+ System.out.println( "Number of worst offenders to remove : " + worst_remove );
+ }
+ if ( av_gap > 0 ) {
+ System.out.println( "Target gap-ratio : " + av_gap );
+ }
+ if ( length > 0 ) {
+ System.out.println( "Target MSA length : " + length );
+ }
+ if ( min_length > 1 ) {
+ System.out.println( "Minimal effective sequence length : " + min_length );
+ }
+ if ( gap_ratio > -1 ) {
+ System.out.println( "Maximum allowed gap ratio per column : " + gap_ratio );
+ }
+ 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 ( normalize_for_effective_seq_length ) {
+ System.out.println( "Normalize : with individual, effective sequence lenghts" );
+ }
+ else {
+ System.out.println( "Normalize : with MSA length" );
+ }
+ 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 );
+ }
+ System.out.println();
+ final int initial_number_of_seqs = msa.getNumberOfSequences();
+ List<MsaProperties> msa_props = null;
+ final MsaCompactor mc = new MsaCompactor( msa );
+ mc.setInfileName( in.getName() );
+ if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) || ( min_length != -1 ) ) {
+ mc.setOutputFormat( output_format );
+ mc.setOutFileBase( out );