+ gap_counts[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ gap_counts[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAvgNumberOfGaps()
+ * avg_gaps_counts_factor );
+ }
+ model.addData( gap_counts, "Mean Gap Count" + " (" + minMaxToString( min_avg_gap_count, max_avg_gap_count )
+ + ")" );
+ model.setSeriesLine( "Series " + "Mean Gap Count", true );
+ model.setSeriesMarker( "Series " + "Mean Gap Count", false );
+ if ( _show_msa_qual ) {
+ final double[][] entropy7 = new double[ _msa_props.size() ][ 2 ];
+ for( int i = 0; i < _msa_props.size(); ++i ) {
+ entropy7[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ entropy7[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy7() * ent7_factor );
+ }
+ model.addData( entropy7, "Entropy norm 7" + " (" + minMaxToString( min_ent7, max_ent7 ) + ")" );
+ model.setSeriesLine( "Series " + "Entropy norm 7", true );
+ model.setSeriesMarker( "Series " + "Entropy norm 7", false );
+ //
+ final double[][] entropy21 = new double[ _msa_props.size() ][ 2 ];
+ for( int i = 0; i < _msa_props.size(); ++i ) {
+ entropy21[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ entropy21[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy21() * ent21_factor );
+ }
+ model.addData( entropy21, "Entropy norm 21" + " (" + minMaxToString( min_ent21, max_ent21 ) + ")" );
+ model.setSeriesLine( "Series " + "Entropy norm 21", true );
+ model.setSeriesMarker( "Series " + "Entropy norm 21", false );