void test()
{
{
MSData tiny;
examples::initializeTiny(tiny);
MSDataFile::WriteConfig writeConfig;
Serializer_mz5 serializer(writeConfig);
IterationListenerRegistry ilr;
serializer.write(testFilename, tiny, &ilr);
MSData dummy;
serializer.read(testFilename, dummy);
// so we don't have any dangling references
//dummy.instrumentPtrs.push_back(InstrumentPtr(new Instrument("LCQ_Deca")));
dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing(
"pwiz_processing")));
dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing(
"CompassXtract processing")));
ChromatogramListPtr sl = dummy.run.chromatogramListPtr;
// check easy functions
unit_assert(sl.get());
unit_assert(sl->size() == 2);
unit_assert(sl->find("tic") == 0);
unit_assert(sl->find("sic") == 1);
// check tic
ChromatogramPtr s = sl->chromatogram(0); // read without binary data
unit_assert(s.get());
unit_assert(s->id == "tic");
unit_assert(s->binaryDataArrayPtrs.empty());
unit_assert(sl->chromatogramIdentity(0).index == 0);
unit_assert(sl->chromatogramIdentity(0).id == "tic");
s = sl->chromatogram(0, true); // read with binary data
vector < TimeIntensityPair > pairs;
s->getTimeIntensityPairs(pairs);
unit_assert(pairs.size() == 15);
for (int i = 0; i < 15; i++)
unit_assert(pairs[i].time == i && pairs[i].intensity == 15 - i);
// check sic
s = sl->chromatogram(1, true);
unit_assert(s.get());
unit_assert(s->id == "sic");
unit_assert(sl->chromatogramIdentity(1).index == 1);
unit_assert(sl->chromatogramIdentity(1).id == "sic");
pairs.clear();
s->getTimeIntensityPairs(pairs);
unit_assert(pairs.size() == 10);
for (int i = 0; i < 10; i++)
unit_assert(pairs[i].time == i && pairs[i].intensity == (10 - i));
}
bfs::remove(testFilename);
}
int main(int argc, char* argv[]){
if(argc!=2) {
cout << "USAGE: mzMLReader <mzML file>" << endl;
exit(0);
}
MSDataFile* msd;
ChromatogramListPtr sl;
ChromatogramPtr s2;
string st=argv[1];
vector<TimeIntensityPair> pairs;
msd = new MSDataFile(argv[1]);
if(!msd->run.chromatogramListPtr->get()) cout << "WTF" << endl;
sl = msd->run.chromatogramListPtr;
for (int j=1; j<(int)sl->size(); j++) {
s2 = sl->chromatogram(j, true);
cout << j << "\t" << s2->id << endl;
s2->getTimeIntensityPairs(pairs);
for(int k=0;k<(int)pairs.size();k++) cout << pairs[k].time << " " << pairs[k].intensity << endl;
}
exit(1);
BasicSpectrum s;
BasicChromatogram chromat;
MzParser sax(&s,&chromat);
sax.load(argv[1]);
bool bLastWasSpectrum=true;
char c='a';
char str[256];
int num;
while(c!='x'){
if(bLastWasSpectrum){
cout << "\nCurrent spectrum:" << endl;
cout << "\tScan number: " << s.getScanNum() << endl;
cout << "\tRetention Time: " << s.getRTime() << endl;
cout << "\tMS Level: " << s.getMSLevel() << endl;
cout << "\tNumber of Peaks: " << s.size() << endl;
} else {
chromat.getIDString(str);
cout << "\nCurrent chromatogram:" << endl;
cout << "\tID: " << str << endl;
cout << "\tNumber of Peaks: " << chromat.size() << endl;
}
cout << "\nMenu:\n\t'c' to grab a new chromatogram\n\t's' to grab a new spectrum\n\t'p' to show peaks\n\t'x' to exit" << endl;
cout << "Please enter your choice: ";
cin >> c;
switch(c){
case 'c':
if(sax.highChromat()==0){
cout << "No chromatograms in the file." << endl;
} else {
cout << "Enter a number from 0 to " << sax.highChromat()-1 << ": ";
cin >> str;
num=(int)atoi(str);
if(num<0 || num>sax.highChromat()-1) {
cout << "Bad number! BOOOOO!" << endl;
} else {
if(!sax.readChromatogram(num)) cout << "Chromatogram number not in file." << endl;
else bLastWasSpectrum=false;
}
}
break;
case 'p':
if(bLastWasSpectrum){
for(unsigned int i=0;i<s.size();i++) printf("%.6lf\t%.1lf\n",s[i].mz,s[i].intensity);
} else {
for(unsigned int i=0;i<chromat.size();i++) printf("%.6lf\t%.1lf\n",chromat[i].time,chromat[i].intensity);
}
break;
case 's':
cout << "Enter a number from " << sax.lowScan() << " to " << sax.highScan() << ": ";
cin >> str;
num=(int)atoi(str);
if(num<sax.lowScan() || num>sax.highScan()) {
cout << "Bad number! BOOOOO!" << endl;
} else {
if(!sax.readSpectrum(num)) cout << "Spectrum number not in file." << endl;
else bLastWasSpectrum=true;
}
break;
case 'x':
break;
default:
cout << "\nInvalid command!" << endl;
break;
}
}
return 0;
}
