X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=a98b10e9067015dc79ca317b8e4bcd782bf9887b;hb=45fa2a2d8465e302f895576a4c841578d2209cda;hp=6950c287bff121b99312c260559dc447ccf45f22;hpb=6d183feafe3e566501af586286bbd1d2107ee5a9;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 6950c28..a98b10e 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -170,7 +170,13 @@ 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 +205,7 @@ 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))
@@ -403,4 +409,20 @@ public class HiddenSequences
 
     return false;
   }
+
+  /**
+   * Answers if a sequence is hidden
+   * 
+   * @param seq
+   *          (absolute) index to test
+   * @return true if sequence at index seq is hidden
+   */
+  public boolean isHidden(int seq)
+  {
+    if (hiddenSequences != null)
+    {
+      return (hiddenSequences[seq] != null);
+    }
+    return false;
+  }
 }