}
final List<Set<String>> features_per_genome_list = new ArrayList<Set<String>>();
boolean first = true;
- for( final PhylogenyNode external_desc : external_descs ) {
- final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
- if ( node.isInternal() ) {
- if ( first ) {
- first = false;
- }
- else {
- out.write( ", " );
+ if ( level >= 1 ) {
+ ////////////
+ ////////////
+ final int node_level = PhylogenyMethods.calculateLevel( node );
+ if ( node_level >= level ) {
+ final List<PhylogenyNode> given_level_descs = PhylogenyMethods
+ .getAllDescendantsOfGivenLevel( node, level );
+ for( final PhylogenyNode given_level_desc : given_level_descs ) {
+ final String spec_name = given_level_desc.getNodeData().isHasTaxonomy()
+ ? given_level_desc.getNodeData().getTaxonomy().getScientificName() : given_level_desc.getName();
}
- out.write( code );
}
- final List<Protein> proteins_per_species = protein_lists_per_species.get( new BasicSpecies( code ) );
- final int node_level = PhylogenyMethods.calculateLevel( node );
- final List<Protein> proteins_per_quasi_species = protein_lists_per_species
- .get( new BasicSpecies( code ) );
- if ( proteins_per_species != null ) {
- final SortedSet<String> features_per_genome = new TreeSet<String>();
- for( final Protein protein : proteins_per_species ) {
- if ( use_domain_architectures ) {
- final String da = protein.toDomainArchitectureString( separator, ie_cutoff );
- features_per_genome.add( da );
+ ///////////
+ ///////////
+ }
+ else {
+ for( final PhylogenyNode external_desc : external_descs ) {
+ final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
+ if ( node.isInternal() ) {
+ if ( first ) {
+ first = false;
}
else {
- List<Domain> domains = protein.getProteinDomains();
- for( final Domain domain : domains ) {
- if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
- features_per_genome.add( domain.getDomainId() );
+ out.write( ", " );
+ }
+ out.write( code );
+ }
+ final List<Protein> proteins_per_species = protein_lists_per_species
+ .get( new BasicSpecies( code ) );
+ if ( proteins_per_species != null ) {
+ final SortedSet<String> features_per_genome = new TreeSet<String>();
+ for( final Protein protein : proteins_per_species ) {
+ if ( use_domain_architectures ) {
+ final String da = protein.toDomainArchitectureString( separator, ie_cutoff );
+ features_per_genome.add( da );
+ }
+ else {
+ List<Domain> domains = protein.getProteinDomains();
+ for( final Domain domain : domains ) {
+ if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
+ features_per_genome.add( domain.getDomainId() );
+ }
}
}
}
+ if ( features_per_genome.size() > 0 ) {
+ features_per_genome_list.add( features_per_genome );
+ }
}
- if ( features_per_genome.size() > 0 ) {
- features_per_genome_list.add( features_per_genome );
- }
- }
- } // for( final PhylogenyNode external_desc : external_descs )
+ } // for( final PhylogenyNode external_desc : external_descs )
+ } // else
if ( features_per_genome_list.size() > 0 ) {
SortedSet<String> intersection = calcIntersection( features_per_genome_list );
out.write( "\t" + intersection.size() + "\t" );