// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import java.util.TreeMap;
import java.util.TreeSet;
+import org.forester.application.surfacing;
import org.forester.go.GoId;
import org.forester.go.GoTerm;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.DomainId;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
}
if ( bdc.contains( dc )
&& ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
- final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc
- .getId1() );
+ final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains()
+ .get( dc.getId1() );
copy_counts.get( dc ).add( count );
}
else {
for( final GenomeWideCombinableDomains genome : genomes ) {
final String species = genome.getSpecies().getSpeciesId();
if ( high_copy_base_species.contains( species ) ) {
- DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc, dc, genome, bdcs_per_genome
- .get( species ) );
+ DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc,
+ dc,
+ genome,
+ bdcs_per_genome.get( species ) );
}
if ( high_copy_target_species.contains( species ) ) {
- DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc, dc, genome, bdcs_per_genome
- .get( species ) );
+ DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc,
+ dc,
+ genome,
+ bdcs_per_genome.get( species ) );
}
if ( low_copy_species.contains( species ) ) {
- DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc, dc, genome, bdcs_per_genome
- .get( species ) );
+ DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc,
+ dc,
+ genome,
+ bdcs_per_genome.get( species ) );
}
}
}
}
html_writer.write( "</td><td>" );
if ( bdcs_per_genome.get( species ).contains( bdc ) && ( copy_means.get( bdc ) > 0 ) ) {
- final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains().get( bdc
- .getId1() );
+ final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains()
+ .get( bdc.getId1() );
html_writer.write( count + "" );
}
else {
+ domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
- SurfacingUtil.extractProteinNames( protein_lists_per_species, domain_id, proteins_file_writer, "\t" );
+ SurfacingUtil.extractProteinNames( protein_lists_per_species,
+ domain_id,
+ proteins_file_writer,
+ "\t",
+ surfacing.LIMIT_SPEC_FOR_PROT_EX );
proteins_file_writer.close();
System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
}