From 60e7c072c017a2a8cec9cc39139b3fca8680d0eb Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Thu, 7 Dec 2017 14:24:14 +0000
Subject: [PATCH] JAL-2872 Redundant Aptx GUI menu items hidden, sorting item
 added

---
 src/jalview/ext/archaeopteryx/AptxInit.java |   62 +++++++++++++++++++++++++--
 1 file changed, 59 insertions(+), 3 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index b9a2266..dfc4387 100644
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -9,6 +9,7 @@ import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Component;
 import java.awt.Dimension;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -18,6 +19,11 @@ import java.net.URL;
 import java.util.HashMap;
 import java.util.Map;
 
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JSeparator;
+
 import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.archaeopteryx.Configuration;
@@ -490,6 +496,7 @@ public final class AptxInit
     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
             APTX_CONFIG, treeTitle);
 
+    adaptAptxGui(aptxApp);
     LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
     bindAptxNodes.associateLeavesToSequences();
@@ -540,13 +547,62 @@ public final class AptxInit
 
   }
 
+  /**
+   * Hides certain redundant Archaeopteryx GUI elements such as the menu items
+   * for reading in trees and adds extra items related to Jalview such as the
+   * tree sorting item.
+   * 
+   * 
+   * @param aptxFrame
+   */
+  private static void adaptAptxGui(MainFrame aptxFrame)
+  {
+    JMenuBar frameBar = aptxFrame.getJMenuBar();
+
+    for (int i = 0; i < frameBar.getMenuCount();i++) {
+      JMenu menu = frameBar.getMenu(i);
+
+      if (menu.getText().contains("File"))
+      {
+        // hide all "Read from ..." and "New" menu items and any Separators that
+        // come directly after them
+        Component previousMenuItem = null;
+        for (Component menuItem : menu.getMenuComponents()) {
+          if (previousMenuItem instanceof JMenuItem)
+          {
+            if (((JMenuItem) previousMenuItem).getText().startsWith("Read")
+                    || ((JMenuItem) previousMenuItem).getText()
+                            .startsWith("New"))
+            {
+              previousMenuItem.setVisible(false);
+
+              if (menuItem instanceof JSeparator)
+              {
+                menuItem.setVisible(false);
+              }
+            }
+          }
+          previousMenuItem = menuItem;
+        }
+      }
+      else if (menu.getText().contains("Inference"))
+      {
+        menu.setVisible(false);
+      }
+      else if (menu.getText().contains("View"))
+      {
+        menu.addSeparator();
+        menu.add(new JMenuItem("Sort alignment by tree"));
+      }
+
+    }
+    aptxFrame.validate();
+  }
+
   public static Map<MainFrame, JalviewBinding> getAllAptxFrames()
   {
     return activeAptx;
   }
 
-  private static void disableRedundantGuiMenus()
-  {
 
-  }
 }
-- 
1.7.10.2