if ( high_copy_base_species.contains( high_copy_target_species )
|| low_copy_species.contains( high_copy_target_species ) ) {
throw new IllegalArgumentException( "species [" + high_copy_target_species
- + "] appears in other list as well" );
+ + "] appears in other list as well" );
}
if ( min_diff < 0 ) {
throw new IllegalArgumentException( "attempt to use negative addition [" + min_diff + "]" );
writeGoIdsToFile( passing_gos_writer, go_ids_of_passing_domains );
}
- //FIXME really needs to be tested!
+ //FIXME really needs to be tested!
private static void addCounts( final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
final BinaryDomainCombination dc,
final GenomeWideCombinableDomains genome,
private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) {
final GoId go_id = go_term.getGoId();
sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
- + "</a>" );
+ + "</a>" );
sb.append( ":" );
sb.append( go_term.getName() );
sb.append( " [" );
final SortedMap<BinaryDomainCombination, Double> low_copy_values,
final SortedSet<BinaryDomainCombination> all_bdcs,
final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome )
- throws IOException {
+ throws IOException {
int counter = 0;
int total_absense_counter = 0;
int not_total_absense_counter = 0;
}
++counter;
html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + bdc.getId0()
- + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
- + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
+ + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
+ + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
html_writer.write( "</td><td>" );
html_writer.write( "<table>" );
for( final GenomeWideCombinableDomains genome : genomes ) {
bdcs_per_genome,
species,
html_writer,
- "#0000FF" );
+ "#0000FF" );
html_writer.write( "</tr>" );
}
else if ( low_copy_species.contains( species ) ) {
bdcs_per_genome,
species,
html_writer,
- "#A0A0A0" );
+ "#A0A0A0" );
html_writer.write( "</tr>" );
}
else if ( high_copy_base_species.contains( species ) ) {
bdcs_per_genome,
species,
html_writer,
- "#404040" );
+ "#404040" );
html_writer.write( "</tr>" );
}
}
final SortedSet<String> all_domains,
final SortedSet<GoId> go_ids_of_passing_domains,
final SortedMap<Species, List<Protein>> protein_lists_per_species )
- throws IOException {
+ throws IOException {
int counter = 0;
int total_absense_counter = 0;
int not_total_absense_counter = 0;
plain_writer.write( domain_id );
plain_writer.write( SurfacingConstants.NL );
html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id
- + "\">" + domain_id + "</a></td><td>" );
+ + "\">" + domain_id + "</a></td><td>" );
html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map )
- .toString() );
+ .toString() );
html_writer.write( "</td><td>" );
html_writer.write( "<table>" );
for( final GenomeWideCombinableDomains genome : genomes ) {
species,
plain_writer,
html_writer,
- "#0000FF" );
+ "#0000FF" );
html_writer.write( "</tr>" );
}
else if ( low_copy_species.contains( species ) ) {
species,
plain_writer,
html_writer,
- "#A0A0A0" );
+ "#A0A0A0" );
html_writer.write( "</tr>" );
}
else if ( high_copy_base_species.contains( species ) ) {
species,
plain_writer,
html_writer,
- "#404040" );
+ "#404040" );
html_writer.write( "</tr>" );
}
}
final SortedMap<Species, List<Protein>> protein_lists_per_species,
final String domain_id ) throws IOException {
final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR
- + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
+ + 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,