// @Test
// public void statMzXMLs() throws IOException
// {
// root = "/Volumes/PPP_Data/JHU DATA/141112 Project 7_MS2/P7M1/Data-QE/";
// //String[] rawfiles =
// {"20081129_Orbi6_NaNa_SA_FASP_blacktips_01","20081129_Orbi6_NaNa_SA_FASP_blacktips_02"};
// String[] rawfiles =
// {"RC-CS-141112_Medimmune_HD_P7M1_Fr19","RC-CS-141112_Medimmune_HD_P7M1_Fr8"};
//
//// Dataframe test = MsReaders.surveyMzXML(rawfiles, root, "/tmp/survey01",
// Range.openClosed(20d, 21d), 2);
// Dataframe test = MsReaders.surveyMzXML(rawfiles, root, "survey01", null, 2);
//
// IOs.write(root+"surveys.txt", test.display().toString());
// }
// @Test
// public void statMzXMLsByFolder() throws IOException
// {
// //root = "/Volumes/PPP_Data/JHU DATA/141112 Project 7_MS2/P7M1/Data-QE/";
// root = "/Volumes/PPP_Data/JHU DATA/141112 Project 7_MS2/P7M2/";
//
// Dataframe test = MsReaders.surveyMzXML(root, "survey02", null, 2);
//
// IOs.write(root+"surveys.txt", test.display().toString());
// }
// @Test
// public void surveyMzXMLs() throws IOException
// {
// LcMsMsDataset test = new MaxQuant("survey");
// test.setRawFilename(root+"20081129_Orbi6_NaNa_SA_FASP_blacktips_01.mzXML");
//
// test = MsReaders.surveyMzXML(test, null, 2);
//
// // write the examples out in MGF format
// Collection<Long> ids = test.getMzRtFileOffset().subset(495.2d, 495.35d, 0d,
// Double.MAX_VALUE);
// RandomAccessFile bin = test.getSpCacheFile(2);
// MgfWriter mgf = new MgfWriter(new File("/tmp/examples495_3.mgf"),
// PeakList.Precision.DOUBLE);
// for (Long id : ids)
// {
// bin.find(id);
// MsnSpectrum ms = MsIO.readSpectrumIdentifier(bin, new MsnSpectrum());
// mgf.write(ms);
// }
// mgf.close(); bin.close();
//
// assertEquals(test.getMzRtFileOffset().size(), 36831);
// }
@Test
public void nextSpec() throws IOException {
Logger.getLogger(MzxmlReader.class.getName()).setLevel(Level.SEVERE);
File data = new File(root + "20081129_Orbi6_NaNa_SA_FASP_blacktips_01.mzXML");
MzxmlReader reader = MzxmlReader.newTolerantReader(data, PeakList.Precision.FLOAT);
int counts = 0;
while (reader.hasNext()) {
MsnSpectrum spec = reader.next();
if (++counts % 100 == 0) System.out.print(".");
if (counts % 10000 == 0) System.out.println(counts);
}
reader.close();
System.out.println("\n" + counts + " spectra imported");
}
private MsnSpectrum[] firstScan(String file, int msLevel, int len) throws IOException {
Logger.getLogger(MzxmlReader.class.getName()).setLevel(Level.SEVERE);
// File data = new File(root+"20081129_Orbi6_NaNa_SA_FASP_blacktips_01.mzXML");
int order = 0;
File data = new File(file);
MsnSpectrum[] spectra = new MsnSpectrum[len];
MzxmlReader reader = MzxmlReader.newTolerantReader(data, PeakList.Precision.FLOAT);
while (reader.hasNext()) {
if (order >= len) break;
MsnSpectrum spec = reader.next();
if (spec != null && spec.getMsLevel() == msLevel) {
spectra[order] = spec;
order++;
}
}
reader.close();
return spectra;
}
