public void testgetEnzymes() {
pepXMLUnmarshaller um = new pepXMLUnmarshaller(pepXMLFile);
Iterator<SampleEnzyme> enzymes = um.getSampleEnzymes();
while (enzymes.hasNext()) {
SampleEnzyme enzyme = enzymes.next();
if (logger.isDebugEnabled()) {
logger.debug("Sample Enzyme: " + enzyme.getName());
}
}
}
public void testProphetSummary() {
pepXMLUnmarshaller um = new pepXMLUnmarshaller(pepXMLFile);
PeptideprophetSummary peptideprophet = um.getPeptideprophetSummary();
if (logger.isDebugEnabled()) {
logger.debug("peptideprophet version: " + peptideprophet.getVersion());
}
InteractSummary interactsummary = um.getInteractSummary();
if (logger.isDebugEnabled()) {
logger.debug("interactsummary base_name: " + interactsummary.getFilename());
}
}
public void testgetMsmsRunSummay() {
pepXMLUnmarshaller um = new pepXMLUnmarshaller(pepXMLFile);
Set<String> msms_run_summaryName = um.getMsmsRunsummaryIDs();
if (logger.isDebugEnabled()) {
logger.debug("MsmsRunSummary basename: " + msms_run_summaryName);
}
try {
MsmsRunSummary runsummary =
um.getMsmsRunsummaryById(
"/regis/sbeams/archive/wyan/HIVHuCell/HIV_S100/HsIPI_v3.21plus/hivs100_14_1");
assertEquals("ThermoFinnigan", runsummary.getMsManufacturer());
} catch (pepXMLUnmarshallerException ex) {
ex.printStackTrace();
}
}
public void testgetSearchSummarybyID() {
// assertTrue(isValidpepXML(pepXMLFile));
pepXMLUnmarshaller um = new pepXMLUnmarshaller(pepXMLFile);
try {
SearchSummary searchsummary =
um.getSearchSummaryById(
"/regis/sbeams/archive/wyan/HIVHuCell/HIV_S100/HsIPI_v3.21plus/hivs100_17_2");
String databaseLocalpath = searchsummary.getSearchDatabase().getLocalPath();
assertEquals("/dbase/users/sbeams/ipi.HUMAN.v3.21plus.fasta", databaseLocalpath);
String enzyme = searchsummary.getEnzymaticSearchConstraint().getEnzyme();
assertEquals("Trypsin", enzyme);
String searchengine = searchsummary.getSearchEngine().value();
assertEquals("SEQUEST", searchengine);
} catch (pepXMLUnmarshallerException ex) {
ex.printStackTrace();
}
}
public void testSpectrumIteration() {
// assertTrue(isValidpepXML(pepXMLFile));
pepXMLUnmarshaller um = new pepXMLUnmarshaller(pepXMLFile);
String path = pepXMLElement.SpectrumQuery.getXpath();
Iterator<SpectrumQuery> iterator =
um.unmarshalCollectionFromXpath(
pepXMLElement.SpectrumQuery.getXpath(), SpectrumQuery.class);
// count the number of spectra we are iterating over
logger.debug("Iterating over all spectra...");
int spectrumCnt = 0;
while (iterator.hasNext()) {
SpectrumQuery spectrum = iterator.next();
if (logger.isDebugEnabled()) {
logger.debug("Spectrum: " + spectrum.getSpectrum());
}
spectrumCnt++;
}
// get the number of spectra entries in the index
int spectrumNo = um.getObjectCountForXpath(pepXMLElement.SpectrumQuery.getXpath());
// compare the two spectra counts
assertEquals(spectrumNo, spectrumCnt);
String spectrumId = null;
String a = null;
try {
spectrumId = um.getSpectrumIDs().iterator().next();
SpectrumQuery testSpectrum = um.getSpectrumById(spectrumId);
assertEquals(testSpectrum.getIndex(), testSpectrum.getIndex());
SpectrumQuery testSpectrumIndex = um.getSpectrumByIndex(2);
assertEquals(3641, testSpectrumIndex.getStartScan());
} catch (pepXMLUnmarshallerException e) {
logger.error("Error reading index for spectrum " + spectrumId, e);
}
}