public void testDB()
throws SQLException, IOException, ClassNotFoundException, SQLException,
ClassNotFoundException, InterruptedException {
String path = this.getClass().getResource("IdentificationDBTest.class").getPath();
path = path.substring(1, path.indexOf("/target/"));
path += "/src/test/resources/experiment/testDB";
try {
ObjectsCache cache = new ObjectsCache();
cache.setAutomatedMemoryManagement(false);
cache.setCacheSize(0);
IdentificationDB idDB = new IdentificationDB(path, "testId", true, cache);
try {
String spectrumKey = "spectrum_file_cus_spectrum_title";
String peptideKey = "PEPTIDE";
String proteinKey = "test_protein";
SpectrumMatch testSpectrumMatch = new SpectrumMatch(spectrumKey);
ArrayList<String> testProteins = new ArrayList<String>();
testProteins.add("test protein1");
testProteins.add("test protein2");
Peptide peptide = new Peptide(peptideKey, new ArrayList<ModificationMatch>());
peptide.setParentProteins(testProteins);
testSpectrumMatch.addHit(
Advocate.mascot.getIndex(),
new PeptideAssumption(
peptide, 1, Advocate.mascot.getIndex(), new Charge(Charge.PLUS, 2), 0.1, "no file"),
false);
idDB.addSpectrumMatch(testSpectrumMatch);
peptide = new Peptide(peptideKey, new ArrayList<ModificationMatch>());
peptide.setParentProteins(testProteins);
PeptideMatch testPeptideMatch = new PeptideMatch(peptide, peptide.getKey());
idDB.addPeptideMatch(testPeptideMatch);
ProteinMatch testProteinMatch = new ProteinMatch(proteinKey);
idDB.addProteinMatch(testProteinMatch);
testSpectrumMatch = idDB.getSpectrumMatch(spectrumKey, true);
Assert.assertTrue(testSpectrumMatch.getKey().equals(spectrumKey));
HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>
assumptionsMap = testSpectrumMatch.getAssumptionsMap();
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> mascotAssumptions =
assumptionsMap.get(Advocate.mascot.getIndex());
Assert.assertTrue(mascotAssumptions.size() == 1);
ArrayList<Double> mascotScores = new ArrayList<Double>(mascotAssumptions.keySet());
Assert.assertTrue(mascotScores.size() == 1);
double bestScore = mascotScores.get(0);
Assert.assertTrue(bestScore == 0.1);
ArrayList<SpectrumIdentificationAssumption> bestAssumptions =
mascotAssumptions.get(bestScore);
PeptideAssumption bestAssumption = (PeptideAssumption) bestAssumptions.get(0);
Peptide bestPeptide = bestAssumption.getPeptide();
Assert.assertTrue(bestPeptide.getParentProteinsNoRemapping().size() == 2);
Assert.assertTrue(
bestPeptide.getParentProteinsNoRemapping().get(0).equals(testProteins.get(0)));
Assert.assertTrue(
bestPeptide.getParentProteinsNoRemapping().get(1).equals(testProteins.get(1)));
ArrayList<String> proteins = new ArrayList<String>();
proteins.add(proteinKey);
bestPeptide.setParentProteins(proteins);
idDB.updateMatch(testSpectrumMatch);
testSpectrumMatch = idDB.getSpectrumMatch(spectrumKey, true);
assumptionsMap = testSpectrumMatch.getAssumptionsMap();
mascotAssumptions = assumptionsMap.get(Advocate.mascot.getIndex());
Assert.assertTrue(mascotAssumptions.size() == 1);
mascotScores = new ArrayList<Double>(mascotAssumptions.keySet());
Assert.assertTrue(mascotScores.size() == 1);
bestScore = mascotScores.get(0);
Assert.assertTrue(bestScore == 0.1);
bestAssumptions = mascotAssumptions.get(bestScore);
bestAssumption = (PeptideAssumption) bestAssumptions.get(0);
bestPeptide = bestAssumption.getPeptide();
Assert.assertTrue(bestPeptide.getParentProteinsNoRemapping().size() == 1);
Assert.assertTrue(bestPeptide.getParentProteinsNoRemapping().get(0).equals(proteinKey));
testPeptideMatch = idDB.getPeptideMatch(peptideKey, true);
Assert.assertTrue(testPeptideMatch.getKey().equals(peptideKey));
testProteinMatch = idDB.getProteinMatch(proteinKey, true);
Assert.assertTrue(testProteinMatch.getKey().equals(proteinKey));
double testScore = 12.3;
PepnovoAssumptionDetails testParameter = new PepnovoAssumptionDetails();
testParameter.setRankScore(testScore);
idDB.addSpectrumMatchParameter(spectrumKey, testParameter);
testParameter =
(PepnovoAssumptionDetails)
idDB.getSpectrumMatchParameter(spectrumKey, testParameter, true);
Assert.assertTrue(testParameter.getRankScore() == testScore);
} finally {
idDB.close();
}
} finally {
File dbFolder = new File(path);
DerbyUtil.closeConnection();
Util.deleteDir(dbFolder);
}
}
