inprogress

diff --git a/forester_applications/src/org/forester/applications/tax_code_cleaner.java b/forester_applications/src/org/forester/applications/tax_code_cleaner.java
index 94820ab..4af65fd 100644 (file)
--- a/forester_applications/src/org/forester/applications/tax_code_cleaner.java
+++ b/forester_applications/src/org/forester/applications/tax_code_cleaner.java
@@ -1,32 +1,8 @@
-// $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
+// ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/org/forester/applications/tax_code_cleaner.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
+// org.forester.applications.tax_code_cleaner
 
 package org.forester.applications;
 
@@ -38,7 +14,6 @@ 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;
@@ -209,13 +184,11 @@ public class tax_code_cleaner {
                         t.setTaxonomyCode( "" );
                     }
                     else if ( tc.length() == 6 ) {
-                        Pattern p = Pattern
-                                .compile( "[A-Z9][A-Z]{2}[A-Z0-9]{2}\\d" );
+                        Pattern p = Pattern.compile( "[A-Z9][A-Z]{2}[A-Z0-9]{2}\\d" );
                         if ( p.matcher( tc ).matches() ) {
                             t.setTaxonomyCode( tc.substring( 0, 5 ) );
                         }
                     }
-                   
                 }
             }
         }