org.forester.surfacing
Class PairwiseGenomeComparator
java.lang.Object
org.forester.surfacing.PairwiseGenomeComparator
public class PairwiseGenomeComparator
- extends Object
Method Summary |
List<DistanceMatrix> |
getDomainDistanceScoresMeans()
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List<DistanceMatrix> |
getSharedBinaryCombinationsBasedDistances()
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List<DistanceMatrix> |
getSharedDomainsBasedDistances()
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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,
PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
DomainSimilarity.DomainSimilarityScoring scoring,
Map<DomainId,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,
boolean display_histograms,
File out_dir,
boolean write_pairwise_comparisons)
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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)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PairwiseGenomeComparator
public PairwiseGenomeComparator()
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,
PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
DomainSimilarity.DomainSimilarityScoring scoring,
Map<DomainId,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,
boolean display_histograms,
File out_dir,
boolean write_pairwise_comparisons)
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)