X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=334d3802ea88e3b21cbbbbdab5688a055b34e789;hb=96356075a122b745936738f478a8ee33ac7e0f0a;hp=a91bb663fde4f4cc22446412cc1f0e0f5376dcd8;hpb=fdda06e4e3b668fb08532ba9192c199bb57fb5bd;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a91bb66..334d380 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4653,7 +4653,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else if (FileFormat.HMMER3.equals(format))
           {
-            HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
+            HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO
+                                                                            // need
+                                                                            // to
+                                                                            // follow
+                                                                            // standard
+                                                                            // pipeline
             hmmFile.parse();
             HiddenMarkovModel hmm = hmmFile.getHMM();
             AlignmentAnnotation annotation = hmm.createAnnotation(