X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=e2ef31886d5542835935e42f1d09c21a4fab0b25;hb=ca160187a050f6d4e50158cd5b51f75c83a7179e;hp=a57dc9c5278064084beab0343e153615491dd4cb;hpb=5c41e4193f3bebb1c8e11c124a4928d1419b052c;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index a57dc9c..e2ef318 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -157,9 +157,10 @@ public class HiddenSequences
     int absAlignmentIndex = alignment.findIndex(sequence);
     int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
-    if (hiddenSequences[alignmentIndex] != null)
+    if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
     {
-      System.out.println("ERROR!!!!!!!!!!!");
+      jalview.bin.Console.outPrintln("ERROR!!!!!!!!!!!");
+      return;
     }
 
     hiddenSequences[alignmentIndex] = sequence;
@@ -221,8 +222,8 @@ public class HiddenSequences
       end = hiddenSequences.length - 1;
     }
 
-    List<SequenceI> asequences;
-    synchronized (asequences = alignment.getSequences())
+    List<SequenceI> asequences = alignment.getSequences();
+    synchronized (asequences)
     {
       for (int index = end; index > start; index--)
       {
@@ -238,8 +239,8 @@ public class HiddenSequences
           }
           else
           {
-            System.out.println(seq.getName()
-                    + " has been deleted whilst hidden");
+            jalview.bin.Console.outPrintln(
+                    seq.getName() + " has been deleted whilst hidden");
           }
         }
       }
@@ -311,7 +312,7 @@ public class HiddenSequences
       return startRow - visibleDistance;
     }
 
-    int index = startRow;
+    int index = Math.min(startRow, hiddenSequences.length - 1);
     int count = 0;
     while ((index > -1) && (count < visibleDistance))
     {