Package org.forester.surfacing
Class PairwiseGenomeComparator
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- org.forester.surfacing.PairwiseGenomeComparator
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public class PairwiseGenomeComparator extends java.lang.Object
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Constructor Summary
Constructors Constructor Description PairwiseGenomeComparator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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, 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)
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)
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Method Detail
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getDomainDistanceScoresMeans
public java.util.List<DistanceMatrix> getDomainDistanceScoresMeans()
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getSharedBinaryCombinationsBasedDistances
public java.util.List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances()
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getSharedDomainsBasedDistances
public java.util.List<DistanceMatrix> getSharedDomainsBasedDistances()
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performPairwiseComparisons
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, 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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performPairwiseComparisonsJacknifed
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)
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