&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
if ( extr_taxonomy_pf_only ) {
( ( NHXParser ) parser )
- .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
replace_underscores = false;
}
else if ( extr_taxonomy ) {
( ( NHXParser ) parser )
- .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
replace_underscores = false;
}
}
System.out.println( "Usage:" );
System.out.println();
System.out
- .println( PRG_NAME
- + " -"
- + FIELD_OPTION
- + "=<field option> [options] <infile in New Hamphshire, NHX, Nexus, ToL XML, or phyloXML format> <outfile>" );
+ .println( PRG_NAME
+ + " -"
+ + FIELD_OPTION
+ + "=<field option> [options] <infile in New Hamphshire, NHX, Nexus, ToL XML, or phyloXML format> <outfile>" );
System.out.println();
System.out.println( " field options: " );
System.out.println();
System.out.println( " " + FIELD_SEQUENCE_SYMBOL + ": transfer name to sequence symbol" );
System.out.println( " " + FIELD_DUMMY + ": to convert NHX formatted trees to phyloXML" );
System.out.println( " " + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1
- + ": transfer/split name to taxonomy uniprot identifier" );
+ + ": transfer/split name to taxonomy uniprot identifier" );
System.out.println( " (split at underscore if \"id_name\" pattern, e.g. \"817_SusD\")" );
System.out.println( " " + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_2
- + ": transfer/split name to taxonomy uniprot identifier" );
+ + ": transfer/split name to taxonomy uniprot identifier" );
System.out.println( " (split at underscore if \"name_id\" pattern, e.g. \"SusD_817\")" );
System.out.println();
System.out.println( " options: " );
System.out.println( " -" + INTERNAL_NAMES_ARE_BOOT_SUPPPORT
- + " : internal names in NH or NHX tree are bootstrap support values" );
+ + " : internal names in NH or NHX tree are bootstrap support values" );
System.out.println( " -" + REPLACE_UNDER_SCORES + " : replace all underscores with spaces" );
System.out.println( " -" + MIDPOINT_REROOT + " : midpoint reroot" );
System.out.println( " -" + ORDER_SUBTREES + " : order subtrees" );
System.out
- .println( " -"
- + EXTRACT_TAXONOMY
- + " : extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: "
- + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" );
+ .println( " -"
+ + EXTRACT_TAXONOMY
+ + " : extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: "
+ + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" );
System.out
- .println( " -"
- + EXTRACT_TAXONOMY_PF
- + " : extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: "
- + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" );
+ .println( " -"
+ + EXTRACT_TAXONOMY_PF
+ + " : extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: "
+ + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" );
System.out.println( " -" + NO_TREE_LEVEL_INDENDATION + " : no tree level indendation in phyloXML output" );
System.out.println( " -" + IGNORE_QUOTES + ": ignore quotes and whitespace (e.g. \"a b\" becomes ab)" );
System.out.println();