From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 28 Jan 2015 11:13:47 +0000 (+0000)
Subject:     JAL-674 patch to make Mapping.compareTransferredToRefPDBAnnot test
X-Git-Tag: Jalview_2_9~103
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c16f0cbe6b789e03e064804f426fbc4399f39b44;p=jalview.git

JAL-674 patch to make Mapping.compareTransferredToRefPDBAnnot test
    pass
        otherwise addAll throws an index not found exception with
	inspos==-1
---

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index ba7e520..2ef1c76 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1155,7 +1155,8 @@ public class AlignSeq
           }
           if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
           {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+            annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+                    Arrays.asList(sq.getAnnotation()));
           }
         }
       }