public class PairwiseGenomeComparator
extends java.lang.Object
Constructor and Description |
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PairwiseGenomeComparator() |
Modifier and Type | Method and Description |
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java.util.List<DistanceMatrix> |
getDomainDistanceScoresMeans() |
java.util.List<DistanceMatrix> |
getSharedBinaryCombinationsBasedDistances() |
java.util.List<DistanceMatrix> |
getSharedDomainsBasedDistances() |
void |
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,
PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
DomainSimilarity.DomainSimilarityScoring scoring,
java.util.Map<DomainId,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,
boolean display_histograms,
java.io.File out_dir,
boolean write_pairwise_comparisons) |
void |
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) |
public java.util.List<DistanceMatrix> getDomainDistanceScoresMeans()
public java.util.List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances()
public java.util.List<DistanceMatrix> getSharedDomainsBasedDistances()
public void 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, PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option, DomainSimilarity.DomainSimilarityScoring scoring, java.util.Map<DomainId,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, boolean display_histograms, java.io.File out_dir, boolean write_pairwise_comparisons)
public void 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)