int length = -1;
int step = 1;
boolean realign = false;
- boolean norm = true;
+ boolean normalize_for_effective_seq_length = true;
String path_to_mafft = null;
int step_for_diagnostics = 1;
int min_length = -1;
msa = DeleteableMsa.createInstance( FastaParser.parseMsa( is ) );
}
else {
- msa = DeleteableMsa.createInstance( GeneralMsaParser.parse( is ) );
+ msa = DeleteableMsa.createInstance( GeneralMsaParser.parseMsa( is ) );
}
final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa );
if (cla.isOptionSet( INFO_ONLY_OPTION ) ) {
path_to_mafft = cla.getOptionValueAsCleanString( PATH_TO_MAFFT_OPTION );
}
if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
- norm = false;
+ normalize_for_effective_seq_length = false;
}
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 );
- 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" );
}
System.out.println( "Realign with MAFFT : " + realign );
if ( realign ) {
if ( removed_seqs_out_base != null ) {
mc.setRemovedSeqsOutBase( removed_seqs_out_base );
}
- mc.setNorm( norm );
+ mc.setNorm( normalize_for_effective_seq_length );
mc.setRealign( realign );
if ( realign ) {
mc.setPathToMafft( path_to_mafft );
msa_props = mc.removeViaLength( length );
}
else {
- msa_props = mc.chart( step, realign, norm );
+ msa_props = mc.chart( step, realign, normalize_for_effective_seq_length );
}
Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
System.out.println();
+ "=<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)" );
+ System.out.println( " -" + DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION
+ + " to normalize gap-contributions with MSA length, instead of individual effective sequence lenghts" );
+
System.out.println();
System.out.println();
System.out.println();