Neeed to know protocol for annotation loading

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 07c56c4..bb722a5 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -592,7 +592,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           dset.deleteSequence(0);
         }
 
-        firePropertyChange("Alignment", null, null);
+        firePropertyChange("Alignment", null, viewport.alignment.getSequences());
 
         updateEditMenuBar();
       }
@@ -990,7 +990,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if(originalSource!=null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-      originalSource.firePropertyChange("alignment", null,null);
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
     }
   }
 
@@ -1014,7 +1016,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if(originalSource!=null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-      originalSource.firePropertyChange("alignment", null,null);
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
     }
   }
 
@@ -1279,7 +1283,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
      }
      else
      {
-       sequences = new FormatAdapter().readFile(str, "Paste", format);
+       sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
      }
 
      AlignmentI alignment = null;
@@ -3283,7 +3287,7 @@ public void drop(DropTargetDropEvent evt)
       }
 
       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
-          alignment, file);
+          alignment, file, protocol);
 
       if (!isAnnotation)
       {