From: jprocter <Jim Procter>
Date: Sun, 17 Jun 2007 12:52:25 +0000 (+0000)
Subject: score only annotation IO
X-Git-Tag: Release_2_4~375
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b650fd1c30becbf43bd58c0513512e1c053e83e7;p=jalview.git

score only annotation IO
---

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index e54ae71..f8c2c2a 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -56,7 +56,7 @@ public class AnnotationFile
       {
         row = annotations[i];
 
-        if (!row.visible)
+        if (!row.visible && !row.hasScore())
         {
           continue;
         }
@@ -127,7 +127,7 @@ public class AnnotationFile
           text.append(row.description + "\t");
         }
 
-        for (int j = 0; j < row.annotations.length; j++)
+        for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)
         {
           if (refSeq != null &&
               jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
@@ -493,7 +493,7 @@ public class AnnotationFile
 
         annotation = new AlignmentAnnotation(label,
                                              description,
-                                             annotations,
+                                             (index==0) ? null : annotations,
                                              0,
                                              0,
                                              graphStyle);