List<ProteinLocation> proteinLocations = new ArrayList<ProteinLocation>();
System.out.println("Generating locations");
GenomeParserImpl genomeParser = new GenomeParserImpl();
genome = genomeParser.parseGenomeFile(genomeFile);
proteinToOLNMap = new EqualProteinOLNMap();
PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
proteinToOLNMap);
List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
.parseResults(searchResultsPaths);