- if ( ( !cla.isOptionSet( LENGTH_OPTION ) && !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) && !cla
- .isOptionSet( AV_GAPINESS_OPTION ) ) && ( ( out != null ) || ( removed_seqs_out_base != null ) ) ) {
- ForesterUtil.fatalError( PRG_NAME,
- "chart only, no outfile(s) produced (no need to indicate output file(s))" );
+ else if ( cla.isOptionSet( MAFFT_OPTIONS ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "no need to indicate MAFFT options without realigning" );
+ }
+ if ( cla.isOptionSet( PERFORM_PHYLOGENETIC_INFERENCE ) ) {
+ perform_phylogenetic_inference = true;
+ }
+ if ( chart_only ) {
+ if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
+ ForesterUtil
+ .fatalError( PRG_NAME,
+ "chart only, no outfile(s) produced, thus no need to indicate output file(s)" );
+ }
+ if ( !realign && cla.isOptionSet( STEP_OPTION ) ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "chart only, no re-aligning, thus no need to use step for output and re-aligning; use -"
+ + STEP_FOR_DIAGNOSTICS_OPTION + " instead" );
+ }
+ }
+ if ( perform_phylogenetic_inference ) {
+ if ( step_for_diagnostics != 1 ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "step for diagnostics reports needs to be set to 1 for tree calculation" );
+ }