+
+ public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException,
+ PhyloXmlDataFormatException {
+ return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
+ }
+
+ public static PhylogenyNode createInstanceFromNhxString( final String nhx,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
+ throws NHXFormatException, PhyloXmlDataFormatException {
+ return new PhylogenyNode( nhx, taxonomy_extraction, false );
+ }
+
+ public static PhylogenyNode createInstanceFromNhxString( final String nhx,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean replace_underscores )
+ throws NHXFormatException, PhyloXmlDataFormatException {
+ return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
+ }
+
+ private PhylogenyNode( final String nhx,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException {
+ // init();
+ NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );
+ setId( PhylogenyNode.getNodeCount() );
+ PhylogenyNode.increaseNodeCount();
+ setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
+ }