Package au.org.intersect.samifier.domain

Examples of au.org.intersect.samifier.domain.PeptideSearchResult

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            peptideSearchResults.addAll(parseResults(searchResultFile));
        }
        //remove all peptides with "X"
        Iterator<PeptideSearchResult> setIterator = peptideSearchResults.iterator();
        while (setIterator.hasNext()) {
            PeptideSearchResult currentElement = setIterator.next();
            if (currentElement.getPeptideSequence().contains("X")) {
                setIterator.remove();
            }
        }
        return peptideSearchResults;
    }
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                        LOG.info("ERR_ACC: " + protein);
                        continue;
                    }
                    int start = Integer.parseInt(proteinPartMatcher.group(2));
                    int stop = Integer.parseInt(proteinPartMatcher.group(3));
                    results.add(new PeptideSearchResult(fileName, id, peptideSequence,
                            protein, start, stop, confidenceScore));
                }
            }
        }
        return results;
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    }

    public void build(String id, String peptideSequence, String protein,
            String start, String end, String confidenceScore) {
        BigDecimal score = new BigDecimal(confidenceScore);
        PeptideSearchResult searchResult = new PeptideSearchResult(fileName, id, peptideSequence, protein, Integer.parseInt(start), Integer.parseInt(end), score);
        results.add(searchResult);
    }
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        String[] params = peptideReferenceMap.get(id);
        if (params == null) {
            LOG.warn("No peptide ref for id " + id);
            return;
        }
        PeptideSearchResult searchResult = new PeptideSearchResult(fileName, id, params[0], protein, Integer.parseInt(start), Integer.parseInt(end), new BigDecimal(params[1]));
        results.add(searchResult);
    }
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            List<PeptideSearchResult> list = peptideSearchResultsParser.parseResults(mascotFile);
            // The parser should find sixteen results - same as mzid file
            System.out.println(list.toString());
            assertEquals("Parser should find seven ", 7, list.size());
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q21_p1", "EFGILK", "KPYK1_YEAST", 469, 474 , new BigDecimal("25.95"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q131_p1", "SVIDNAR", "KPYK1_YEAST", 62, 68 , new BigDecimal("40.45"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q217_p1", "INFGIEK", "KPYK1_YEAST", 460, 466 , new BigDecimal("37.51"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q376_p2", "TGIAIGLNK", "RL36B_YEAST", 5, 13 , new BigDecimal("35.86"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q887_p1", "KRNEEEDAK", "RL31A_YEAST", 78, 86 , new BigDecimal("40.09"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q1009_p2", "EYTINLHKR", "RL31A_YEAST", 11, 19 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "q2365_p1", "NEEEDAKNPLFSYVEPVLVASAK", "RL31A_YEAST", 80, 102 , new BigDecimal("20.69"))));
        }
        catch(Exception e)
        {
            fail("Unexpected exception: " + e.getMessage());
            e.printStackTrace();
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            ProteinToOLNMap proteinToOLNMap = proteinToOLNParser.parseMappingFile(mapFile);
            PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(proteinToOLNMap);

            List<PeptideSearchResult> list = peptideSearchResultsParser.parseResults(mascotFile);
            assertEquals("Parser should find sixteen ", 16, list.size());
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_11_1_KPYK1_YEAST_0_469_474", "EFGILK", "KPYK1_YEAST", 469, 474 , new BigDecimal("25.95"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_11_2_KPYK1_YEAST_0_62_68", "SVIDNAR", "KPYK1_YEAST", 62, 68 , new BigDecimal("40.45"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_11_3_KPYK1_YEAST_0_460_466", "INFGIEK", "KPYK1_YEAST", 460, 466 , new BigDecimal("37.51"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_11_4_RL36B_YEAST_0_5_13", "TGIAIGLNK", "RL36B_YEAST", 5, 13 , new BigDecimal("35.86")))); 
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_1_RL31A_YEAST_0_78_86", "KRNEEEDAK", "RL31A_YEAST", 78, 86 , new BigDecimal("40.09"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_2_RL31B_YEAST_0_78_86", "KRNEEEDAK", "RL31B_YEAST", 78, 86 , new BigDecimal("40.09"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_3_RL31A_YEAST_0_11_19", "EYTINLHKR", "RL31A_YEAST", 11, 19 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_4_RL31B_YEAST_0_11_19", "EYTINLHKR", "RL31B_YEAST", 11, 19 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_5_RL31_ASHGO_0_11_19", "EYTINLHKR", "RL31_ASHGO", 11, 19 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_6_RL31_CYAPA_0_18_26", "EYTINLHKR", "RL31_CYAPA", 18, 26 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_7_RL31_DICDI_0_10_18", "EYTINLHKR", "RL31_DICDI", 10, 18 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_8_RL31_NICGU_0_16_24", "EYTINLHKR", "RL31_NICGU", 16, 24 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_9_RL31_PANGI_0_16_24", "EYTINLHKR", "RL31_PANGI", 16, 24 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_10_RL31_PERFR_0_17_25", "EYTINLHKR", "RL31_PERFR", 17, 25 , new BigDecimal("52.75"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_11_RL31A_YEAST_0_80_102", "NEEEDAKNPLFSYVEPVLVASAK", "RL31A_YEAST", 80, 102 , new BigDecimal("20.69"))));
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_14_12_RL31B_YEAST_0_80_102", "NEEEDAKNPLFSYVEPVLVASAK", "RL31B_YEAST", 80, 102 , new BigDecimal("20.69"))));
        }
        catch(Exception e)
        {
            fail("Unexpected exception: " + e.getMessage());
            e.getCause().printStackTrace();
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    @Test
    public void testConfidenceScoreEqual()
    {
        BigDecimal confidenceScore = new BigDecimal("10.20");
        PeptideSearchResult peptideSearchResult = new PeptideSearchResult(null, null,null,null,0,0, confidenceScore);

        assertTrue(filter.accepts(peptideSearchResult));
    }
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    @Test
    public void testConfidenceScoreGreater()
    {
        BigDecimal confidenceScore = new BigDecimal("11.20");
        PeptideSearchResult peptideSearchResult = new PeptideSearchResult(null, null,null,null,0,0, confidenceScore);

        assertTrue(filter.accepts(peptideSearchResult));
    }
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    @Test
    public void testConfidenceScoreSmaller()
    {
        BigDecimal confidenceScore = new BigDecimal("1.20");
        PeptideSearchResult peptideSearchResult = new PeptideSearchResult(null, null,null,null,0,0, confidenceScore);

        assertFalse(filter.accepts(peptideSearchResult));
    }
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Related Classes of au.org.intersect.samifier.domain.PeptideSearchResult

  • au.org.intersect.samifier.filter.ConfidenceScoreFilterUnitTest
  • au.org.intersect.samifier.parser.mzidentml.MzidReader
  • au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl
  • au.org.intersect.samifier.parser.PeptideSearchResultsParserImplUnitTest
  • org.apache.commons.lang3.builder.EqualsBuilder
  • org.apache.commons.lang3.builder.HashCodeBuilder
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