From d429962a1e4d2413e0c18fd88227cffee8bfa502 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 2 Nov 2005 16:06:05 +0000
Subject: [PATCH] Add jvsuffix and dbref to menu

---
 src/jalview/appletgui/AlignFrame.java    |   17 ++++++++---
 src/jalview/jbappletgui/GAlignFrame.java |   48 +++++++++++++++++++++---------
 2 files changed, 47 insertions(+), 18 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4fc6208..6e2d32b 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -241,8 +241,9 @@ 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)
@@ -863,13 +864,21 @@ 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());
diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java
index 5123317..6eb72d9 100755
--- a/src/jalview/jbappletgui/GAlignFrame.java
+++ b/src/jalview/jbappletgui/GAlignFrame.java
@@ -85,7 +85,7 @@ public class GAlignFrame extends Frame {
     MenuItem pasteThis = new MenuItem();
     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
     protected MenuItem font = new MenuItem();
-    protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
+    protected CheckboxMenuItem dbref = new CheckboxMenuItem();
     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
@@ -98,8 +98,9 @@ public class GAlignFrame extends Frame {
     Menu helpMenu = new Menu();
     MenuItem documentation = new MenuItem();
     MenuItem about = new MenuItem();
+  protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
 
-    public GAlignFrame() {
+  public GAlignFrame() {
         try {
             jbInit();
             setMenuBar(alignFrameMenuBar);
@@ -462,12 +463,13 @@ public class GAlignFrame extends Frame {
                     font_actionPerformed(e);
                 }
             });
-        fullSeqId.setLabel("Show Full Sequence ID");
-        fullSeqId.setState(true);
-        fullSeqId.addItemListener(new java.awt.event.ItemListener() {
+    dbref.setLabel("ShowSequence DB Refs");
+    dbref.setActionCommand("");
+    dbref.setState(true);
+    dbref.addItemListener(new java.awt.event.ItemListener() {
                 public void itemStateChanged(ItemEvent e) {
-                    fullSeqId_actionPerformed(null);
-                }
+        dbref_actionPerformed(e);
+      }
             });
         scaleAbove.setLabel("Scale Above");
         scaleAbove.setState(true);
@@ -528,8 +530,17 @@ public class GAlignFrame extends Frame {
                     about_actionPerformed(e);
                 }
             });
+          seqLimits.setState(true);
+    seqLimits.setLabel("Show Sequence Limits");
+    seqLimits.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        seqLimits_itemStateChanged(e);
+      }
+    });
 
-        alignFrameMenuBar.add(fileMenu);
+    alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
         alignFrameMenuBar.add(searchMenu);
         alignFrameMenuBar.add(viewMenu);
@@ -560,13 +571,15 @@ public class GAlignFrame extends Frame {
         searchMenu.add(findMenuItem);
         viewMenu.add(font);
         viewMenu.addSeparator();
-        viewMenu.add(wrapMenuItem);
+        viewMenu.add(dbref);
+        viewMenu.add(seqLimits);
+        viewMenu.addSeparator();
+    viewMenu.add(wrapMenuItem);
         viewMenu.add(scaleAbove);
         viewMenu.add(scaleLeft);
         viewMenu.add(scaleRight);
         viewMenu.addSeparator();
-        viewMenu.add(fullSeqId);
-        viewMenu.add(viewBoxesMenuItem);
+    viewMenu.add(viewBoxesMenuItem);
         viewMenu.add(viewTextMenuItem);
         viewMenu.add(colourTextMenuItem);
         viewMenu.add(renderGapsMenuItem);
@@ -787,9 +800,6 @@ public class GAlignFrame extends Frame {
     protected void font_actionPerformed(ActionEvent e) {
     }
 
-    protected void fullSeqId_actionPerformed(ActionEvent e) {
-    }
-
     protected void epsFile_actionPerformed(ActionEvent e) {
     }
 
@@ -828,4 +838,14 @@ public class GAlignFrame extends Frame {
 
     protected void about_actionPerformed(ActionEvent e) {
     }
+
+  public void dbref_actionPerformed(ItemEvent e)
+  {
+
+  }
+
+  public void seqLimits_itemStateChanged(ItemEvent e)
+  {
+
+  }
 }
-- 
1.7.10.2