+ 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 );
+ }
+ //
+ if ( worst_remove > 0 ) {
+ MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
+ }
+ else if ( av_gap > 0 ) {
+ MsaCompactor.reduceGapAverage( msa, av_gap, step, realign, norm, path_to_mafft, out );
+ }
+ else if ( length > 0 ) {
+ // TODO if < shortest seq -> error
+ MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
+ }
+ else {
+ MsaCompactor.chart( msa, step, realign, norm, path_to_mafft );