Uses of Class
org.forester.surfacing.DomainSimilarity.PRINT_OPTION
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Packages that use DomainSimilarity.PRINT_OPTION Package Description org.forester.surfacing -
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Uses of DomainSimilarity.PRINT_OPTION in org.forester.surfacing
Methods in org.forester.surfacing that return DomainSimilarity.PRINT_OPTION Modifier and Type Method Description static DomainSimilarity.PRINT_OPTION
DomainSimilarity.PRINT_OPTION. valueOf(java.lang.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 Description static void
SurfacingUtil. checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option, java.lang.String[][] input_file_properties, java.lang.String automated_pairwise_comparison_suffix, java.io.File outdir)
void
PairwiseGenomeComparator. performPairwiseComparisons(java.lang.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, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, java.util.List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, java.lang.String automated_pairwise_comparison_suffix, boolean verbose, java.lang.String automated_pairwise_comparison_prefix, java.lang.String command_line_prg_name, java.io.File out_dir, boolean write_pairwise_comparisons, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)
java.lang.StringBuffer
DomainSimilarity. toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy)
static void
SurfacingUtil. writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc, java.lang.StringBuilder html_title, java.io.Writer simple_tab_writer, java.io.Writer single_writer, java.util.Map<java.lang.Character,java.io.Writer> split_writers, java.util.SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, java.util.List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy, java.util.Set<java.lang.String> pos_filter_doms)
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