Merge branch 'develop' into feature/JAL-2611

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 1daaf43..32443d8 100755 (executable)
--- 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!!!!!!!!!!!");
+      return;
     }
 
     hiddenSequences[alignmentIndex] = sequence;
@@ -170,7 +171,13 @@ public class HiddenSequences
   public List<SequenceI> showAll(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> revealedSeqs = new ArrayList<>();
+
+    if (hiddenSequences == null)
+    {
+      return revealedSeqs;
+    }
+
     for (int i = 0; i < hiddenSequences.length; i++)
     {
       if (hiddenSequences[i] != null)
@@ -199,7 +206,7 @@ public class HiddenSequences
   public List<SequenceI> showSequence(int alignmentIndex,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> revealedSeqs = new ArrayList<>();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if (repSequence != null && hiddenRepSequences != null
             && hiddenRepSequences.containsKey(repSequence))
@@ -247,7 +254,8 @@ public class HiddenSequences
   }
 
   /**
-   * Convert absolute alignment index to visible alignment index
+   * Convert absolute alignment index to visible alignment index (or -1 if
+   * before the first visible sequence)
    * 
    * @param alignmentIndex
    * @return
@@ -304,7 +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))
     {