeak].intensity - centroid.intensity) / centroid.intensity * 100) > 10 ||
//not a good check for infinity
centroid.intensity>999999999999.9 ||
centroid.intensity < 0 ) {
centroid.intensity=s[bestPeak].intensity;
}
//Centroided peaks must fall within spectrum mass range
if(centroid.mz<minMZ || centroid.mz>maxMZ) {
//do nothing if invalid mz, but perhaps find a better way to handle this one day.
} else {
out.add(centroid);
}
}
}
}
}
//returns whether or not the peak is still valid. true if peak still exists, false if peak was solved already.
bool CHardklor2::CheckForPeak(vector<Result>& vMR, Spectrum& s, int index){
double dif=100.0;
double massDif;
bool match=false;
int mid=s.size()/2;
int upper=s.size();
int lower=0;
double FWHM=CalcFWHM(vMR[index].mass,cs.res400,cs.msType);
if(vMR[index].mass>=s[s.size()-1].mz) {
mid=s.size()-1;
} else if(vMR[index].mass<=s[0].mz) {
mid=0;
} else {
while(s[mid].mz!=vMR[index].mass){
if(lower>=upper) break;
if(s[mid].mz>vMR[index].mass){
upper=mid-1;
mid=(lower+upper)/2;
} else {
lower=mid+1;
mid=(lower+upper)/2;
}
}
}
dif=fabs(s[mid].mz-vMR[index].mass);
if(mid>0){
massDif=fabs(s[mid-1].mz-vMR[index].mass);
if(massDif<dif) {
dif=massDif;
mid--;
}
}
if(mid<s.size()-1){
massDif=fabs(s[mid+1].mz-vMR[index].mass);
if(massDif<dif) {
dif=massDif;
mid++;
}
}
if(dif<FWHM){
if(mask[mid].intensity>0.1) return false;
else return true;
}
return false;
}
int CHardklor2::CompareBPI(const void *p1, const void *p2){
const pepHit d1 = *(pepHit *)p1;
const pepHit d2 = *(pepHit *)p2;
if(d1.basePeakIndex<d2.basePeakIndex) return -1;
else if(d1.basePeakIndex>d2.basePeakIndex) return 1;
else return 0;
}
double CHardklor2::LinReg(vector<float>& mer, vector<float>& obs){
int i,sz;
double sxx=0,syy=0,sxy=0;
//Cosine angle correlation
sxy=0;
sxx=0;
syy=0;
sz=(int)mer.size();
for(i=0;i<sz;i++){
sxy += (mer[i]*obs[i]);
sxx += (mer[i]*mer[i]);
syy += (obs[i]*obs[i]);
}
if(sxx>0 && syy>0 && sxy>0) return sxy/sqrt(sxx*syy);
else return 0;
}
bool CHardklor2::MatchSubSpectrum(Spectrum& s, int peakIndex, pepHit& pep){
int i,k,n;
size_t varCount;
size_t v;
float max=s[peakIndex].intensity;
int maxMercuryIndex[3];
vector<int> charges;
double dif;
vector<float> obs;
vector<float> mer;
vector<int> vMatchIndex;
vector<float> vMatchPeak;
vector<Result> vMR;
Result r;
double corr;
double da;
//keep track of best hits
double bestCorr;
double bestDA;
int bestCharge;
double bestMass;
vector<int> bestMatchIndex;
vector<float> bestMatchPeak;
int matchCount;
int bestMatchCount;
int thisMaxIndex=0;
int bestVariant;
mercuryModel* model=NULL;
double deltaM = CalcFWHM(s[peakIndex].mz,cs.res400,cs.msType);
QuickCharge(s,peakIndex,charges);
bestCorr=0.0;
bestMatchCount=0;
//Mark number of variants to analyze
if(cs.noBase) varCount=cs.variant->size();
else varCount=cs.variant->size()+1;
//iterate through all charge states
for(i=0;i<(int)charges.size();i++){
for(v=0;v<varCount;v++){
//get model from library
dif=0;
model=models->getModel(charges[i],(int)v,s[peakIndex].mz);
for(k=0; k<model->size; k++) {
if(model->peaks[k].intensity>dif){
dif = model->peaks[k].intensity;
maxMercuryIndex[0]=k;
}
}
if(k==0) maxMercuryIndex[1]=-1;
else maxMercuryIndex[1]=maxMercuryIndex[0]-1; //allow right shift
maxMercuryIndex[2]=maxMercuryIndex[0]+1; //allow left shift
//Apply shift and find mz boundaries
n=0;
while(n<3){
if(maxMercuryIndex[n]<0) {
n++;
continue;
}
//Align the mercury distribution (MD) to the observed peak. The MD can shift in
//either direction for one peak to adjust for system noise. The width of the MD
//determines the boundaries for correlation to the observed data.
double lower=5000.0;
double upper=0.0;
double shft = s[peakIndex].mz - model->peaks[maxMercuryIndex[n]].mz;
vMR.clear();
for(k=0; k<model->size; k++) {
r.data=model->peaks[k].intensity;
r.mass=model->peaks[k].mz+shft;
vMR.push_back(r);
if(model->peaks[k].intensity>99.999) thisMaxIndex=(int)vMR.size()-1;
if(r.mass<lower) lower=r.mass;
if(r.mass>upper) upper=r.mass;
}
da=model->area;
//Add a little buffer to the bounds
lower-=0.1;
upper+=0.1;
//Match predictions to the observed peaks and record them in the proper array.
corr=PeakMatcherB(vMR,s,lower,upper,deltaM/2,peakIndex,matchCount,vMatchIndex,vMatchPeak);
//cout << "\tMSS: " << s[peakIndex].mz << " " << s[peakIndex].intensity << "\t" << charges[i] << "\t" << matchCount << "\t" << corr << endl;
if(corr>bestCorr || (corr>cs.corr && corr+0.025*(matchCount-bestMatchCount)>bestCorr) ){
bestMatchIndex=vMatchIndex;
bestMatchPeak=vMatchPeak;
bestMatchCount=matchCount;
bestCorr=corr;
bestMass=model->zeroMass+shft*charges[i];
bestCharge=charges[i];
bestDA=da;
bestVariant=(int)v;
}
n++;
}//while
}//for v (variant)
}//for i (charge)
model=NULL;
//if above threshold, erase peaks.
if(bestCorr>cs.corr){
pep.area=(float)bestDA;
strcpy(pep.averagine,"");
pep.basePeakIndex=0;
pep.charge=bestCharge;
pep.corr=bestCorr;
pep.highMZ=0;
pep.lowMZ=0;
pep.massShift=0;
pep.monoMass=bestMass;
pep.intensity=s[peakIndex].intensity;
pep.variantIndex=bestVariant;
//mark which peaks contributed to this analysis
for(k=0;k<(int)bestMatchIndex.size();k++){
if(bestMatchPeak[k]*max/s[bestMatchIndex[k]].intensity>0.5) s[bestMatchIndex[k]].intensity=-s[bestMatchIndex[k]].intensity;
else s[bestMatchIndex[k]].intensity-=bestMatchPeak[k]*max;
}
return true;
}
return false;
}
double CHardklor2::PeakMatcher(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, int& indexOverlap, vector<int>& vMatchIndex, vector<float>& vMatchIntensity){
vMatchIndex.clear();
vMatchIntensity.clear();
vector<float> obs;
vector<float> mer;
bool match;
bool bMax=false;
double corr=0.0;
double dif;
double massDif;
matchCount=0;
indexOverlap=-1;
int j,k;
for(k=0;k<(int)vMR.size();k++) {
if(vMR[k].data>99.9) bMax=true;
match=false;
dif=deltaM;
//look left
j=matchIndex;
while(j>-1 && s[j].mz>=lower){
massDif=s[j].mz-vMR[k].mass;
if(massDif<-deltaM) break;
if(fabs(massDif)<dif){
dif=fabs(massDif);
match=true;
matchIndex=j;
}
j--;
}
//look right
j=matchIndex+1;
while(j<s.size() && s[j].mz<=upper){
massDif=s[j].mz-vMR[k].mass;
if(massDif>deltaM) break;
if(fabs(massDif)<dif){
dif=fabs(massDif);
match=true;
matchIndex=j;
}
j++;
}
if(!match) {
//if expected peak is significant (above 50 rel abun) and has no match, match it to 0.
