X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=0f57a02344893ff958940b7ce4c1fc2f9aae7637;hb=bb73060aba34b1a61bd863dcfcf969e49a3a5d16;hp=dcc5f269dd0ca57654ae8c3053ec12cb625ecebf;hpb=cdb40eae73b3a9a7ca68c9b882e38a2e1dd3d03e;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index dcc5f26..0f57a02 100755
--- 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;