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

                        .getPeptideSequence(peptideSearchResult);
                if (peptideSequence == null) {
                    LOG.warn("Error while geting peptide sequnce for " + peptideSearchResult.getId());
                    continue;
                }
                ResultsAnalyserOutputter outputter;
                outputter = new ResultsAnalyserOutputter(peptideSearchResult,
                        proteinToOLNMap, genome, peptideSequence,
                        translationTable);
                if (outputter.isValid()) {
                    output.write(outputter.toString());
                    output.write(System.getProperty("line.separator"));
                }
            }


        } else {
            for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
                PeptideSequence peptideSequence = sequenceGenerator
                        .getPeptideSequence(peptideSearchResult);
                if (peptideSequence == null) {
                    LOG.warn("Error while geting peptide sequnce for " + peptideSearchResult.getId());
                    continue;
                }
                ResultsAnalyserOutputter outputter;
                outputter = new ResultsAnalyserOutputter(peptideSearchResult,
                        proteinToOLNMap, genome, peptideSequence);
                if (outputter.isValid()) {
                    output.write(outputter.toString());
                    output.write(System.getProperty("line.separator"));
                }
            }


        }

                continue;
            }
            if (DebuggingFlag.get_sbi_debug_flag() == 1) {
                CodonTranslationTable translationTable = CodonTranslationTable
                        .parseTableFile(translationTableFile);
                ResultsAnalyserOutputter outputter = new ResultsAnalyserOutputter(
                        peptideSearchResult, proteinToOLNMap, genome,
                        peptideSequence, translationTable);
                if (outputter.isValid()) {
                    String query = outputter.toQuery();
                // System.out.println(query);
                    hsqldb.execute(query);
                }
            } else {
                ResultsAnalyserOutputter outputter = new ResultsAnalyserOutputter(
                        peptideSearchResult, proteinToOLNMap, genome,
                        peptideSequence);
                if (outputter.isValid()) {
                    hsqldb.execute(outputter.toQuery());
                }
            }
        }


        Collection<String> resultSet = hsqldb.filterResult(sqlQuery);

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

Related Classes of au.org.intersect.samifier.domain.ResultsAnalyserOutputter