void IDRipper::getProteinIdentification_(ProteinIdentification & result, PeptideIdentification pep_ident, std::vector<ProteinIdentification> & prot_idents)
{
const String & identifier = pep_ident.getIdentifier();
for (vector<ProteinIdentification>::iterator prot_it = prot_idents.begin(); prot_it != prot_idents.end(); ++prot_it)
{
if (identifier.compare(prot_it->getIdentifier()) == 0)
{
result = *prot_it;
break;
}
}
}
END_SECTION
START_SECTION(void load(const String &filename, ProteinIdentification &protein_ids, PeptideIdentification &peptide_ids))
{
ProtXMLFile f;
ProteinIdentification proteins;
PeptideIdentification peptides;
String prot_file;
StringList ids = ListUtils::create<String>("16627578304933075941,13229490167902618598");
// we do this twice, just to check that members are correctly reset etc..
for (Int i=0;i<2;++i)
{
prot_file = OPENMS_GET_TEST_DATA_PATH("ProtXMLFile_input_1.protXML");
f.load(prot_file, proteins, peptides);
TEST_EQUAL(proteins.getIdentifier(), ids[i]);
TEST_EQUAL(peptides.getIdentifier(), ids[i]);
// groups
TEST_EQUAL(proteins.getProteinGroups().size(), 7);
TEST_EQUAL(proteins.getProteinGroups()[0].probability, 0.9990);
TEST_EQUAL(proteins.getProteinGroups()[0].accessions.size(), 1);
TEST_EQUAL(proteins.getProteinGroups()[3].accessions.size(), 2);
TEST_EQUAL(proteins.getProteinGroups()[3].accessions[0],
"P01876|IGHA1_HUMAN");
TEST_EQUAL(proteins.getProteinGroups()[3].accessions[1],
"P01877|IGHA2_HUMAN");
TEST_EQUAL(proteins.getProteinGroups()[6].probability, 0.2026);
TEST_EQUAL(proteins.getProteinGroups()[6].accessions.size(), 1);
TEST_EQUAL(proteins.getIndistinguishableProteins().size(), 7);
TEST_EQUAL(proteins.getIndistinguishableProteins()[0].accessions.size(), 1);
TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions.size(), 2);
TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions[0],
"P01876|IGHA1_HUMAN");
TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions[1],
"P01877|IGHA2_HUMAN");
TEST_EQUAL(proteins.getIndistinguishableProteins()[6].accessions.size(), 1);
// proteins
TEST_EQUAL(proteins.getHits().size(), 9);
TEST_EQUAL(proteins.getHits()[0].getAccession(), "P02787|TRFE_HUMAN");
TEST_EQUAL(proteins.getHits()[0].getCoverage(), 8.6);
TEST_EQUAL(proteins.getHits()[0].getScore(), 0.9990);
// this one is indistinguishable... therefore it should have minimal infos
TEST_EQUAL(proteins.getHits()[6].getAccession(), "P00739|HPTR_HUMAN");
TEST_EQUAL(proteins.getHits()[6].getCoverage(), -1);
TEST_EQUAL(proteins.getHits()[6].getScore(), -1);
TEST_EQUAL(proteins.getHits()[8].getAccession(), "P04217|A1BG_HUMAN");
TEST_EQUAL(proteins.getHits()[8].getCoverage(), 2.0);
TEST_EQUAL(proteins.getHits()[8].getScore(), 0.2026);
// peptides
TEST_EQUAL(peptides.getHits().size(), 16);
AASequence aa_seq("MYLGYEYVTAIR");
TEST_EQUAL(peptides.getHits()[0].getSequence(), aa_seq);
TEST_EQUAL(peptides.getHits()[0].getCharge(), 2);
TEST_EQUAL(peptides.getHits()[0].getScore(), 0.8633);
TEST_EQUAL(peptides.getHits()[0].getProteinAccessions().size(), 1);
TEST_EQUAL(peptides.getHits()[0].getProteinAccessions()[0], "P02787|TRFE_HUMAN");
TEST_EQUAL(peptides.getHits()[0].getMetaValue("is_unique"), true);
TEST_EQUAL(peptides.getHits()[0].getMetaValue("is_contributing"), true);
// load 2 nd file and
prot_file = OPENMS_GET_TEST_DATA_PATH("ProtXMLFile_input_2.protXML");
}
}