From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 1 Jun 2018 14:04:43 +0000 (+0100)
Subject: JAL-3012 JAL-2937 TODO avoid creating data copies by instrumenting output alignment... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=061c304150f3db1f126b2e8e274d3f7da4846887;p=jalview.git

JAL-3012 JAL-2937 TODO avoid creating data copies by instrumenting output alignment object
---

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 6fcd6db..b3cca40 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -196,7 +196,9 @@ public class HMMBuild extends HmmerCommand
           copy.add(seq);
         }
       }
-
+      // TODO rather than copy alignment data we should anonymize in situ -
+      // export/File import could use anonymization hash to reinstate references
+      // at import level ?
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
       Hashtable sequencesHash = stashSequences(copyArray);