public StringBuffer toNewHampshireX( final Phylogeny tree ) throws IOException { setOutputFormt( FORMAT.NHX ); return getOutput( tree ); }
public StringBuffer toPhyloXML( final Phylogeny tree, final int phyloxml_level ) throws IOException { final StringWriter string_writer = new StringWriter(); final Writer writer = new BufferedWriter( string_writer ); setPhyloXmlLevel( phyloxml_level ); setOutputFormt( FORMAT.PHYLO_XML ); writePhyloXmlStart( writer ); writeOutput( writer, tree ); writePhyloXmlEnd( writer ); writer.flush(); writer.close(); return string_writer.getBuffer(); }
private void toPhyloXMLNoPhyloXmlSource( final Writer writer, final Phylogeny tree, final int phyloxml_level ) throws IOException { setPhyloXmlLevel( phyloxml_level ); setOutputFormt( FORMAT.PHYLO_XML ); writeOutput( writer, tree ); }
public StringBuffer toNewHampshire( final Phylogeny tree, final boolean nh_write_distance_to_parent ) throws IOException { setOutputFormt( FORMAT.NH ); setWriteDistanceToParentInNH( nh_write_distance_to_parent ); return getOutput( tree ); }
public StringBuffer toNewHampshire( final Phylogeny tree, final boolean nh_write_distance_to_parent, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException { setOutputFormt( FORMAT.NH ); setNhConversionSupportStyle( svs ); setWriteDistanceToParentInNH( nh_write_distance_to_parent ); return getOutput( tree ); }
public void toPhyloXML( final Writer writer, final Phylogeny tree, final int phyloxml_level ) throws IOException { setPhyloXmlLevel( phyloxml_level ); setOutputFormt( FORMAT.PHYLO_XML ); writePhyloXmlStart( writer ); writeOutput( writer, tree ); writePhyloXmlEnd( writer ); }