From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Thu, 17 Aug 2017 09:18:53 +0000 (+0100)
Subject: JAL-2599 some slight renaming of variables and methods
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b938d55838925c0fa1426c166f670871e2614ebf;p=jalview.git

JAL-2599 some slight renaming of variables and methods
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index abbd8e3..fa0ca2f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1991,7 +1991,7 @@ public class Alignment implements AlignmentI
    * with HMMs. If remove is set to true, the consensus sequences will be
    * removed from the alignment.
    */
-  @Override
+  @Override // TODO make this more efficient.
   public List<SequenceI> getHMMConsensusSequences(boolean remove)
   {
     List<SequenceI> seqs = new ArrayList<>();
diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
index 1f3318c..28aa62f 100644
--- a/src/jalview/io/HMMFile.java
+++ b/src/jalview/io/HMMFile.java
@@ -725,9 +725,6 @@ public class HMMFile extends AlignFile
     SequenceI hmmSeq = hmm.initHMMSequence();
     SequenceI[] seq = new SequenceI[1];
     seq[0] = hmmSeq;
-    // view.initInformation();
-    // view.updateInformation(view.panel);
-    // getViewport().alignmentChanged(alignPanel);
     return seq;
 
   }