in progress

diff --git a/forester_applications/src/org/forester/applications/tax_code_cleaner.java b/forester_applications/src/org/forester/applications/tax_code_cleaner.java
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+// $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
+// javac -cp ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
+// ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/org/forester/applications/simple_node_processor.java
+// java -Xmx2048m -cp
+// /home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/:/home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
+// org.forester.applications.simple_node_processor
+
+package org.forester.applications;
+
+import java.io.File;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+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.data.Identifier;
+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;
+import org.forester.util.ForesterUtil;
+
+public class tax_code_cleaner {
+
+    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();
+            int i = 0;
+            while ( it.hasNext() ) {
+                final PhylogenyNode node = it.next();
+                processNode( node, i );
+                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 ) throws PhyloXmlDataFormatException {
+        if ( node.isExternal() ) {
+            if ( node.getNodeData().isHasTaxonomy() ) {
+                final Taxonomy t = node.getNodeData().getTaxonomy();
+                if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) ) {
+                    final String tc = t.getTaxonomyCode();
+                    if ( tc.equals( "ACRALC" ) ) {
+                        t.setScientificName( "Acremonium alcalophilum" );
+                        t.setTaxonomyCode( "AALXX" );
+                    }
+                    else if ( tc.equals( "AMPQU" ) ) {
+                        t.setScientificName( "Amphimedon queenslandica" );
+                        t.setTaxonomyCode( "AMPQE" );
+                    }
+                    else if ( tc.equals( "AQUAE" ) ) {
+                        t.setScientificName( "Aquifex aeolicus (strain VF5)" );
+                    }
+                    else if ( tc.equals( "ASTSPC" ) ) {
+                        t.setScientificName( "Asterochloris sp. Cgr/DA1pho" );
+                        t.setTaxonomyCode( "ASCXX" );
+                    }
+                    else if ( tc.equals( "BAUCOM" ) ) {
+                        t.setScientificName( "Baudoinia compniacensis" );
+                        t.setTaxonomyCode( "BCOXX" );
+                    }
+                    else if ( tc.equals( "CAP" ) ) {
+                        t.setScientificName( "Capitella sp.1" );
+                        t.setTaxonomyCode( "CTEXX" );
+                    }
+                    else if ( tc.equals( "CAPOWC" ) ) {
+                        t.setScientificName( "Capsaspora owczarzaki (strain ATCC 30864)" );
+                        t.setTaxonomyCode( "CAPO3" );
+                    }
+                    else if ( tc.equals( "CHLVUL" ) ) {
+                        t.setScientificName( "Chlorella variabilis" );
+                        t.setTaxonomyCode( "CHLVA" );
+                    }
+                    else if ( tc.equals( "CITCLE" ) ) {
+                        t.setScientificName( "Citrus clementina" );
+                        t.setTaxonomyCode( "CCLXX" );
+                    }
+                    else if ( tc.equals( "CLAGRA" ) ) {
+                        t.setScientificName( "Cladonia grayi" );
+                        t.setTaxonomyCode( "" );
+                    }
+                    else if ( tc.equals( "COEREV" ) ) {
+                        t.setScientificName( "Coemansia reversa" );
+                        t.setTaxonomyCode( "CREXX" );
+                    }
+                    else if ( tc.equals( "CONPUT" ) ) {
+                        t.setScientificName( "Coniophora puteana" );
+                        t.setTaxonomyCode( "CPUXX" );
+                    }
+                    else if ( tc.equals( "DICSQU" ) ) {
+                        t.setScientificName( "Dichomitus squalens" );
+                        t.setTaxonomyCode( "DICSQ" );
+                    }
+                    else if ( tc.equals( "FOMPIN" ) ) {
+                        t.setScientificName( "Fomitopsis pinicola" );
+                        t.setTaxonomyCode( "FPIXX" );
+                    }
+                    else if ( tc.equals( "GONPRO" ) ) {
+                        t.setScientificName( "Gonapodya prolifera" );
+                        t.setTaxonomyCode( "GONPR" );
+                    }
+                    else if ( tc.equals( "GYMLUX" ) ) {
+                        t.setScientificName( "Gymnopus luxurians" );
+                        t.setTaxonomyCode( "" );
+                    }
+                    else if ( tc.equals( "HYDPIN" ) ) {
+                        t.setScientificName( "Hydnomerulius pinastri" );
+                        t.setTaxonomyCode( "" );
+                    }
+                    else if ( tc.equals( "JAAARG" ) ) {
+                        t.setScientificName( "Jaapia argillacea" );
+                        t.setTaxonomyCode( "" );
+                    }
+                    else if ( tc.equals( "MYCPOP" ) ) {
+                        t.setScientificName( "Mycosphaerella populorum" );
+                        t.setTaxonomyCode( "MYCPS" );
+                    }
+                    else if ( tc.equals( "MYCTHE" ) ) {
+                        t.setScientificName( "Myceliophthora thermophila" );
+                        t.setTaxonomyCode( "THIHA" );
+                    }
+                    else if ( tc.equals( "OIDMAI" ) ) {
+                        t.setScientificName( "Oidiodendron maius" );
+                        t.setTaxonomyCode( "" );
+                    }
+                    else if ( tc.equals( "PANVIR" ) ) {
+                        t.setScientificName( "Panicum virgatum" );
+                        t.setTaxonomyCode( "PANVG" );
+                    }
+                    else if ( tc.equals( "PIRSPE" ) ) {
+                        t.setScientificName( "Piromyces sp. E2" );
+                        t.setTaxonomyCode( "PIRSE" );
+                    }
+                    else if ( tc.equals( "SAICOM" ) ) {
+                        t.setScientificName( "Saitoella complicata" );
+                        t.setTaxonomyCode( "" );
+                    }
+                    else if ( tc.equals( "SERLAC" ) ) {
+                        t.setScientificName( "Serpula lacrymans" );
+                        t.setTaxonomyCode( "SERL9" );
+                    }
+                    else if ( tc.equals( "SPHARC" ) ) {
+                        t.setScientificName( "Sphaeroforma arctica" );
+                        t.setTaxonomyCode( "SARXX" );
+                    }
+                    else if ( tc.equals( "THETRA" ) ) {
+                        t.setScientificName( "Thecamonas trahens" );
+                        t.setTaxonomyCode( "TTRXX" );
+                    }
+                    else if ( tc.equals( "THITER" ) ) {
+                        t.setScientificName( "Thielavia terrestris (strain ATCC 38088 / NRRL 8126)" );
+                        t.setTaxonomyCode( "THITE" );
+                    }
+                    else if ( tc.equals( "WOLCOC" ) ) {
+                        t.setScientificName( "Wolfiporia cocos MD-104 SS10" );
+                        t.setTaxonomyCode( "WOLCO" );
+                    }
+                    else if ( tc.equals( "XANPAR" ) ) {
+                        t.setScientificName( "Xanthoria parietina 46-1" );
+                        t.setTaxonomyCode( "" );
+                    }
+                }
+            }
+        }
+    }
+}