JAL-1479 improved SiftsClient test coverage and implemented previously unimplemented...

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index bfeafd6..db4c858 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -254,6 +254,12 @@ public class HiddenSequences
     return alignmentIndex;
   }
 
+  /**
+   * makes a copy of the alignment with hidden sequences included. Using the
+   * copy for anything other than simple output is not recommended. Note - this
+   * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+   * @return
+   */
   public AlignmentI getFullAlignment()
   {
     int isize = hiddenSequences.length;
@@ -272,17 +278,26 @@ public class HiddenSequences
         index++;
       }
     }
-
-    return new Alignment(seq);
+    Alignment fAlignmt = new Alignment(seq);
+    fAlignmt.annotations = alignment.getAlignmentAnnotation();
+    fAlignmt.alignmentProperties = alignment.getProperties();
+    fAlignmt.groups = alignment.getGroups();
+    fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+    fAlignmt.setSeqrep(alignment.getSeqrep());
+
+    return fAlignmt;
   }
 
   public boolean isHidden(SequenceI seq)
   {
-    for (int i = 0; i < hiddenSequences.length; i++)
+    if (hiddenSequences != null)
     {
-      if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+      for (int i = 0; i < hiddenSequences.length; i++)
       {
-        return true;
+        if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+        {
+          return true;
+        }
       }
     }