import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
break;
case NH:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( true );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
( ( NHXParser ) parser )
- .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
- .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NHX:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
phylogeny.setRerootable( false );
phylogeny.setRooted( true );
- ForesterUtil.transferInternalNodeNamesToConfidence( phylogeny );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny );
}
if ( client.getProcessingInstructions() != null ) {
WebserviceUtil.processInstructions( client, phylogeny );
}
if ( client.getNodeField() != null ) {
- ForesterUtil.transferNodeNameToField( phylogeny, client.getNodeField() );
+ PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField() );
}
phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
_main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );