private double extractRetentionTime(Spectrum spectrum) {
ScanList scanListElement = spectrum.getScanList();
if (scanListElement == null) return 0;
List<Scan> scanElements = scanListElement.getScan();
if (scanElements == null) return 0;
for (Scan scan : scanElements) {
List<CVParam> cvParams = scan.getCvParam();
if (cvParams == null) continue;
for (CVParam param : cvParams) {
String accession = param.getAccession();
String unitAccession = param.getUnitAccession();
String value = param.getValue();
if ((accession == null) || (value == null)) continue;
// Retention time (actually "Scan start time") MS:100001
if (accession.equals("MS:1000016")) {
// MS:1000038 is used in mzML 1.0, while UO:0000031
// is used in mzML 1.1.0 :-/
double retentionTime;
if ((unitAccession == null)
|| (unitAccession.equals("MS:1000038"))
|| unitAccession.equals("UO:0000031")) {
retentionTime = Double.parseDouble(value);
} else {
retentionTime = Double.parseDouble(value) / 60d;
}
return retentionTime;
}
}
}
return 0;
}
public void testReadingOfreferenceableParamGroupWithoutSpectrumCaching() {
URL url = this.getClass().getClassLoader().getResource("sample_small.mzML");
assertNotNull(url);
MzMLUnmarshaller um = new MzMLUnmarshaller(url, false);
MzML mz = um.unmarshall();
assertNotNull(mz);
assertNotNull(mz.getRun());
// First pass.
List<Spectrum> spectra = mz.getRun().getSpectrumList().getSpectrum();
for (Spectrum spectrum : spectra) {
if (spectrum.getId().equalsIgnoreCase("scan=21")) {
// skip this spectrum, since it does not contain scan data
} else {
if (spectrum.getScanList() != null) {
Scan scan = spectrum.getScanList().getScan().get(0); // get first scan
if (scan != null) {
Assert.assertEquals(5, scan.getCvParam().size());
Assert.assertEquals(2, scan.getUserParam().size());
}
}
}
}
// Second pass. See if it keeps adding the referenceable ones.
spectra = mz.getRun().getSpectrumList().getSpectrum();
for (Spectrum spectrum : spectra) {
if (spectrum.getId().equalsIgnoreCase("scan=21")) {
// skip this spectrum, since it does not contain scan data
} else {
if (spectrum.getScanList() != null) {
Scan scan = spectrum.getScanList().getScan().get(0); // get first scan
if (scan != null) {
Assert.assertEquals(5, scan.getCvParam().size());
Assert.assertEquals(2, scan.getUserParam().size());
}
}
}
}
}
public void testReferenceableParamGroupMarshallingWithoutSpectrumCaching() {
URL url = this.getClass().getClassLoader().getResource("sample_small.mzML");
assertNotNull(url);
MzMLUnmarshaller um = new MzMLUnmarshaller(url, false);
MzML mz = um.unmarshall();
MzMLMarshaller marshaller = new MzMLMarshaller();
try {
// Try a single pass.
File output =
File.createTempFile(
"testReferenceableParamGroupMarshallingWithoutSpectrumCaching", ".mzML");
output.deleteOnExit();
BufferedWriter bw = new BufferedWriter(new FileWriter(output));
marshaller.marshall(mz, bw);
bw.flush();
bw.close();
um = new MzMLUnmarshaller(output, false, null);
mz = um.unmarshall();
// First pass.
List<Spectrum> spectra = mz.getRun().getSpectrumList().getSpectrum();
for (Spectrum spectrum : spectra) {
if (spectrum.getId().equalsIgnoreCase("scan=21")) {
// skip this spectrum, since it does not contain scan data
} else {
if (spectrum.getScanList() != null) {
Scan scan = spectrum.getScanList().getScan().get(0); // get first scan
if (scan != null) {
Assert.assertEquals(5, scan.getCvParam().size());
Assert.assertEquals(2, scan.getUserParam().size());
Assert.assertEquals(
2,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getCvParam()
.size());
Assert.assertEquals(
1,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getUserParam()
.size());
}
}
}
}
// Second pass. See if it keeps adding the referenceable ones.
spectra = mz.getRun().getSpectrumList().getSpectrum();
for (Spectrum spectrum : spectra) {
if (spectrum.getId().equalsIgnoreCase("scan=21")) {
// skip this spectrum, since it does not contain scan data
} else {
if (spectrum.getScanList() != null) {
Scan scan = spectrum.getScanList().getScan().get(0); // get first scan
if (scan != null) {
Assert.assertEquals(5, scan.getCvParam().size());
Assert.assertEquals(2, scan.getUserParam().size());
Assert.assertEquals(
2,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getCvParam()
.size());
Assert.assertEquals(
1,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getUserParam()
.size());
}
}
}
}
// Try a double pass.
output = File.createTempFile("tempTestReferenceableParamGroupMarshalling", "mzML");
output.deleteOnExit();
bw = new BufferedWriter(new FileWriter(output));
marshaller.marshall(mz, bw);
bw.flush();
bw.close();
File output2 = File.createTempFile("tempTestReferenceableParamGroupMarshalling2", "mzML");
output2.deleteOnExit();
bw = new BufferedWriter(new FileWriter(output2));
marshaller.marshall(mz, bw);
bw.flush();
bw.close();
// Check wether this one still makes sense.
um = new MzMLUnmarshaller(output2, false, null);
mz = um.unmarshall();
// First pass.
spectra = mz.getRun().getSpectrumList().getSpectrum();
for (Spectrum spectrum : spectra) {
if (spectrum.getId().equalsIgnoreCase("scan=21")) {
// skip this spectrum, since it does not contain scan data
} else {
if (spectrum.getScanList() != null) {
Scan scan = spectrum.getScanList().getScan().get(0); // get first scan
if (scan != null) {
Assert.assertEquals(5, scan.getCvParam().size());
Assert.assertEquals(2, scan.getUserParam().size());
Assert.assertEquals(
2,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getCvParam()
.size());
Assert.assertEquals(
1,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getUserParam()
.size());
}
}
}
}
// Second pass. See if it keeps adding the referenceable ones.
spectra = mz.getRun().getSpectrumList().getSpectrum();
for (Spectrum spectrum : spectra) {
if (spectrum.getId().equalsIgnoreCase("scan=21")) {
// skip this spectrum, since it does not contain scan data
} else {
if (spectrum.getScanList() != null) {
Scan scan = spectrum.getScanList().getScan().get(0); // get first scan
if (scan != null) {
Assert.assertEquals(5, scan.getCvParam().size());
Assert.assertEquals(2, scan.getUserParam().size());
Assert.assertEquals(
2,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getCvParam()
.size());
Assert.assertEquals(
1,
scan.getReferenceableParamGroupRef()
.get(0)
.getReferenceableParamGroup()
.getUserParam()
.size());
}
}
}
}
} catch (IOException ioe) {
ioe.printStackTrace();
fail("IOException when creating a temproray file to marshall to!\n" + ioe.getMessage());
}
}
