// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
// 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
// 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.
// 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
//
// Contact: phylosoft @ gmail . com
// 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
//
// Contact: phylosoft @ gmail . com
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
for( final GenomeWideCombinableDomains genome : genomes ) {
final String species = genome.getSpecies().getSpeciesId();
if ( high_copy_base_species.contains( species ) ) {
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 ) );
- 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 ) );
- 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 ) ) {
}
html_writer.write( "</td><td>" );
if ( bdcs_per_genome.get( species ).contains( bdc ) && ( copy_means.get( bdc ) > 0 ) ) {
for( final BinaryDomainCombination bdc : all_bdcs ) {
if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
&& ( high_copy_base_values.get( bdc ) >= low_copy_values.get( bdc ) ) ) {
for( final BinaryDomainCombination bdc : all_bdcs ) {
if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
&& ( high_copy_base_values.get( bdc ) >= low_copy_values.get( bdc ) ) ) {
for( final DomainId domain_id : all_domains ) {
if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
&& ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
for( final DomainId domain_id : all_domains ) {
if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
&& ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
- if ( high_copy_target_values.get( domain_id ) >= min_diff
- + ( factor * low_copy_values.get( domain_id ) ) ) {
+ if ( high_copy_target_values.get( domain_id ) >= ( min_diff + ( factor * low_copy_values
+ .get( domain_id ) ) ) ) {
+ 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 ) );
+ 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,
+ -1 );
proteins_file_writer.close();
System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
}
proteins_file_writer.close();
System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
}