From 23b2281dd8846acd591369f298cbcd8466a85beb Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 8 Oct 2013 02:57:59 +0000 Subject: [PATCH] inprogress --- .../forester/applications/tax_code_cleaner.java | 33 ++------------------ 1 file changed, 3 insertions(+), 30 deletions(-) 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 --- 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 ) ); } } - } } } -- 1.7.10.2