JAL-3664 hmm related TODOs

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 0c47c1d..0bda090 100644 (file)
--- 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 (executable)
--- 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);