path_to_mafft = cla.getOptionValueAsCleanString( PATH_TO_MAFFT_OPTION );
}
if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
path_to_mafft = cla.getOptionValueAsCleanString( PATH_TO_MAFFT_OPTION );
}
if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
}
if ( cla.isOptionSet( STEP_FOR_DIAGNOSTICS_OPTION ) ) {
step_for_diagnostics = cla.getOptionValueAsInt( STEP_FOR_DIAGNOSTICS_OPTION );
}
if ( cla.isOptionSet( STEP_FOR_DIAGNOSTICS_OPTION ) ) {
step_for_diagnostics = cla.getOptionValueAsInt( STEP_FOR_DIAGNOSTICS_OPTION );
}
System.out.println( "Step for diagnostics reports : " + step_for_diagnostics );
System.out.println( "Calculate normalized Shannon Entropy : " + report_entropy );
}
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 );
+ if ( normalize_for_effective_seq_length ) {
+ System.out.println( "Normalize : with individual, effective sequence lenghts" );
+ }
+ else {
+ System.out.println( "Normalize : with MSA length" );
}
Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
}
Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
- System.out.println( "MSA length : " + msa.getLength() );
- System.out.println( "Number of sequences : " + msa.getNumberOfSequences() );
- System.out.println( "Median sequence length : " + NF_1.format( msa_stats.median() ) );
- System.out.println( "Mean sequence length : "
+ System.out.println( "MSA length : " + msa.getLength() );
+ System.out.println( "Number of sequences : " + msa.getNumberOfSequences() );
+ System.out.println( "Median sequence length : " + NF_1.format( msa_stats.median() ) );
+ System.out.println( "Mean sequence length : "
- System.out.println( "Max sequence length : " + ( ( int ) msa_stats.getMax() ) );
- System.out.println( "Min sequence length : " + ( ( int ) msa_stats.getMin() ) );
- System.out.println( "Gap ratio : "
+ System.out.println( "Max sequence length : " + ( ( int ) msa_stats.getMax() ) );
+ System.out.println( "Min sequence length : " + ( ( int ) msa_stats.getMin() ) );
+ System.out.println( "Gap ratio : "
+ "=<decimal> maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" );
System.out.println( " -" + PERFORM_PHYLOGENETIC_INFERENCE
+ " to calculate a simple phylogenetic tree (Kimura distances, NJ)" );
+ "=<decimal> maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" );
System.out.println( " -" + PERFORM_PHYLOGENETIC_INFERENCE
+ " to calculate a simple phylogenetic tree (Kimura distances, NJ)" );