//#ifdef _MSC_VER
//#ifndef MSSINGLESCAN_MAIN
//int mssinglescan_main(int argc, char * argv[] ) {
//#else
//int main(int argc, char *argv[]){
//#endif
//#else
int main(int argc, char *argv[]){
//#endif
//Here are all the variable we are going to need
MSReader r;
Spectrum s;
int j;
if(argc==1){
printf("DESCRIPTION: Reads an MS/MS spectrum from any MSToolkit supported file type and outputs to screen in MS2 format.\n\n");
printf("USAGE: MSSingleScan [scan number] [file]\n");
exit(0);
};
r.readFile(argv[2],s,atoi(argv[1]));
if(s.getScanNumber()==0) exit(-1);
printf("S\t%d\t%d\t%.*f\n",s.getScanNumber(),s.getScanNumber(),2,s.getMZ());
if(s.getRTime()>0) printf("I\tRTime\t%.*f\n",4,s.getRTime());
for(j=0;j<s.sizeZ();j++){
printf("Z\t%d\t%.*f\n",s.atZ(j).z,2,s.atZ(j).mz);
};
for(j=0;j<s.size();j++){
printf("%.4f %.4f\n",s.at(j).mz,s.at(j).intensity);
};
return 0;
};
bool CPeptideDatabase::readMascot(char* mascotFile, char* dataFile){
MSReader r;
MascotParser p;
Spectrum s;
MascotLite m;
int i;
int percent=0;
p.clear();
p.readText(mascotFile);
if(p.isDistiller()){
cout << mascotFile << "\t" << p.size() << " peptides from Distiller, no need for RT lookup." << endl;
} else if(p.hasRTime()){
cout << mascotFile << "\t" << p.size() << " peptides have RT already, no need for lookup." << endl;
} else {
cout << mascotFile << "\tLooking up retention times for " << p.size() << " Mascot peptides..." << endl;
cout << percent;
r.readFile(dataFile,s);
}
for(i=0;i<p.size();i++){
if(p.isDistiller()||p.hasRTime()){
m.rTime=p[i].rTime;
} else {
if( (int)i*100/p.size() > percent){
percent=(int)i*100/p.size();
cout << "\b\b\b" << percent;
}
r.readFile(NULL,s,p[i].scanNum);
if(s.getScanNumber()==0){
cout << "Scan not found. Please check that correct data file is used. Stopping Mascot parsing." << endl;
return false;
}
m.rTime=s.getRTime();
}
m.charge=p[i].charge;
m.fileID=fileID;
m.monoMass=p[i].zeroMass;
m.scanNum=p[i].scanNum;
strcpy(m.peptide,p[i].sequence_Long);
strcpy(m.protein,p[i].gene);
mascot.push_back(m);
}
cout << " Done!" << endl;
fileID++;
return true;
}
//First derivative method taken from CSpecAnalyze, returns base peak intensity of the set
void CNoiseReduction::FirstDerivativePeaks(Spectrum& sp, int winSize){
int i,j;
float maxIntensity;
int bestPeak;
bool bLastPos;
Spectrum gp;
int nextBest;
double FWHM;
Peak_T centroid;
bLastPos=false;
for(i=0;i<sp.size()-winSize;i++){
if(sp.at(i).intensity<sp.at(i+winSize).intensity) {
bLastPos=true;
continue;
} else {
if(bLastPos){
bLastPos=false;
//find max and add peak
maxIntensity=0;
for(j=i;j<i+winSize;j++){
if (sp.at(j).intensity>maxIntensity){
maxIntensity=sp.at(j).intensity;
bestPeak = j;
}
}
//Best estimate of Gaussian centroid
//Get 2nd highest point of peak
if(bestPeak==sp.size()-1){
nextBest=bestPeak-1;
} else if(sp.at(bestPeak-1).intensity > sp.at(bestPeak+1).intensity){
nextBest=bestPeak-1;
} else {
nextBest=bestPeak+1;
}
//Get FWHM
FWHM = calcFWHM(sp.at(bestPeak).mz);
//Calc centroid MZ (in three lines for easy reading)
centroid.mz = pow(FWHM,2)*log(sp.at(bestPeak).intensity/sp.at(nextBest).intensity);
centroid.mz /= GC*(sp.at(bestPeak).mz-sp.at(nextBest).mz);
centroid.mz += (sp.at(bestPeak).mz+sp.at(nextBest).mz)/2;
//Calc centroid intensity
centroid.intensity=(float)(sp.at(bestPeak).intensity/exp(-pow((sp.at(bestPeak).mz-centroid.mz)/FWHM,2)*GC));
//some peaks are funny shaped and have bad gaussian fit.
//if error is more than 10%, keep existing intensity
if( fabs((sp.at(bestPeak).intensity - centroid.intensity) / centroid.intensity * 100) > 10 ||
//not a good check for infinity
centroid.intensity>999999999999.9 ||
centroid.intensity < 0 ) {
centroid.intensity=sp.at(bestPeak).intensity;
}
//Hack until I put in mass ranges
if(centroid.mz<0 || centroid.mz>2000) {
//do nothing if invalid mz
} else {
gp.add(centroid);
}
i+=winSize-1;
}
}
}
int scanNumber=sp.getScanNumber();
int scanNumber2=sp.getScanNumber(false);
float rTime=sp.getRTime();
sp = gp;
sp.setRTime(rTime);
sp.setScanNumber(scanNumber);
sp.setScanNumber(scanNumber2,true);
}
bool CNoiseReduction::ScanAveragePlusDeNoise(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
Spectrum ts;
Spectrum ps;
//MSReader r;
vector<int> v;
vector<int> vPos;
int i;
int j;
int k;
int widthCount=0;
int numScans=1;
int match;
double dif;
double prec;
double dt;
double c;
bool bLeft=true;
int posLeft=ps.getScanNumber()-1;
int posRight=ps.getScanNumber()+1;
int index;
char cFilter1[256];
//char cFilter2[256];
sp.clear();
//if file is not null, create new buffer
if(file!=NULL){
strcpy(lastFile,file);
bs.clear();
if(scanNum>0) r->readFile(file,ts,scanNum);
else r->readFile(file,ts);
if(ts.getScanNumber()==0) return false;
bs.push_back(ts);
ps=bs[0];
c=CParam(ps,3);
posA=0;
} else {
posA++;
//cout << "ER: " << posA << " " << bs.size() << endl;
if(posA>=(int)bs.size()) return false; //end of buffer, no more data
ps=bs[posA];
c=CParam(ps,3);
}
//set our pivot spectrum
//ps=bs[posA];
ps.getRawFilter(cFilter1,256);
//cout << "Averaging: " << ps.getScanNumber() << endl;
posLeft=posA;
posRight=posA;
while(widthCount<(width*2)){
index=-1;
//Alternate looking left and right
if(bLeft){
bLeft=false;
widthCount++;
while(true){
posLeft--;
//cout << posLeft << endl;
if(posLeft<0) { //buffer is too short on left, add spectra
i=bs[0].getScanNumber();
while(true){
i--;
//cout << "I: " << i << endl;
if(i==0) break;
r->readFile(lastFile,ts,i);
if(ts.getScanNumber()==0) continue;
else break;
}
if(i==0) break;
bs.push_front(ts);
for(i=0;i<(int)v.size();i++)v[i]++;
posA++;
posRight++;
posLeft=0;
//ts.getRawFilter(cFilter2,256);
if(ts.getMsLevel()==cs.msLevel) {
index=posLeft;
break;
}
} else {
//bs[posLeft].getRawFilter(cFilter2,256);
if(bs[posLeft].getMsLevel()==cs.msLevel) {
index=posLeft;
break;
}
}
}
} else {
bLeft=true;
widthCount++;
while(true){
posRight++;
if(posRight>=(int)bs.size()) { //buffer is too short on right, add spectra
r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
r->readFile(NULL,ts);
if(ts.getScanNumber()==0) {
posRight--;
break;
}
bs.push_back(ts);
//ts.getRawFilter(cFilter2,256);
if(ts.getMsLevel()==cs.msLevel) {
index=posRight;
break;
}
} else {
//bs[posRight].getRawFilter(cFilter2,256);
if(bs[posRight].getMsLevel()==cs.msLevel) {
index=posRight;
break;
}
}
}
}
if(index==-1) continue;
//ts=bs[index];
v.push_back(index);
numScans++;
}
//cout << "Still Averaging: " << ps.getScanNumber() << endl;
//cout << " with: ";
//for(i=0;i<v.size();i++) cout << bs[v[i]].getScanNumber() << " ";
//cout << endl;
//cout << numScans << " " << v.size() << endl;
//Match peaks between pivot scan and neighbors
for(i=0;i<(int)v.size();i++) vPos.push_back(0);
for(i=0;i<(int)ps.size();i++){ //iterate all points
prec = c * ps.at(i).mz * ps.at(i).mz / 2;
match=1;
for(k=0;k<(int)v.size();k++){ //iterate all neighbors
dif=100000.0;
//cout << "Checking " << bs[v[k]].getScanNumber() << " pos " << vPos[k] << endl;
for(j=vPos[k];j<bs[v[k]].size();j++){ //check if point is a match
dt=fabs(ps.at(i).mz-bs[v[k]].at(j).mz);
if(dt<=dif) {
if(dt<prec) {
ps.at(i).intensity+=bs[v[k]].at(j).intensity;
vPos[k]=j+1;
match++;
break;
}
dif=dt;
} else {
vPos[k]=j-1;
break;
}
}
}
//if data point was not visible across enough scans, set it to 0
if(match<cs.boxcarFilter && match<(int)v.size()) ps.at(i).intensity=0.0;
}
//Average points and apply cutoff
for(i=0;i<ps.size();i++) {
ps.at(i).intensity/=numScans;
sp.add(ps.at(i));
//if(ps.at(i).intensity>=cutoff) sp.add(ps.at(i));
}
sp.setScanNumber(ps.getScanNumber());
sp.setScanNumber(ps.getScanNumber(true),true);
sp.setRTime(ps.getRTime());
sp.setRawFilter(cFilter1);
//clear unused buffer
if(posLeft>0){
while(posLeft>0){
bs.pop_front();
posLeft--;
posA--;
}
}
//cout << "Done averaging" << endl;
return true;
}
