- for( final GapContribution stat : stats ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( stat.getId() );
- sb.append( "\t" );
- sb.append( NF_4.format( stat.getValue() ) );
- sb.append( "\t" );
- // sb.append( NF_4.format( stat.median() ) );
- // sb.append( "\t" );
- // sb.append( NF_4.format( stat.getMin() ) );
- // sb.append( "\t" );
- // sb.append( NF_4.format( stat.getMax() ) );
- //sb.append( "\t" );
- System.out.println( sb );
+ // for( final GapContribution stat : stats ) {
+ // final StringBuilder sb = new StringBuilder();
+ // sb.append( stat.getId() );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.getValue() ) );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.median() ) );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.getMin() ) );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.getMax() ) );
+ //sb.append( "\t" );
+ //System.out.println( sb );
+ // }
+ return stats;
+ }
+
+ private static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( int c = from; c <= to; ++c ) {
+ stats.addValue( MsaMethods.calculateIdentityRatio( msa, c ) );