| 33 | START_SECTION(~ProtXMLFile()) |
| 34 | delete ptr; |
| 35 | END_SECTION |
| 36 | |
| 37 | START_SECTION(void load(const String &filename, ProteinIdentification &protein_ids, PeptideIdentification &peptide_ids)) |
| 38 | { |
| 39 | ProtXMLFile f; |
| 40 | ProteinIdentification proteins; |
| 41 | PeptideIdentification peptides; |
| 42 | String prot_file; |
| 43 | |
| 44 | StringList ids = ListUtils::create<String>("16627578304933075941,13229490167902618598"); |
| 45 | // we do this twice, just to check that members are correctly reset etc.. |
| 46 | for (Int i=0;i<2;++i) |
| 47 | { |
| 48 | prot_file = OPENMS_GET_TEST_DATA_PATH("ProtXMLFile_input_1.protXML"); |
| 49 | f.load(prot_file, proteins, peptides); |
| 50 | |
| 51 | // groups |
| 52 | TEST_EQUAL(proteins.getProteinGroups().size(), 7); |
| 53 | TEST_EQUAL(proteins.getProteinGroups()[0].probability, 0.9990); |
| 54 | TEST_EQUAL(proteins.getProteinGroups()[0].accessions.size(), 1); |
| 55 | TEST_EQUAL(proteins.getProteinGroups()[3].accessions.size(), 2); |
| 56 | TEST_EQUAL(proteins.getProteinGroups()[3].accessions[0], |
| 57 | "P01876|IGHA1_HUMAN"); |
| 58 | TEST_EQUAL(proteins.getProteinGroups()[3].accessions[1], |
| 59 | "P01877|IGHA2_HUMAN"); |
| 60 | TEST_EQUAL(proteins.getProteinGroups()[6].probability, 0.2026); |
| 61 | TEST_EQUAL(proteins.getProteinGroups()[6].accessions.size(), 1); |
| 62 | |
| 63 | TEST_EQUAL(proteins.getIndistinguishableProteins().size(), 7); |
| 64 | TEST_EQUAL(proteins.getIndistinguishableProteins()[0].accessions.size(), 1); |
| 65 | TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions.size(), 2); |
| 66 | TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions[0], |
| 67 | "P01876|IGHA1_HUMAN"); |
| 68 | TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions[1], |
| 69 | "P01877|IGHA2_HUMAN"); |
| 70 | TEST_EQUAL(proteins.getIndistinguishableProteins()[6].accessions.size(), 1); |
| 71 | |
| 72 | // proteins |
| 73 | TEST_EQUAL(proteins.getHits().size(), 9); |
| 74 | TEST_EQUAL(proteins.getHits()[0].getAccession(), "P02787|TRFE_HUMAN"); |
| 75 | TEST_EQUAL(proteins.getHits()[0].getCoverage(), 8.6); |
| 76 | TEST_EQUAL(proteins.getHits()[0].getScore(), 0.9990); |
| 77 | // this one is indistinguishable... therefore no coverage (but the score |
| 78 | // got transferred from the "leader" protein): |
| 79 | TEST_EQUAL(proteins.getHits()[6].getAccession(), "P00739|HPTR_HUMAN"); |
| 80 | TEST_EQUAL(proteins.getHits()[6].getCoverage(), -1); |
| 81 | TEST_EQUAL(proteins.getHits()[6].getScore(), 0.2663); |
| 82 | |
| 83 | TEST_EQUAL(proteins.getHits()[8].getAccession(), "P04217|A1BG_HUMAN"); |
| 84 | TEST_EQUAL(proteins.getHits()[8].getCoverage(), 2.0); |
| 85 | TEST_EQUAL(proteins.getHits()[8].getScore(), 0.2026); |
| 86 | |
| 87 | // peptides |
| 88 | TEST_EQUAL(peptides.getHits().size(), 16); |
| 89 | AASequence aa_seq = AASequence::fromString("MYLGYEYVTAIR"); |
| 90 | TEST_EQUAL(peptides.getHits()[0].getSequence(), aa_seq); |
| 91 | TEST_EQUAL(peptides.getHits()[0].getCharge(), 2); |
| 92 | TEST_EQUAL(peptides.getHits()[0].getScore(), 0.8633); |
no test coverage detected