// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
break;
case NH:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( true );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
- ( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
- ( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NHX:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;