JAL-715 - allow rest service attributes to be exported and imported as a | separated...

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1a0d82c..4e279d3 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -143,7 +143,7 @@ public class Alignment implements AlignmentI
    */
   public SequenceI getSequenceAt(int i)
   {
-    if (i < sequences.size())
+    if (i>-1 && i < sequences.size())
     {
       return (SequenceI) sequences.elementAt(i);
     }
@@ -652,6 +652,11 @@ public class Alignment implements AlignmentI
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+  
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -683,7 +688,9 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      unhookAnnotation(aa);
+      if (unhook) {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }