// returns number of peaks that were stored
int PeakList::readPeaksToLocalAllocation(const SpectraAggregator& sa,
const SingleSpectrumHeader* header)
{
// create a basic PeakList read function
header_ = header;
if (localAllocationSize_>0 && peaks_)
delete [] peaks_;
localAllocationSize_ = header->getOriginalNumPeaks();
peaks_ = new Peak[localAllocationSize_];
if (! peaks_)
{
cout << "Error: couldn't allocate memory for spectrum!" << endl;
exit(1);
}
const int numPeaksRead = sa.readPeakList(header, peaks_);
numPeaks_ = numPeaksRead;
if (header->getFileType() != IFT_MZXML &&
( numPeaksRead != header->getOriginalNumPeaks() ||
peaks_[0].mass != header->getFirstPeakMass()) )
{
cout << "Error reading scan " << header->getScanNumber() << ": " << header_->getTitle()
<< " in file " << sa.getSpectraFile(header_->getSpectraFileIndexInList()).getFilePath() << endl;
if (numPeaksRead != header->getOriginalNumPeaks())
cout << "Num peaks read " << numPeaksRead << ", expecting " << header->getScanNumber() << endl;
if (peaks_[0].mass != header->getFirstPeakMass())
cout << setprecision(5) << "First peak mass " << peaks_[0].mass
<<", expecting " << header->getFirstPeakMass() << endl;
cout << "Could possibly be a dos/unix problem with the files, try running dos2unix (or unix2dos)..." << endl;
cout <<"Skipping spectrum..." << endl;
const int numPeaksRead = sa.readPeakList(header, peaks_);
return 0;
}
return numPeaks_;
}
// function assumes that the buffer is sufficently large for all peaks being read
// returns number of peaks that were stored
int PeakList::readPeaksToBuffer(const SpectraAggregator& sa,
const SingleSpectrumHeader* header,
Peak* peakBuffer)
{
// create a basic PeakList read function
header_ = header;
if (localAllocationSize_>0 && peaks_)
delete [] peaks_;
localAllocationSize_ = 0;
peaks_ = peakBuffer;
const int numPeaksRead = sa.readPeakList(header, peaks_);
numPeaks_ = numPeaksRead;
return numPeaks_;
}
