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 (executable)
--- 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 (file)
--- 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;
 
   }