JAL-2629 add documentation to previous work

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ed26833..ebce25b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -179,6 +179,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public AlignViewControllerI avc;
 
+  /*
+   * The selected HMM for this align frame
+   */
   HiddenMarkovModel selectedHMM = null;
 
   List<AlignmentPanel> alignPanels = new ArrayList<>();
@@ -498,6 +501,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  /**
+   * Adds all menu items to the HMMER menu
+   */
   private void buildHMMERMenu()
   {
     hmmerMenu.removeAll();
@@ -5697,11 +5703,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  /**
+   * Sets the status of the HMMER menu
+   * 
+   * @param status
+   */
   public void updateHMMERStatus(boolean status)
   {
     hmmerMenu.setEnabled(status);
   }
 
+  /**
+   * Returns the selected hidden Markov model.
+   * 
+   * @return
+   */
   public HiddenMarkovModel getSelectedHMM()
   {
     return selectedHMM;