+ mc.setPeformPhylogenticInference( perform_phylogenetic_inference );
+ if ( removed_seqs_out_base != null ) {
+ mc.setRemovedSeqsOutBase( removed_seqs_out_base );
+ }
+ mc.setNorm( norm );
+ mc.setRealign( realign );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ mc.setMafftOptions( mafft_options );
+ }
+ mc.setStep( step );
+ mc.setStepForDiagnostics( step_for_diagnostics );
+ mc.setCalculateNormalizedShannonEntropy( report_entropy );
+ if ( worst_remove > 0 ) {
+ msa_props = mc.removeWorstOffenders( worst_remove );
+ }
+ else if ( av_gap > 0 ) {
+ msa_props = mc.removeViaGapAverage( av_gap );
+ }
+ else if ( length > 0 ) {
+ msa_props = mc.removeViaLength( length );
+ }
+ else {
+ msa_props = mc.chart( step, realign, norm );
+ }
+ Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );