final static private String OUTPUT_REMOVED_SEQS_OPTION = "ro";
final static private String MAFFT_OPTIONS = "mo";
final static private String PERFORM_PHYLOGENETIC_INFERENCE = "t";
- //
+ //
final static private String PATH_TO_MAFFT_OPTION = "mafft";
final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
final static private String PRG_NAME = "msa_compactor";
}
if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION );
- if ( ( worst_remove < 1 ) || ( worst_remove >= msa.getNumberOfSequences() - 1 ) ) {
+ if ( ( worst_remove < 1 ) || ( worst_remove >= ( msa.getNumberOfSequences() - 1 ) ) ) {
ForesterUtil.fatalError( PRG_NAME, "number of worst offender sequences to remove is out of range: "
+ worst_remove );
}
if ( length >= msa.getLength() ) {
ForesterUtil.fatalError( PRG_NAME,
"target length is out of range [longer than MSA (" + msa.getLength()
- + ")]: " + length );
+ + ")]: " + length );
}
else if ( length < initial_msa_stats.getMin() ) {
ForesterUtil.fatalError( PRG_NAME,
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)" );
+ .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,
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" );
+ "step for diagnostics reports needs to be set to 1 for tree calculation" );
}
}
ForesterUtil.printProgramInformation( PRG_NAME,
else {
if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION
- + "=<path to MAFFT>\" option" );
+ + "=<path to MAFFT>\" option" );
}
else {
ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" );
System.out.println( " options: " );
System.out.println();
System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION
- + "=<integer> number of worst offender sequences to remove" );
+ + "=<integer> number of worst offender sequences to remove" );
System.out.println( " -" + LENGTH_OPTION + "=<integer> target MSA length" );
System.out.println( " -" + AV_GAPINESS_OPTION + "=<decimal> target gap-ratio (0.0-1.0)" );
System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment );
System.out.println( " -" + MAFFT_OPTIONS + "=<string> options for MAFFT (default: --auto)" );
System.out.println( " -" + STEP_OPTION + "=<integer> step for output and re-aligning (default: 1)" );
System.out.println( " -" + STEP_FOR_DIAGNOSTICS_OPTION
- + "=<integer> step for diagnostics reports (default: 1)" );
+ + "=<integer> step for diagnostics reports (default: 1)" );
System.out.println( " -" + REPORT_ENTROPY
- + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" );
+ + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" );
System.out.println( " -" + OUTPUT_FORMAT_OPTION
- + "=<f|p|n> format for output alignments: f for fasta (default), p for phylip, or n for nexus" );
+ + "=<f|p|n> format for output alignments: f for fasta (default), p for phylip, or n for nexus" );
System.out.println( " -" + OUTPUT_REMOVED_SEQS_OPTION + "=<file> to output the removed sequences" );
System.out.println( " -" + MIN_LENGTH_OPTION
- + "=<integer> minimal effecive sequence length (for deleting of shorter sequences)" );
+ + "=<integer> minimal effecive sequence length (for deleting of shorter sequences)" );
System.out.println( " -" + GAP_RATIO_LENGTH_OPTION
- + "=<decimal> maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" );
+ + "=<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)" );
+ + " to calculate a simple phylogenetic tree (Kimura distances, NJ)" );
System.out.println();
System.out.println();
System.out.println();