org.forester.surfacing
Class DomainCountsDifferenceUtil

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

public final class DomainCountsDifferenceUtil
extends java.lang.Object

Nested Class Summary

static class

DomainCountsDifferenceUtil.COPY_CALCULATION_MODE

Constructor Summary

DomainCountsDifferenceUtil()

Method Summary

static void

calculateCopyNumberDifferences(java.util.List<GenomeWideCombinableDomains> genomes, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.List<java.lang.String> high_copy_base_species, java.util.List<java.lang.String> high_copy_target_species, java.util.List<java.lang.String> low_copy_species, int min_diff, java.lang.Double factor, java.io.File plain_output_dom, java.io.File html_output_dom, java.io.File html_output_dc, java.util.Map<DomainId,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, java.io.File all_domains_go_ids_out_dom, java.io.File passing_domains_go_ids_out_dom, java.io.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(java.util.List<GenomeWideCombinableDomains> genomes,
                                                  java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species,
                                                  java.util.List<java.lang.String> high_copy_base_species,
                                                  java.util.List<java.lang.String> high_copy_target_species,
                                                  java.util.List<java.lang.String> low_copy_species,
                                                  int min_diff,
                                                  java.lang.Double factor,
                                                  java.io.File plain_output_dom,
                                                  java.io.File html_output_dom,
                                                  java.io.File html_output_dc,
                                                  java.util.Map<DomainId,java.util.List<GoId>> domain_id_to_go_ids_map,
                                                  java.util.Map<GoId,GoTerm> go_id_to_term_map,
                                                  java.io.File all_domains_go_ids_out_dom,
                                                  java.io.File passing_domains_go_ids_out_dom,
                                                  java.io.File proteins_file_base)
                                           throws java.io.IOException

Throws:

java.io.IOException