+ else if ( av_gap > 0 ) {
+ System.out.println( ": " + av_gap );
+ }
+ else if ( length > 0 ) {
+ System.out.println( ": " + length );
+ }
+ if ( out != null || removed_seqs_out_base != null ) {
+ System.out.println( "Output format: " + ( output_format == MSA_FORMAT.FASTA ? "fasta" : "phylip" ) );
+ }
+ System.out.println( "Step for output and re-aligning) : " + step );
+ System.out.println( "Step for dia: " + step_for_diagnostics );
+ System.out.println( "Step for diagnostics reports: " + report_aln_mean_identity );
+ if ( !norm ) {
+ System.out.println( "Normalize: " + norm );
+ }
+ System.out.println( "Realign: " + realign );
+ if ( realign ) {
+ System.out.println( "MAFFT options: " + mafft_options );
+ }
+ if ( min_length > -1 ) {
+ System.out.println( "Minimal effective sequence length: " + min_length );
+ }
+ if ( gap_ratio > -1 ) {
+ System.out.println( ": " + gap_ratio );
+ }
+ //