X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Fphyloxml%2Fdata%2FAnnotationParser.java;h=66023d4e35e2ad11665efac3bfcb4ed2dd2dd27c;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=00494f59b4ce53a51590edb264f83b0e2c3e9da8;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

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 00494f5..66023d4 100644
--- a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java
@@ -21,13 +21,13 @@
 // 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;