@Test public void testModificationPosition() throws Exception { // in proteins and peptides MUST be reported with the position set to 0 (N-terminal) // or the amino acid length +1 (C-terminal) respectively. String dataLine = "PEP\t" + "EIEIL\t" + "P02768\t" + "0\t" + "UniProtKB\t" + "2011_11\t" + "[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]\t" + "2\t" + "2\t" + "3\t" + "8-MOD:00397\t" + // position overflow "10.2\t" + "1123.2|1145.3\t" + "2\t" + "1234.4\t" + "http://www.ebi.ac.uk/pride/link/to/peptide\t" + "ms_run[1]:index=5"; pepParser.parse(1, dataLine, errorList); assertError(LogicalErrorType.ModificationPosition); }
@Test public void testUnique() throws Exception { pepParser.checkUnique(pehFactory.findColumnByHeader("unique"), "x"); assertError(FormatErrorType.MZBoolean); }