midpoint rooting is faster

[jalview.git] / forester / java / src / org / forester / phylogeny / data / Annotation.java

diff --git a/forester/java/src/org/forester/phylogeny/data/Annotation.java b/forester/java/src/org/forester/phylogeny/data/Annotation.java
index a1d6b22..829707a 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Annotation.java
+++ b/forester/java/src/org/forester/phylogeny/data/Annotation.java
@@ -47,23 +47,28 @@ public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annot
 
     public Annotation( final String ref ) {
         if ( ForesterUtil.isEmpty( ref ) ) {
-            throw new IllegalArgumentException( "illegal attempt to create Annotation with null or empty reference" );
+            throw new IllegalArgumentException( "annotation reference is empty or null" );
         }
-        if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.length() < 3 ) ) {
-            throw new IllegalArgumentException( "illegal format for Annotation reference: [" + ref + "]" );
+        if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 ) || ( ref.length() < 3 ) ) {
+            throw new IllegalArgumentException( "illegal format for annotation reference: [" + ref + "]" );
         }
         _ref = ref;
         init();
     }
 
+    public Annotation() {
+        _ref = "";
+        init();
+    }
+
     @Override
     public StringBuffer asSimpleText() {
-        return new StringBuffer( getDesc() );
+        return new StringBuffer( !ForesterUtil.isEmpty( getRef() ) ? getRef() : getDesc() );
     }
 
     @Override
     public StringBuffer asText() {
-        return new StringBuffer( getDesc() );
+        return asSimpleText();
     }
 
     @Override