private void init() { _e_value_maximum = HmmPfamOutputParser.E_VALUE_MAXIMUM_DEFAULT; setIgnoreDufs( HmmPfamOutputParser.IGNORE_DUFS_DEFAULT ); setReturnType( HmmPfamOutputParser.RETURN_TYPE_DEFAULT ); _max_allowed_overlap = HmmPfamOutputParser.MAX_ALLOWED_OVERLAP_DEFAULT; setIndividualDomainScoreCutoffs( null ); setIgnoreEngulfedDomains( false ); setIgnoreVirusLikeIds( false ); setAllowNonUniqueQuery( false ); setVerbose( false ); intitCounts(); }
+ "hmmpfam_output3" ), "human", "ls" ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); List<Protein> proteins = null; HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); proteins = null; HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); proteins = null; HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); proteins = null; HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); proteins = null;
+ ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); List<?> domain_collections = null; + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" ); parser2.setEValueMaximum( 0.2 ); parser2.setIgnoreDufs( true ); parser2.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); List<Protein> domain_collections2 = null;
+ ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); final List<Protein> domain_collections = parser.parse();