Removed to reduce jar size

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

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