if(vMR[k].data>50.0) {
//cout << "xM: " << vMR[k].mass << "\t0" << endl;
mer.push_back((float)vMR[k].data);
obs.push_back(0.0f);
if(bMax) break;
}
} else {
mer.push_back((float)vMR[k].data);
//cout << "xM: " << vMR[k].mass << "\t" << s[matchIndex].mz << endl;
if(mask[matchIndex].intensity>0.1 && vMR[k].data>50) {
if(indexOverlap<0) indexOverlap=matchIndex;
}
if(s[matchIndex].intensity<0.1) {
obs.push_back(0.0f);
} else {
matchCount++;
obs.push_back(s[matchIndex].intensity);
}
vMatchIndex.push_back(matchIndex);
vMatchIntensity.push_back((float)vMR[k].data/100.0f);
}
}
if(matchCount<2) corr=0.0;
else corr=LinReg(mer,obs);
//for(j=0;j<mer.size();j++){
// cout << "M:" << mer[j] << "\t" << "O:" << obs[j] << endl;
//}
//cout << "Corr: " << corr << "(" << matchCount << ")" << endl;
//remove last matched peaks (possibly overlap with other peaks) but only if they are of low abundance.
int tmpCount=matchCount;
while(corr<0.90 && matchCount>2 && mer[mer.size()-1]<50.0){
mer.pop_back();
obs.pop_back();
matchCount--;
double corr2=LinReg(mer,obs);
//cout << "Old corr: " << corr << "(" << matchCount+1 << ")" << " New corr: " << corr2 << endl;
if(corr2>corr) {
corr=corr2;
tmpCount=matchCount;
}
}
matchCount=tmpCount;
return corr;
}
double CHardklor2::PeakMatcherB(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, vector<int>& vMatchIndex, vector<float>& vMatchIntensity){
vMatchIndex.clear();
vMatchIntensity.clear();
vector<float> obs;
vector<float> mer;
bool match;
bool bMax=false;
double corr=0.0;
double dif;
double massDif;
matchCount=0;
int j,k;
for(k=0;k<(int)vMR.size();k++) {
if(vMR[k].data>99.9) bMax=true;
else bMax=false;
match=false;
dif=deltaM;
//look left
j=matchIndex;
while(j>-1 && s[j].mz>=lower){
massDif=s[j].mz-vMR[k].mass;
if(massDif<-deltaM) break;
if(fabs(massDif)<dif){
dif=fabs(massDif);
match=true;
matchIndex=j;
}
j--;
}
//look right
j=matchIndex+1;
while(j<s.size() && s[j].mz<=upper){
massDif=s[j].mz-vMR[k].mass;
if(massDif>deltaM) break;
if(fabs(massDif)<dif){
dif=fabs(massDif);
match=true;
matchIndex=j;
}
j++;
}
if(!match) {
break;
} else {
mer.push_back((float)vMR[k].data);
if(s[matchIndex].intensity<0.1) {
obs.push_back(0.0f);
} else {
matchCount++;
obs.push_back(s[matchIndex].intensity);
}
vMatchIndex.push_back(matchIndex);
vMatchIntensity.push_back((float)vMR[k].data/100.0f);
}
}
if(matchCount<2) corr=0.0;
else corr=LinReg(mer,obs);
int tmpCount=matchCount;
while(corr<0.90 && matchCount>2){
mer.pop_back();
obs.pop_back();
matchCount--;
double corr2=LinReg(mer,obs);
if(corr2>corr) {
corr=corr2;
tmpCount=matchCount;
}
}
matchCount=tmpCount;
return corr;
}
void CHardklor2::QuickCharge(Spectrum& s, int index, vector<int>& v){
int i,j;
double dif;
double rawCh;
double rawChR;
int ch;
int charge[1000];
float minIntensity=s[index].intensity/4;
for(i=cs.minCharge;i<=cs.maxCharge;i++) charge[i]=0;
//check forward
for(j=index+1;j<s.size();j++){
if(s[j].intensity<minIntensity) continue;
dif = s[j].mz - s[index].mz;
if(dif > 1.1) break;
rawCh=1/dif;
ch = (int)(rawCh+0.5);
rawChR=rawCh-(int)rawCh;
if(rawChR>0.2 && rawChR<0.8) continue;
if(ch<cs.minCharge || ch>cs.maxCharge) continue;
charge[ch]=1;
}
//if no forward charge, exit now.
bool bMatch=false;
for(i=cs.minCharge;i<=cs.maxCharge;i++){
if(charge[i]>0) {
bMatch=true;
break;
}
}
if(!bMatch) {
v.clear();
return;
}
//check backward
for(j=index-1;j>=0;j--){
if (s[j].intensity<minIntensity) continue;
dif = s[index].mz - s[j].mz;
if(dif > 1.1) break;
rawCh=1/dif;
ch = (int)(rawCh+0.5);
rawChR=rawCh-(int)rawCh;
if(rawChR>0.2 && rawChR<0.8) continue;
if(ch<cs.minCharge || ch>cs.maxCharge) continue;
charge[ch]=1;
}
v.clear();
for(i=cs.minCharge;i<=cs.maxCharge;i++){
if(charge[i]>0) v.push_back(i);
}
}
void CHardklor2::QuickHardklor(Spectrum& s, vector<pepHit>& vPeps) {
//iterators
int i,j,k,n,m,x;
size_t varCount;
size_t v;
//tracking spectrum peak intensities
float maxHeight=9999999999999.9f;
float max=0.0f;
float lowPoint=9999999999999.9f;
//Mercury storage and variables aligning mercury data (including 1 da shifts)
mercuryModel* model;
vector<Result> vMR;
Result r;
int maxIndex;
int thisMaxIndex;
int maxMercuryIndex[3];
double da;
double lower;
double upper;
double shft;
//peak variables
vector<int> charges;
double deltaM;
double dif;
double corr;
vector<float> obs;
vector<float> mer;
vector<int> vMatchIndex;
vector<float> vMatchPeak;
vector<int> vMatchIndex2;
vector<float> vMatchPeak2;
int matchCount,matchCount2;
int indexOverlap;
double top3[3];
//refinement variables
bool keepPH;
pepHit ph2;
//pepHit bestKeepPH;
int lowIndex;
int highIndex;
bool corr2;
double corr3;
//best hit variables
double bestCorr;
double bestLow;
double bestHigh;
double bestDA;
int bestCharge;
double bestMass;
vector<int> bestMatchIndex;
vector<float> bestMatchPeak;
int bestMatchCount;
pepHit bestPH;
bool bestKeepPH;
int bestOverlap;
int bestLowIndex;
int bestHighIndex;
int bestVariant;
//Results
pepHit ph;
//Spectrum variables
Spectrum origSpec=s;
Spectrum refSpec=s;
Spectrum tmpSpec;
//create mask
mask.clear();
for(i=0;i<s.size();i++) mask.add(s[i].mz,0);
//find lowest intensity;
for(i=0;i<s.size();i++){
//printf("%.6lf\t%.1f\n",s[i].mz, s[i].intensity);
if(s[i].intensity<1) continue; //zero is not allowed as a low point
if(s[i].intensity<lowPoint) lowPoint=s[i].intensity;
}
//clear results vector
vPeps.clear();
//Mark number of variants to analyze
if(cs.noBase) varCount=cs.variant->size();
else varCount=cs.variant->size()+1;
//start the loop through all peaks
while(true){
//Find most intense peak. Note that sorting is not possible because
//peaks change in intensity as they are deconvolved. Also it is advantageous
//to keep peaks in m/z order
max=0.0f;
for(i=0;i<s.size();i++){
if(s[i].intensity<maxHeight && s[i].intensity>max){
max=s[i].intensity;
maxIndex=i;
}
}
//stop searching when we reach lowest original point
//this prevents overfitting with lots of partial noise peaks
if(max<lowPoint) break;