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 dcc5f26..db4c858 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -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;
@@ -277,6 +283,7 @@ public class HiddenSequences
     fAlignmt.alignmentProperties = alignment.getProperties();
     fAlignmt.groups = alignment.getGroups();
     fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+    fAlignmt.setSeqrep(alignment.getSeqrep());
 
     return fAlignmt;
   }