work for rrm project (ComPhy 2012 Moscow)

[jalview.git] / forester / java / src / org / forester / io / writers / PhyloXmlNodeWriter.java

diff --git a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java
index 586a709..67d38d4 100644 (file)
--- a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2000-2009 Christian M. Zmasek
 // Copyright (C) 2007-2009 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
@@ -15,7 +15,7 @@
 // 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
@@ -39,13 +39,13 @@ public class PhyloXmlNodeWriter {
     public static void toPhyloXml( final Writer w, final PhylogenyNode node, final int level, final String indentation )
             throws IOException {
         String ind = "";
-        if ( indentation.length() > 0 ) {
+        if ( ( indentation != null ) && ( indentation.length() > 0 ) ) {
             ind = indentation + PhylogenyWriter.PHYLO_XML_INTENDATION_BASE;
         }
         if ( !ForesterUtil.isEmpty( node.getName() ) ) {
             PhylogenyDataUtil.appendElement( w, PhyloXmlMapping.NODE_NAME, node.getName(), indentation );
         }
-        if ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+        if ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
             PhylogenyDataUtil.appendElement( w, PhyloXmlMapping.BRANCH_LENGTH, String.valueOf( ForesterUtil.round( node
                     .getDistanceToParent(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), indentation );
         }