rejiggered loadDataFile and parseFeatureFile so JNet annotation parsing is attempted...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 99227e1..a714ce6 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3761,9 +3761,10 @@ public void showTranslation_actionPerformed(ActionEvent e)
 }
 
 /**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
+ * Try to load a features file onto the alignment.
+ * @param file contents or path to retrieve file 
+ * @param type access mode of file (see jalview.io.AlignFile)
+ * @return true if features file was parsed corectly.
  */
 public boolean parseFeaturesFile(String file, String type)
 {
@@ -3864,12 +3865,15 @@ public void drop(DropTargetDropEvent evt)
     }
 }
 
-  // This method will attempt to load a "dropped" file first by testing
-  // whether its and Annotation file, then features file. If both are
-  // false then the user may have dropped an alignment file onto this
-  // AlignFrame
+  /**     
+   * Attempt to load a "dropped" file: First by testing
+   * whether it's and Annotation file, then a JNet file, and finally a features file. If all are
+   * false then the user may have dropped an alignment file onto this
+   * AlignFrame.
+   * @param file either a filename or a URL string.
+   */
    public void loadJalviewDataFile(String file)
-  {
+   {
     try
     {
       String protocol = "File";
@@ -3884,34 +3888,37 @@ public void drop(DropTargetDropEvent evt)
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file,protocol);
-        if (!isGroupsFile)
+        // try to see if its a JNet 'concise' style annotation file *before* we try to parse it as a features file
+        String format = new IdentifyFile().Identify(file, protocol);
+        if(format.equalsIgnoreCase("JnetFile"))
         {
-          String format = new IdentifyFile().Identify(file, protocol);
-
-          if(format.equalsIgnoreCase("JnetFile"))
-          {
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                file, protocol);
-            new JnetAnnotationMaker().add_annotation(predictions,
+          jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                  file, protocol);
+          new JnetAnnotationMaker().add_annotation(predictions,
                 viewport.getAlignment(),
                 0, false);
-            alignPanel.adjustAnnotationHeight();
-            alignPanel.paintAlignment(true);
-          }
-          else
+          isAnnotation=true;
+        }
+        else
+        {
+          // try to parse it as a features file
+          boolean isGroupsFile = parseFeaturesFile(file,protocol);
+          // if it wasn't a features file then we just treat it as a general alignment file to load into the current view.
+          if (!isGroupsFile)
           {
             new FileLoader().LoadFile(viewport, file, protocol, format);
+          } else {
+            alignPanel.paintAlignment(true);
+          }
         }
       }
-      }
-      else
+      if (isAnnotation)
       {
-        // (isAnnotation)
+        
         alignPanel.adjustAnnotationHeight();
         buildSortByAnnotationScoresMenu();
+        alignPanel.paintAlignment(true);
       }
-
     }
     catch (Exception ex)
     {