From bb73060aba34b1a61bd863dcfcf969e49a3a5d16 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 21 Jun 2016 10:18:12 +0100 Subject: [PATCH] JAL-1369 HUGE WARNING: datamodel.HiddenSequences is NOT SAFE --- src/jalview/datamodel/HiddenSequences.java | 6 ++++++ 1 file changed, 6 insertions(+) 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; -- 1.7.10.2