From e938eeede696247b82e988dff7f94a18acc5da60 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 25 Oct 2013 01:03:03 +0000
Subject: [PATCH] moved

---
 .../application/simple_node_processor.java         |   99 --------------------
 1 file changed, 99 deletions(-)
 delete mode 100644 forester/java/src/org/forester/application/simple_node_processor.java

diff --git a/forester/java/src/org/forester/application/simple_node_processor.java b/forester/java/src/org/forester/application/simple_node_processor.java
deleted file mode 100644
index 7420bc2..0000000
--- a/forester/java/src/org/forester/application/simple_node_processor.java
+++ /dev/null
@@ -1,99 +0,0 @@
-
-package org.forester.application;
-
-import java.io.File;
-
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.CommandLineArguments;
-
-public class simple_node_processor {
-
-    private final static String BASE = "b_";
-
-    public static void main( final String args[] ) {
-        File in = null;
-        File out = null;
-        try {
-            CommandLineArguments cla = null;
-            cla = new CommandLineArguments( args );
-            in = cla.getFile( 0 );
-            out = cla.getFile( 1 );
-            if ( out.exists() ) {
-                System.out.println( out + " already exists" );
-                System.exit( -1 );
-            }
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhyloXmlParser xml_parser = new PhyloXmlParser();
-            final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
-            final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
-            // final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
-            final PhylogenyNodeIterator it = phylogeny_0.iteratorExternalForward();
-            int i = 0;
-            while ( it.hasNext() ) {
-                final PhylogenyNode node = it.next();
-                processNode( node, i, out.toString() );
-                i++;
-            }
-            //   final PhylogenyWriter writer = new PhylogenyWriter();
-            //   writer.toPhyloXML( out, phylogeny_0, 0 );
-        }
-        catch ( final Exception e ) {
-            System.out.println( e.getLocalizedMessage() );
-            e.printStackTrace();
-            System.exit( -1 );
-        }
-    }
-
-    //    private static void processNode( final PhylogenyNode node, final int i ) {
-    //        node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
-    //        if ( !node.isExternal() ) {
-    //            if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
-    //                node.setName( BASE + i );
-    //            }
-    //        }
-    //    }
-    private static void processNode( final PhylogenyNode node, final int i, final String label ) {
-        //if ( node.isExternal() ) {
-        //    final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
-        //    final String s = node.getNodeData().getTaxonomy().getScientificName();
-        //    System.out.println( s + "\t" + c );
-        //}
-        //        if ( !node.isExternal() ) {
-        //            if ( !node.getNodeData().isHasTaxonomy() ) {
-        //                if ( !ForesterUtil.isEmpty( node.getName() ) ) {
-        //                    if ( ( node.getName().indexOf( "_" ) < 0 ) && ( node.getName().indexOf( "&" ) < 0 )
-        //                            && ( node.getName().indexOf( " " ) < 0 ) ) {
-        //                        Taxonomy t = new Taxonomy();
-        //                        t.setScientificName( node.getName() );
-        //                        node.getNodeData().addTaxonomy( t );
-        //                        node.setName( "" );
-        //                    }
-        //                }
-        //            }
-        //        }
-        if ( node.isExternal() ) {
-            if ( node.getNodeData().isHasTaxonomy() ) {
-                //  final Taxonomy t = node.getNodeData().getTaxonomy();
-                //  t.setIdentifier( null );
-                //if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) && t.getTaxonomyCode().length() == 5 ) {
-                //    if ( node.getName().equalsIgnoreCase( t.getTaxonomyCode() ) ) {
-                //        node.setName( "" );
-                //    }
-                //}
-                // node.setName( "" );
-                final Taxonomy t = node.getNodeData().getTaxonomy();
-                System.out.println( t.getTaxonomyCode() + "\t" + t.getScientificName() + "\t" + t.getCommonName()
-                        + "\t" + label );
-            }
-            else {
-                //System.out.println( "node " + node + " has not tax" );
-            }
-        }
-    }
-}
\ No newline at end of file
-- 
1.7.10.2