From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 22 Jun 2020 11:19:02 +0000 (+0100)
Subject: JAL-3664 hmm related TODOs
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fjims%2Fwork_on_2_12%2FJAL-3664_hmmer_ux;p=jalview.git

JAL-3664 hmm related TODOs
---

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 0c47c1d..0bda090 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -201,6 +201,7 @@ public class HMMBuild extends HmmerCommand
       // at import level ?
 
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
+      // TODO: when copy contains the alignment sequences, you actually see the alignment sequences change to 'Sequence0'... if a redraw occurs!
       Hashtable sequencesHash = stashSequences(copyArray);
 
       exportStockholm(copyArray, alignmentFile, ac);
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 7061938..1126de6 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -441,6 +441,7 @@ public class FileLoader implements Runnable
             viewport.addAlignment(al, title);
             if (source instanceof HMMFile)
             {
+              // TODO: absorb into viewport.addAlignment above ?
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
                       .getSequenceAt(alignment.getHeight() - 1);