/** Test of getValidatedPSMs method, of class AnalyzeOutcomes. */
@Test
public void testGetValidatedPSMs() throws Exception {
System.out.println("getValidatedPSMs");
AnalyzeOutcomes instance = new AnalyzeOutcomesImpl();
ArrayList<XilmassResult> res = new ArrayList<XilmassResult>();
// start with Xilmass objects
File folder =
new File(
"C:\\Users\\Sule\\Documents\\NetBeansProjects\\CrossLinkedPeptides\\Data\\Test\\analyze\\xilmass_validated_testing\\test_mc4_TMSAm_HCD_contaminants");
// folder = new
// File("C:\\Users\\Sule\\Documents\\PhD\\XLinked\\XLinkData_Freiburg\\competetives\\xilmass\\runs\\mc4_TMSAm_HCD_contaminants\\output\\elite");
for (File f : folder.listFiles()) {
System.out.println(f.getName());
BufferedReader br = new BufferedReader(new FileReader(f));
String line = "";
while ((line = br.readLine()) != null) {
if (!line.startsWith("SpectrumFile") && (!line.startsWith("File")) && !line.isEmpty()) {
// make sure that a PSM is not contaminant-derived
if (!line.contains("contaminant")) {
XilmassResult r = new XilmassResult(line, "ScoreName");
// set if it is target or decoy..
r.setTarget_decoy(instance.getTargetDecoy(r.getProteinA(), r.getProteinB()));
res.add(r);
}
}
}
}
// now sort these
Collections.sort(res, XilmassResult.ScoreDSCBasedTDs);
ArrayList<Outcome> resOutcome = new ArrayList<Outcome>();
for (XilmassResult r : res) {
resOutcome.add(r);
}
System.out.println("Validated list...");
double fdr = 0.01;
instance.isPIT = false;
// it contains only TTs not, TDs or DDs
ArrayList<Outcome> result = instance.getValidatedPSMs(resOutcome, fdr, true);
assertEquals(24, result.size());
fdr = 0.05;
result = instance.getValidatedPSMs(resOutcome, fdr, true);
assertEquals(29, result.size());
// update to calculate PLink-FDR
resOutcome.get(26).setTarget_decoy("DD");
instance.isPIT = false;
result = instance.getValidatedPSMs(resOutcome, 0.05, true);
assertEquals(30, result.size());
// try if DD is found before finding any TD..
resOutcome.get(25).setTarget_decoy("DD");
result = instance.getValidatedPSMs(resOutcome, 0.05, true);
assertEquals(24, result.size());
}
/** Test of getTargetDecoy method, of class AnalyzeOutcomes. */
@Test
public void testGetTargetDecoy() {
System.out.println("getTargetDecoy");
String proteinA = "DECOY" + "Q145", proteinB = "P145";
AnalyzeOutcomes instance = new AnalyzeOutcomesImpl();
String expResult = "TD";
String result = instance.getTargetDecoy(proteinA, proteinB);
assertEquals(expResult, result);
proteinA = "Q145";
proteinB = "DECOY" + "P145";
instance = new AnalyzeOutcomesImpl();
expResult = "TD";
result = instance.getTargetDecoy(proteinA, proteinB);
assertEquals(expResult, result);
proteinA = "Q145";
proteinB = "DECOY" + "P145";
instance = new AnalyzeOutcomesImpl();
expResult = "TD";
result = instance.getTargetDecoy(proteinA, proteinB);
assertEquals(expResult, result);
proteinA = "DECOY" + "Q145";
proteinB = "DECOY" + "P145";
instance = new AnalyzeOutcomesImpl();
expResult = "DD";
result = instance.getTargetDecoy(proteinA, proteinB);
assertEquals(expResult, result);
proteinA = "Q145";
proteinB = "REVERSED" + "P145";
instance = new AnalyzeOutcomesImpl();
expResult = "TD";
result = instance.getTargetDecoy(proteinA, proteinB);
assertEquals(expResult, result);
proteinA = "Q145";
proteinB = "P145";
instance = new AnalyzeOutcomesImpl();
expResult = "TT";
result = instance.getTargetDecoy(proteinA, proteinB);
assertEquals(expResult, result);
}
