+
+ public static void domainsPerProteinsStatistics( final String genome,
+ final List<Protein> protein_list,
+ final DescriptiveStatistics all_genomes_domains_per_potein_stats,
+ final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+ final SortedSet<String> domains_which_are_always_single,
+ final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
+ final SortedSet<String> domains_which_never_single,
+ final Writer writer ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final Protein protein : protein_list ) {
+ final int domains = protein.getNumberOfProteinDomains();
+ //System.out.println( domains );
+ stats.addValue( domains );
+ all_genomes_domains_per_potein_stats.addValue( domains );
+ if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
+ all_genomes_domains_per_potein_histo.put( domains, 1 );
+ }
+ else {
+ all_genomes_domains_per_potein_histo.put( domains,
+ 1 + all_genomes_domains_per_potein_histo.get( domains ) );
+ }
+ if ( domains == 1 ) {
+ final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
+ if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+ if ( domains_which_never_single.contains( domain ) ) {
+ domains_which_never_single.remove( domain );
+ domains_which_are_sometimes_single_sometimes_not.add( domain );
+ }
+ else {
+ domains_which_are_always_single.add( domain );
+ }
+ }
+ }
+ else if ( domains > 1 ) {
+ for( final Domain d : protein.getProteinDomains() ) {
+ final String domain = d.getDomainId().getId();
+ // System.out.println( domain );
+ if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+ if ( domains_which_are_always_single.contains( domain ) ) {
+ domains_which_are_always_single.remove( domain );
+ domains_which_are_sometimes_single_sometimes_not.add( domain );
+ }
+ else {
+ domains_which_never_single.add( domain );
+ }
+ }
+ }
+ }
+ }
+ try {
+ writer.write( genome );
+ writer.write( "\t" );
+ if ( stats.getN() >= 1 ) {
+ writer.write( stats.arithmeticMean() + "" );
+ writer.write( "\t" );
+ if ( stats.getN() >= 2 ) {
+ writer.write( stats.sampleStandardDeviation() + "" );
+ }
+ else {
+ writer.write( "" );
+ }
+ writer.write( "\t" );
+ writer.write( stats.median() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getN() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMin() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMax() + "" );
+ }
+ else {
+ writer.write( "\t" );
+ writer.write( "\t" );
+ writer.write( "\t" );
+ writer.write( "0" );
+ writer.write( "\t" );
+ writer.write( "\t" );
+ }
+ writer.write( "\n" );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }