X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=692c2fde137e81d89d6e25a2cbda80a00d0d7e4f;hb=a0d1b1826f8ab0792c589946746d52ad0316fc99;hp=4fc6208a753a374ae5d785396aefc6bd8fc843dd;hpb=6e21be7d86ab4ac3936e1e7691b31ebcf9080cdf;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4fc6208..692c2fd 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -35,7 +35,7 @@ public class AlignFrame
     extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
+  public final AlignViewport viewport;
   int NEW_WINDOW_WIDTH = 700;
   int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
@@ -241,14 +241,14 @@ public class AlignFrame
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
+                                              viewport.getAlignment().getSequences(),
+                                                      viewport.showDBPrefix,
+                                                      viewport.showJVSuffix));
   }
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
     PaintRefresher.components.remove(viewport.alignment);
-    dispose();
     if(PaintRefresher.components.size()==0 && applet==null)
       System.exit(0);
   }
@@ -863,13 +863,21 @@ public class AlignFrame
     new FontChooser(alignPanel);
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void dbref_actionPerformed(ItemEvent e)
   {
-    viewport.setShowJVSuffix(fullSeqId.getState());
+    viewport.showDBPrefix = dbref.getState();
     alignPanel.fontChanged();
     alignPanel.repaint();
   }
 
+  public void seqLimits_itemStateChanged(ItemEvent e)
+  {
+    viewport.setShowJVSuffix(seqLimits.getState());
+    alignPanel.fontChanged();
+    alignPanel.repaint();
+  }
+
+
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.getState());
@@ -1201,7 +1209,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }