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(); }
public HmmscanPerDomainTableParser( final File input_file, final String species, final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to, final boolean allow_proteins_with_same_name ) { _input_file = input_file; _species = species; _filter = null; _filter_type = FilterType.NONE; _ind_cutoff = individual_cutoff_applies_to; _allow_proteins_with_same_name = allow_proteins_with_same_name; init(); }
private void init() { _fs_e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT; _i_e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT; setIgnoreDufs( HmmscanPerDomainTableParser.IGNORE_DUFS_DEFAULT ); setReturnType( HmmscanPerDomainTableParser.RETURN_TYPE_DEFAULT ); _max_allowed_overlap = HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT; setIndividualScoreCutoffs( null ); setIgnoreEngulfedDomains( false ); setIgnoreVirusLikeIds( false ); intitCounts(); }
static public Msa parseMsa( final File f ) throws IOException { return parseMsa( new FileInputStream( f ) ); }
private void init() { setInputMatrixType( INPUT_MATRIX_TYPE_DEFAULT ); reset(); }
@Override public synchronized Phylogeny[] create( final Object source, final Object parser ) throws IOException { if ( !( parser instanceof PhylogenyParser ) ) { throw new IllegalArgumentException( "attempt to use object of type other than PhylogenyParser as creator for ParserBasedPhylogenyFactory" ); } final PhylogenyParser my_parser = ( PhylogenyParser ) parser; my_parser.setSource( source ); return my_parser.parse(); }
public DistanceMatrix[] parse( final Object source ) throws IOException { reset(); final List<BasicTable<String>> tables = BasicTableParser.parse( source, VALUE_SEPARATOR, false, false, COMMENT, true ); final DistanceMatrix[] distance_matrices = new DistanceMatrix[ tables.size() ]; int i = 0; for( final BasicTable<String> table : tables ) { distance_matrices[ i++ ] = transform( table ); } return distance_matrices; }
public HmmPfamOutputParser( final File input_file, final String species, final String model_type ) { _input_file = input_file; _species = species; _filter = null; _filter_type = FilterType.NONE; init(); }
static public List<MolecularSequence> parse( final File f ) throws IOException { return parse( new FileInputStream( f ) ); }
private void reset() { setMatrixSize( -1 ); }
public static SymmetricalDistanceMatrixParser createInstance() { return new SymmetricalDistanceMatrixParser(); }
private SymmetricalDistanceMatrixParser() { init(); }
static public boolean isLikelyFasta( final File f ) throws IOException { return isLikelyFasta( new FileInputStream( f ) ); }
static public Msa parseMsa( final String s ) throws IOException { return parseMsa( s.getBytes() ); }
public HmmscanPerDomainTableParser( final File input_file, final String species, final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) { _input_file = input_file; _species = species; _filter = null; _filter_type = FilterType.NONE; _ind_cutoff = individual_cutoff_applies_to; _allow_proteins_with_same_name = false; init(); }
public HmmPfamOutputParser( final File input_file, final String species, final Set<String> filter, final FilterType filter_type ) { _input_file = input_file; _species = species; _filter = filter; _filter_type = filter_type; init(); }
static public Msa parseMsa( final InputStream is ) throws IOException { return BasicMsa.createInstance( parse( is ) ); }
static public Msa parseMsa( final byte[] bytes ) throws IOException { return parseMsa( new ByteArrayInputStream( bytes ) ); }
public HmmscanPerDomainTableParser( final File input_file, final String species, final Set<String> filter, final FilterType filter_type, final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) { _input_file = input_file; _species = species; _filter = filter; _filter_type = filter_type; _ind_cutoff = individual_cutoff_applies_to; _allow_proteins_with_same_name = false; init(); }
public HmmscanPerDomainTableParser( final File input_file, final String species, final Set<String> filter, final FilterType filter_type, final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to, final boolean allow_proteins_with_same_name ) { _input_file = input_file; _species = species; _filter = filter; _filter_type = filter_type; _ind_cutoff = individual_cutoff_applies_to; _allow_proteins_with_same_name = allow_proteins_with_same_name; init(); }