From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 21 Jun 2016 09:18:12 +0000 (+0100)
Subject: JAL-1369 HUGE WARNING: datamodel.HiddenSequences is NOT SAFE
X-Git-Tag: Release_2_10_0~161^2~5^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bb73060aba34b1a61bd863dcfcf969e49a3a5d16;p=jalview.git

JAL-1369 HUGE WARNING: datamodel.HiddenSequences is NOT SAFE
---

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;