From ce957421712f63416c9da127f1d4695f6e64c15a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 19 Apr 2006 14:32:11 +0000
Subject: [PATCH] Alignment might not have any annotations

---
 src/jalview/gui/AlignFrame.java |   54 +++++++++++++++++++--------------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 87cd9a9..0d744d6 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2514,42 +2514,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
   jalview.datamodel.AlignmentAnnotation[] annotations
       = viewport.alignment.getAlignmentAnnotation();
   int a, aSize;
-  for (int i = 0; i < annotations.length; i++)
+  if(annotations!=null)
   {
-
-    if (annotations[i].label.equals("Quality") ||
-        annotations[i].label.equals("Conservation") ||
-        annotations[i].label.equals("Consensus"))
+    for (int i = 0; i < annotations.length; i++)
     {
-      continue;
-    }
-
+      if (annotations[i].label.equals("Quality") ||
+          annotations[i].label.equals("Conservation") ||
+          annotations[i].label.equals("Consensus"))
+      {
+        continue;
+      }
 
-    aSize = viewport.alignment.getWidth()/3;
-    jalview.datamodel.Annotation [] anots =
-        new jalview.datamodel.Annotation[aSize];
+      aSize = viewport.alignment.getWidth() / 3;
+      jalview.datamodel.Annotation[] anots =
+          new jalview.datamodel.Annotation[aSize];
 
-    for(a=0; a<viewport.alignment.getWidth(); a++)
-    {
-     if( annotations[i].annotations[a]==null
-      || annotations[i].annotations[a]==null)
-       continue;
+      for (a = 0; a < viewport.alignment.getWidth(); a++)
+      {
+        if (annotations[i].annotations[a] == null
+            || annotations[i].annotations[a] == null)
+          continue;
 
-      anots[a/3] = new Annotation(
-     annotations[i].annotations[a].displayCharacter,
-     annotations[i].annotations[a].description,
-     annotations[i].annotations[a].secondaryStructure,
-     annotations[i].annotations[a].value,
-     annotations[i].annotations[a].colour);
-    }
+        anots[a / 3] = new Annotation(
+            annotations[i].annotations[a].displayCharacter,
+            annotations[i].annotations[a].description,
+            annotations[i].annotations[a].secondaryStructure,
+            annotations[i].annotations[a].value,
+            annotations[i].annotations[a].colour);
+      }
 
-    jalview.datamodel.AlignmentAnnotation aa
+      jalview.datamodel.AlignmentAnnotation aa
           = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-       annotations[i].description, anots );
-     al.addAnnotation(aa);
+          annotations[i].description, anots);
+      al.addAnnotation(aa);
+    }
   }
 
-
     AlignFrame af = new AlignFrame(al);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              NEW_WINDOW_WIDTH,
-- 
1.7.10.2