import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
-import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.io.parsers.FastaParser;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
private static enum NDF {
NodeName( "NN" ),
TaxonomyCode( "TC" ),
- TaxonomyCommonName( "CN" ),
+ TaxonomyCommonName( "TN" ),
TaxonomyScientificName( "TS" ),
TaxonomyIdentifier( "TI" ),
TaxonomySynonym( "SY" ),
n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
break;
}
+ case CLADE_NAME:
+ n.setName( name );
+ break;
default: {
throw new IllegalArgumentException( "don't know what to do with " + field );
}
}
}
-
+ public final static PhylogenyNode getFirstExternalNode( final PhylogenyNode node ) {
+ PhylogenyNode n = node;
+ while ( n.isInternal() ) {
+ n = n.getFirstChildNode();
+ }
+ return n;
+ }
+
+ public final static PhylogenyNode getLastExternalNode( final PhylogenyNode node ) {
+ PhylogenyNode n = node;
+ while ( n.isInternal() ) {
+ n = n.getLastChildNode();
+ }
+ return n;
+ }
+
+ public final static boolean isHasCollapsedNodes( final Phylogeny phy ) {
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() && ( n.isCollapse() ) ) {
+ return true;
+ }
+ }
+ return false;
+ }
}