private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
private boolean _editable = true;
private boolean _nh_parsing_replace_underscores = false;
- private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
private boolean _internal_number_are_confidence_for_nh_parsing = false;
private boolean _display_sequence_relations = false;
private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
}
boolean isAntialiasScreen() {
- // if ( AptxUtil.isMac() ) {
- // Apple Macintosh graphics are slow, turn off anti-alias.
- // return false;
- //}
+ if ( ForesterUtil.isMac() ) {
+ //Apple Macintosh graphics are slow, turn off anti-alias.
+ return false;
+ }
return _antialias_screen;
}
if ( s.equalsIgnoreCase( "no" ) ) {
setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
}
- else if ( s.equalsIgnoreCase( "yes" ) ) {
+ else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
}
- else if ( s.equalsIgnoreCase( "pfam" ) ) {
+ else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
}
+ else if ( s.equalsIgnoreCase( "aggressive" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
}
if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
ForesterUtil