}
else {
ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
- + "\" option: \"" + field_str + "\"" );
+ + "\" option: \"" + field_str + "\"" );
}
}
}
}
catch ( final Exception e ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
- + "] [" + e.getMessage() + "]" );
+ + "] [" + e.getMessage() + "]" );
}
Map<String, String> map = null;
if ( !advanced_table ) {
if ( ( phylogenies.length > 1 )
&& ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME,
- "attempt to set same name or id on more than one phylogeny" );
+ "attempt to set same name or id on more than one phylogeny" );
}
if ( !ForesterUtil.isEmpty( tree_name ) ) {
phylogenies[ 0 ].setName( tree_name );
}
if ( ForesterUtil.isEmpty( seqs ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
- + "] is devoid of fasta-formatted sequences" );
+ + "] is devoid of fasta-formatted sequences" );
}
final Map<String, String> map = new HashMap<String, String>();
for( final MolecularSequence seq : seqs ) {
if ( ForesterUtil.isEmpty( seq.getIdentifier() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
- + "] contains sequence with empty identifier" );
+ + "] contains sequence with empty identifier" );
}
if ( map.containsKey( seq.getIdentifier() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "sequence identifier [" + seq.getIdentifier()
- + "] is not unique" );
+ + "] is not unique" );
}
if ( seq.getLength() < 1 ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "sequence [" + seq.getIdentifier() + "] is empty" );
System.out.println();
System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
System.out.println( " " + SEQUENCE_ANNOTATION_DESC
- + " : sequence annotation description" );
+ + " : sequence annotation description" );
System.out.println( " " + DS_FILED + " : domain structure" );
System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
- + ": taxonomy scientific name" );
+ + ": taxonomy scientific name" );
System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
System.out.println( " " + MOL_SEQ + " : molecular sequence" );
System.out.println( " -k=<n> : key column in mapping table (0 based)," );
System.out.println( " -v=<n> : value column in mapping table (0 based)," );
System.out.println( " data which with to decorate - default is 1" );
System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
- + " : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
+ + " : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION
- + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
+ + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
System.out.println( " -s=<c> : column separator in mapping file, default is tab" );
System.out.println( " -c : cut name after first space (only for -f=n)" );
System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
- + " : trim node name to be replaced after tilde" );
+ + " : trim node name to be replaced after tilde" );
System.out.println( " -" + decorator.MIDPOINT_ROOT_OPTION + " : to midpoint-root the tree" );
System.out.println( " -" + decorator.ORDER_TREE_OPTION + " : to order tree branches" );
System.out.println( " -" + decorator.VERBOSE_OPTION + " : verbose" );