inprogress

[jalview.git] / 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
index a190edf..42442ab 100644 (file)
--- a/forester/java/src/org/forester/application/simple_node_processor.java
+++ b/forester/java/src/org/forester/application/simple_node_processor.java
@@ -1,33 +1,10 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org
 
 package org.forester.application;
 
 import java.io.File;
 
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
@@ -41,16 +18,16 @@ public class simple_node_processor {
 
     public static void main( final String args[] ) {
         File in = null;
-        final File out = 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 );
-            //  }
+            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 );
@@ -62,8 +39,8 @@ public class simple_node_processor {
                 processNode( node, i );
                 i++;
             }
-            //  final PhylogenyWriter writer = new PhylogenyWriter();
-            //  writer.toPhyloXML( out, phylogeny_0, 0 );
+            final PhylogenyWriter writer = new PhylogenyWriter();
+            writer.toPhyloXML( out, phylogeny_0, 0 );
         }
         catch ( final Exception e ) {
             System.out.println( e.getLocalizedMessage() );
@@ -81,10 +58,38 @@ public class simple_node_processor {
     //        }
     //    }
     private static void processNode( final PhylogenyNode node, final int i ) {
+        //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() ) {
-            final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
-            final String s = node.getNodeData().getTaxonomy().getScientificName();
-            System.out.println( s + "\t" + c );
+            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( "" );
+            }
+            else {
+                System.out.println( "node " + node + " has not tax" );
+            }
         }
     }
-}
+}
\ No newline at end of file