org.forester.surfacing
Class DomainCountsDifferenceUtil

java.lang.Object
  extended by org.forester.surfacing.DomainCountsDifferenceUtil

public final class DomainCountsDifferenceUtil
extends Object


Nested Class Summary
static class DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
           
 
Constructor Summary
DomainCountsDifferenceUtil()
           
 
Method Summary
static void calculateCopyNumberDifferences(List<GenomeWideCombinableDomains> genomes, SortedMap<Species,List<Protein>> protein_lists_per_species, List<String> high_copy_base_species, List<String> high_copy_target_species, List<String> low_copy_species, int min_diff, Double factor, File plain_output_dom, File html_output_dom, File html_output_dc, Map<DomainId,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, File all_domains_go_ids_out_dom, File passing_domains_go_ids_out_dom, File proteins_file_base)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DomainCountsDifferenceUtil

public DomainCountsDifferenceUtil()
Method Detail

calculateCopyNumberDifferences

public static void calculateCopyNumberDifferences(List<GenomeWideCombinableDomains> genomes,
                                                  SortedMap<Species,List<Protein>> protein_lists_per_species,
                                                  List<String> high_copy_base_species,
                                                  List<String> high_copy_target_species,
                                                  List<String> low_copy_species,
                                                  int min_diff,
                                                  Double factor,
                                                  File plain_output_dom,
                                                  File html_output_dom,
                                                  File html_output_dc,
                                                  Map<DomainId,List<GoId>> domain_id_to_go_ids_map,
                                                  Map<GoId,GoTerm> go_id_to_term_map,
                                                  File all_domains_go_ids_out_dom,
                                                  File passing_domains_go_ids_out_dom,
                                                  File proteins_file_base)
                                           throws IOException
Throws:
IOException