Uses of Class
org.forester.surfacing.DomainSimilarity.PRINT_OPTION

Packages that use DomainSimilarity.PRINT_OPTION

Package	Description
org.forester.surfacing

Uses of DomainSimilarity.PRINT_OPTION in org.forester.surfacing

Methods in org.forester.surfacing that return DomainSimilarity.PRINT_OPTION

Modifier and Type	Method and Description
static DomainSimilarity.PRINT_OPTION	DomainSimilarity.PRINT_OPTION.valueOf(String name) Returns the enum constant of this type with the specified name.
static DomainSimilarity.PRINT_OPTION[]	DomainSimilarity.PRINT_OPTION.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.forester.surfacing with parameters of type DomainSimilarity.PRINT_OPTION

Modifier and Type	Method and Description
static void	SurfacingUtil.checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option, String[][] input_file_properties, String automated_pairwise_comparison_suffix, File outdir)
void	PairwiseGenomeComparator.performPairwiseComparisons(StringBuilder html_desc, boolean sort_by_species_count_first, DomainSimilarityCalculator.Detailedness detailedness, boolean ignore_domains_without_combs_in_all_spec, boolean ignore_domains_specific_to_one_species, DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field, DomainSimilarity.PRINT_OPTION domain_similarity_print_option, DomainSimilarity.DomainSimilarityScoring scoring, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, String automated_pairwise_comparison_suffix, boolean verbose, String automated_pairwise_comparison_prefix, String command_line_prg_name, File out_dir, boolean write_pairwise_comparisons, Map<String,Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)
StringBuffer	DomainSimilarity.toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, Map<String,Integer> tax_code_to_id_map, Phylogeny phy)
static void	SurfacingUtil.writeDomainSimilaritiesToFile(StringBuilder html_desc, StringBuilder html_title, Writer simple_tab_writer, Writer single_writer, Map<Character,Writer> split_writers, SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, Map<String,Integer> tax_code_to_id_map, Phylogeny phy, Set<String> pos_filter_doms)