org.forester.surfacing

Class PairwiseGenomeComparator

java.lang.Object

org.forester.surfacing.PairwiseGenomeComparator

public class PairwiseGenomeComparator
extends Object

Constructor Summary

Constructors

Constructor and Description
PairwiseGenomeComparator()

Method Summary

Modifier and Type	Method and Description
List<DistanceMatrix>	getDomainDistanceScoresMeans()
List<DistanceMatrix>	getSharedBinaryCombinationsBasedDistances()
List<DistanceMatrix>	getSharedDomainsBasedDistances()
void	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)
void	performPairwiseComparisonsJacknifed(Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, boolean verbose, int number_of_resamplings, double jacknife_ratio, long random_seed)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PairwiseGenomeComparator

public PairwiseGenomeComparator()

Method Detail

getDomainDistanceScoresMeans

public List<DistanceMatrix> getDomainDistanceScoresMeans()

getSharedBinaryCombinationsBasedDistances

public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances()

getSharedDomainsBasedDistances

public List<DistanceMatrix> getSharedDomainsBasedDistances()

performPairwiseComparisons

public void 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)

performPairwiseComparisonsJacknifed

public void performPairwiseComparisonsJacknifed(Species[] species,
                                                int number_of_genomes,
                                                List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
                                                boolean verbose,
                                                int number_of_resamplings,
                                                double jacknife_ratio,
                                                long random_seed)