transferred the storage position of the HMM to annotations

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 080e260..a91bb66 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -54,6 +54,7 @@ import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -4652,15 +4653,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else if (FileFormat.HMMER3.equals(format))
           {
-            HMMFile hmm = new HMMFile(new FileParse(file, sourceType));
-            hmm.parse();
-
-            getViewport().getAlignment().setHMM(hmm.getHMM());
-
-
-
-
-
+            HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
+            hmmFile.parse();
+            HiddenMarkovModel hmm = hmmFile.getHMM();
+            AlignmentAnnotation annotation = hmm.createAnnotation(
+                    getViewport().getAlignment().getWidth());
+            getViewport().getAlignment().addAnnotation(annotation);
+            annotation.setHMM(hmm);
+            isAnnotation = true;
           }
           else if (FileFormat.Jnet.equals(format))
           {