import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
+import org.forester.phylogeny.Phylogeny;
import org.forester.species.Species;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.util.DescriptiveStatistics;
private List<DistanceMatrix> _shared_domains_based_distances;
private List<DistanceMatrix> _shared_binary_combinations_based_distances;
- //private List<HistogramData> _histogram_datas;
public PairwiseGenomeComparator() {
init();
}
return _domain_distance_scores_means;
}
- //public List<HistogramData> getHistogramDatas() {
- // return _histogram_datas;
- //}
public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
return _shared_binary_combinations_based_distances;
}
}
private void init() {
- //_histogram_datas = new ArrayList<HistogramData>();
_domain_distance_scores_means = new ArrayList<DistanceMatrix>();
_shared_domains_based_distances = new ArrayList<DistanceMatrix>();
_shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
final String command_line_prg_name,
final File out_dir,
final boolean write_pairwise_comparisons,
- final Map<String, Integer> tax_code_to_id_map ) {
+ final Map<String, Integer> tax_code_to_id_map,
+ final boolean calc_similarity_scores,
+ final Phylogeny phy ) {
init();
final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
}
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
sort_by_species_count_first,
- true );
+ true,
+ calc_similarity_scores );
final SortedSet<DomainSimilarity> similarities = calc
.calculateSimilarities( pw_calc,
genome_pair,
}
break;
}
- DescriptiveStatistics pw_stats = null;
if ( write_pairwise_comparisons ) {
try {
final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
: out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
- pw_stats = SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
- new StringBuilder( species_i + "-"
- + species_j ),
- writer,
- null,
- similarities,
- true,
- null,
- domain_similarity_print_option,
- scoring,
- false,
- tax_code_to_id_map,
- false );
+ SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
+ new StringBuilder( species_i + "-" + species_j ),
+ null,
+ writer,
+ null,
+ similarities,
+ true,
+ null,
+ domain_similarity_print_option,
+ scoring,
+ false,
+ tax_code_to_id_map,
+ phy );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
+ pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
}
}
- if ( pw_stats != null ) {
- if ( pw_stats.getMin() >= pw_stats.getMax() ) {
- ForesterUtil
- .printWarningMessage( command_line_prg_name, "for [" + species_i + "-" + species_j
- + "] score minimum is [" + pw_stats.getMin() + "] while score maximum is ["
- + pw_stats.getMax()
- + "], possibly indicating that a genome is compared to itself" );
- }
- }
}
}
getDomainDistanceScoresMeans().add( domain_distance_scores_means );