From 061c304150f3db1f126b2e8e274d3f7da4846887 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 1 Jun 2018 15:04:43 +0100 Subject: [PATCH] JAL-3012 JAL-2937 TODO avoid creating data copies by instrumenting output alignment object --- src/jalview/hmmer/HMMBuild.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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); -- 1.7.10.2