- model.addData( seqs_gaps, "Gaps" );
- model.setSeriesLine( "Series " + "Gaps", true );
- model.setSeriesMarker( "Series " + "Gaps", false );
- final double[][] seqs_identity = new double[ _msa_props.size() ][ 2 ];
- for( int i = 0; i < _msa_props.size(); ++i ) {
- seqs_identity[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
- seqs_identity[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAverageIdentityRatio() * 100 );
+ model.addData( seqs_gaps, "Gap ratio" );
+ model.setSeriesLine( "Series " + "Gap ratio", true );
+ model.setSeriesMarker( "Series " + "Gap ratio", false );
+ if ( _show_msa_qual ) {
+ final double[][] seqs_identity = new double[ _msa_props.size() ][ 2 ];
+ for( int i = 0; i < _msa_props.size(); ++i ) {
+ seqs_identity[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ seqs_identity[ i ][ 1 ] = ForesterUtil
+ .roundToInt( _msa_props.get( i ).getAverageIdentityRatio() * 200 );
+ }
+ model.addData( seqs_identity, "mean MSA column identity" );
+ model.setSeriesLine( "Series " + "mean MSA column identity", true );
+ model.setSeriesMarker( "Series " + "mean MSA column identity", false );