Пример #1
0
  /** 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());
  }
Пример #2
0
  /** 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);
  }