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[jalview.git] / forester / java / src / org / forester / io / parsers / phyloxml / data / AnnotationParser.java

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java
index 8f25921..66023d4 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java
@@ -5,7 +5,7 @@
 // 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
@@ -15,19 +15,19 @@
 // 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/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.io.parsers.phyloxml.data;
 
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
 import org.forester.io.parsers.phyloxml.XmlElement;
-import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.PhylogenyData;
@@ -51,15 +51,14 @@ public class AnnotationParser implements PhylogenyDataPhyloXmlParser {
     }
 
     @Override
-    public PhylogenyData parse( final XmlElement element ) throws PhylogenyParserException {
-        String ref;
+    public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException {
+        final Annotation annotation;
         if ( element.isHasAttribute( PhyloXmlMapping.ANNOTATION_REF_ATTR ) ) {
-            ref = element.getAttribute( PhyloXmlMapping.ANNOTATION_REF_ATTR );
+            annotation = new Annotation( element.getAttribute( PhyloXmlMapping.ANNOTATION_REF_ATTR ) );
         }
         else {
-            ref = "_:_";
+            annotation = new Annotation();
         }
-        final Annotation annotation = new Annotation( ref );
         if ( element.isHasAttribute( PhyloXmlMapping.ANNOTATION_TYPE_ATTR ) ) {
             annotation.setType( element.getAttribute( PhyloXmlMapping.ANNOTATION_TYPE_ATTR ) );
         }
@@ -85,7 +84,7 @@ public class AnnotationParser implements PhylogenyDataPhyloXmlParser {
                     annotation.setProperties( new PropertiesMap() );
                 }
                 annotation.getProperties()
-                        .addProperty( ( Property ) PropertyParser.getInstance().parse( child_element ) );
+                .addProperty( ( Property ) PropertyParser.getInstance().parse( child_element ) );
             }
         }
         return annotation;