2 package org.forester.archaeopteryx;
6 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
7 import org.forester.io.writers.PhylogenyWriter;
8 import org.forester.phylogeny.Phylogeny;
9 import org.forester.phylogeny.PhylogenyNode;
10 import org.forester.phylogeny.data.Taxonomy;
11 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
12 import org.forester.phylogeny.factories.PhylogenyFactory;
13 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
14 import org.forester.util.CommandLineArguments;
16 public class simple_node_processor {
18 private final static String BASE = "b_";
20 public static void main( final String args[] ) {
24 CommandLineArguments cla = null;
25 cla = new CommandLineArguments( args );
26 in = cla.getFile( 0 );
27 out = cla.getFile( 1 );
29 System.out.println( out + " already exists" );
32 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
33 final PhyloXmlParser xml_parser = new PhyloXmlParser();
34 final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
35 final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
36 final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
38 while ( it.hasNext() ) {
39 final PhylogenyNode node = it.next();
40 processNode( node, i );
43 final PhylogenyWriter writer = new PhylogenyWriter();
44 writer.toPhyloXML( out, phylogeny_0, 0 );
46 catch ( final Exception e ) {
47 System.out.println( e.getLocalizedMessage() );
53 // private static void processNode( final PhylogenyNode node, final int i ) {
54 // node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
55 // if ( !node.isExternal() ) {
56 // if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
57 // node.setName( BASE + i );
61 private static void processNode( final PhylogenyNode node, final int i ) {
62 //if ( node.isExternal() ) {
63 // final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
64 // final String s = node.getNodeData().getTaxonomy().getScientificName();
65 // System.out.println( s + "\t" + c );
67 // if ( !node.isExternal() ) {
68 // if ( !node.getNodeData().isHasTaxonomy() ) {
69 // if ( !ForesterUtil.isEmpty( node.getName() ) ) {
70 // if ( ( node.getName().indexOf( "_" ) < 0 ) && ( node.getName().indexOf( "&" ) < 0 )
71 // && ( node.getName().indexOf( " " ) < 0 ) ) {
72 // Taxonomy t = new Taxonomy();
73 // t.setScientificName( node.getName() );
74 // node.getNodeData().addTaxonomy( t );
75 // node.setName( "" );
80 if ( node.isExternal() ) {
81 if ( node.getNodeData().isHasTaxonomy() ) {
82 final Taxonomy t = node.getNodeData().getTaxonomy();
83 t.setIdentifier( null );
84 //if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) && t.getTaxonomyCode().length() == 5 ) {
85 // if ( node.getName().equalsIgnoreCase( t.getTaxonomyCode() ) ) {
86 // node.setName( "" );