static void |
DomainCountsDifferenceUtil.calculateCopyNumberDifferences(java.util.List<GenomeWideCombinableDomains> genomes,
java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species,
java.util.List<java.lang.String> high_copy_base_species,
java.util.List<java.lang.String> high_copy_target_species,
java.util.List<java.lang.String> low_copy_species,
int min_diff,
java.lang.Double factor,
java.io.File plain_output_dom,
java.io.File html_output_dom,
java.io.File html_output_dc,
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,
java.io.File all_domains_go_ids_out_dom,
java.io.File passing_domains_go_ids_out_dom,
java.io.File proteins_file_base) |
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java.util.SortedSet<DomainSimilarity> |
BasicDomainSimilarityCalculator.calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator,
java.util.List<GenomeWideCombinableDomains> cdc_list,
boolean ignore_domains_without_combinations_in_any_genome,
boolean ignore_domains_specific_to_one_genome) |
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java.util.SortedSet<DomainSimilarity> |
DomainSimilarityCalculator.calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator,
java.util.List<GenomeWideCombinableDomains> cdc_list,
boolean ignore_domains_without_combinations_in_any_genome,
boolean ignore_domains_specific_to_one_genome) |
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static DomainParsimonyCalculator |
DomainParsimonyCalculator.createInstance(Phylogeny phylogeny,
java.util.List<GenomeWideCombinableDomains> gwcd_list) |
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static DomainParsimonyCalculator |
DomainParsimonyCalculator.createInstance(Phylogeny phylogeny,
java.util.List<GenomeWideCombinableDomains> gwcd_list,
java.util.Map<java.lang.String,java.util.Set<java.lang.String>> domain_id_to_secondary_features_map) |
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static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> |
DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list) |
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static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> |
DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list,
java.util.SortedSet<java.lang.String> positive_filter) |
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static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> |
DomainParsimonyCalculator.createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list,
java.util.Map<java.lang.String,java.lang.String> domain_id_to_second_features_map) |
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static java.util.SortedSet<java.lang.String> |
SurfacingUtil.getAllDomainIds(java.util.List<GenomeWideCombinableDomains> gwcd_list) |
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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) |
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void |
PairwiseGenomeComparator.performPairwiseComparisonsJacknifed(Species[] species,
int number_of_genomes,
java.util.List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
boolean verbose,
int number_of_resamplings,
double jacknife_ratio,
long random_seed) |
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static void |
SurfacingUtil.writePresentToNexus(java.io.File output_file,
java.io.File positive_filter_file,
java.util.SortedSet<java.lang.String> filter,
java.util.List<GenomeWideCombinableDomains> gwcd_list) |
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static void |
SurfacingUtil.writeProteinListsForAllSpecies(java.io.File output_dir,
java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species,
java.util.List<GenomeWideCombinableDomains> gwcd_list,
double domain_e_cutoff,
java.util.Set<java.lang.String> pos_filter_doms) |
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