+ if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
+ System.out.print( "Output format : " );
+ if ( output_format == MSA_FORMAT.FASTA ) {
+ System.out.println( "fasta" );
+ }
+ else if ( output_format == MSA_FORMAT.PHYLIP ) {
+ System.out.println( "phylip" );
+ }
+ else if ( output_format == MSA_FORMAT.NEXUS ) {
+ System.out.println( "nexus" );
+ }
+ }
+ if ( min_length == -1 ) {
+ if ( chart_only && !realign ) {
+ System.out.println( "Step for output and re-aligning : n/a" );
+ }
+ else {
+ if ( chart_only ) {
+ System.out.println( "Step for re-aligning : " + step );
+ }
+ else {
+ System.out.println( "Step for output and re-aligning : " + step );
+ }
+ }
+ System.out.println( "Step for diagnostics reports : " + step_for_diagnostics );
+ System.out.println( "Calculate normalized Shannon Entropy : " + report_entropy );
+ if ( !norm ) {
+ System.out.println( "Normalize : " + norm );
+ }
+ System.out.println( "Realign with MAFFT : " + realign );
+ if ( realign ) {
+ System.out.println( "MAFFT options : " + mafft_options );
+ }
+ System.out.println( "Simple tree (Kimura distances, NJ) : " + perform_phylogenetic_inference );
+ }