From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 11 Dec 2017 20:34:15 +0000 (+0000)
Subject: JAL-1953 start on making everything interface based
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ef887ebe817cd6595b6275f5f51001677c377214;p=jalview.git

JAL-1953 start on making everything interface based
---

diff --git a/forester b/forester
index 5642da5..835739d 160000
--- a/forester
+++ b/forester
@@ -1 +1 @@
-Subproject commit 5642da5f473ab9ae57fee86c0cb3b33525a2e916
+Subproject commit 835739d782b7099677aadf653ecc682cf74fc87f
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bb3dbcc..058cc72 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -29,6 +29,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
 import jalview.util.QuickSort;
 
 import java.util.ArrayList;
@@ -37,10 +39,6 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-
 /**
  * Routines for manipulating the order of a multiple sequence alignment TODO:
  * this class retains some global states concerning sort-order which should be
@@ -74,7 +72,7 @@ public class AlignmentSorter
 
   static TreeModel lastTree = null;
 
-  static Phylogeny lastAptxTree = null;
+  static ExternalTreeI lastExternalTree = null;
 
   static boolean sortTreeAscending = true;
 
@@ -470,16 +468,16 @@ public class AlignmentSorter
 
 
 
-  private static List<SequenceI> getOrderByTree(Phylogeny aptxTree,
-          Map<PhylogenyNode, SequenceI> nodesWithBoundSeqs)
+  private static List<SequenceI> getOrderByTree(ExternalTreeI aptxTree,
+          Map<ExternalTreeNodeI, SequenceI> nodesWithBoundSeqs)
   {
     List<SequenceI> seqsByTreeOrder = new ArrayList<>();
     if (!aptxTree.isEmpty())
     {
-      for (final PhylogenyNodeIterator iter = aptxTree
-              .iteratorPreorder(); iter.hasNext();)
+      for (final Iterator<ExternalTreeNodeI> iter = aptxTree
+              .iterateInPreOrder(); iter.hasNext();)
       {
-        PhylogenyNode treeNode = iter.next();
+        ExternalTreeNodeI treeNode = iter.next();
         seqsByTreeOrder.add(nodesWithBoundSeqs.get(treeNode));
       }
 
@@ -532,17 +530,17 @@ public class AlignmentSorter
    *          tree which has
    */
   public static void sortByTree(AlignmentI align,
-          Map<PhylogenyNode, SequenceI> aptxNodesWithSeqs,
-          Phylogeny aptxTree) throws IllegalArgumentException
+          Map<ExternalTreeNodeI, SequenceI> nodesBoundToSequences,
+          ExternalTreeI externalTreeI) throws IllegalArgumentException
   {
-    List<SequenceI> tmp = getOrderByTree(aptxTree, aptxNodesWithSeqs);
+    List<SequenceI> tmp = getOrderByTree(externalTreeI, nodesBoundToSequences);
 
     if (!tmp.isEmpty())
     {
-      if (lastAptxTree != aptxTree)
+      if (lastExternalTree != externalTreeI)
       {
         sortTreeAscending = true;
-        lastAptxTree = aptxTree;
+        lastExternalTree = externalTreeI;
       }
       else
       {
diff --git a/src/jalview/ext/archaeopteryx/AptxConfig.java b/src/jalview/ext/archaeopteryx/AptxConfig.java
new file mode 100644
index 0000000..9563a0a
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/AptxConfig.java
@@ -0,0 +1,14 @@
+package jalview.ext.archaeopteryx;
+
+import org.forester.archaeopteryx.Configuration;
+
+public class AptxConfig
+{
+  private final Configuration config;
+
+  public AptxConfig(Configuration aptxConfig)
+  {
+    config = aptxConfig;
+  }
+
+}
diff --git a/src/jalview/ext/archaeopteryx/AptxControlPanel.java b/src/jalview/ext/archaeopteryx/AptxControlPanel.java
new file mode 100644
index 0000000..6c1bfb4
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/AptxControlPanel.java
@@ -0,0 +1,31 @@
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.ExternalTreeControlsI;
+
+import org.forester.archaeopteryx.ControlPanel;
+
+public class AptxControlPanel implements ExternalTreeControlsI
+{
+  ControlPanel aptxCp;
+
+  public AptxControlPanel(ControlPanel aptxControlPanel)
+  {
+    aptxCp = aptxControlPanel;
+
+  }
+
+  @Override
+  public void defaultSettings()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void displayEntireTree()
+  {
+    aptxCp.showWhole();
+
+  }
+
+}
diff --git a/src/jalview/ext/archaeopteryx/AptxFrame.java b/src/jalview/ext/archaeopteryx/AptxFrame.java
index f0c535b..4223147 100644
--- a/src/jalview/ext/archaeopteryx/AptxFrame.java
+++ b/src/jalview/ext/archaeopteryx/AptxFrame.java
@@ -1,27 +1,123 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreePanelI;
-import jalview.ext.treeviewer.ExternalTreeViewerI;
+import jalview.ext.treeviewer.ExternalTreeControlsI;
+import jalview.ext.treeviewer.ExternalTreeFrame;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreePanel;
+
+import java.awt.Component;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JSeparator;
 
 import org.forester.archaeopteryx.MainFrame;
 
-public class Aptx implements ExternalTreeViewerI
+public class AptxFrame extends ExternalTreeFrame
 {
-  private final MainFrame aptxApp;
+  private final MainFrame aptxFrame;
 
-  public Aptx(MainFrame aptx)
+  public AptxFrame(MainFrame aptx)
   {
-    aptxApp = aptx;
+    aptxFrame = aptx;
+    adaptAptxGui(aptxFrame);
 
+  }
+  /**
+   * 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 void adaptAptxGui(MainFrame aptxFrame)
+  {
+    JMenuBar frameBar = aptxFrame.getJMenuBar();
 
+    for (int i = 0; i < frameBar.getMenuCount(); i++)
+    {
+      JMenu menu = frameBar.getMenu(i);
 
+      if (menu.getText().startsWith("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().startsWith("Inference"))
+      {
+        menu.setVisible(false);
+      }
+      else if (menu.getText().startsWith("View"))
+      {
+        menu.addSeparator();
+        JMenuItem sortMenuItem = new JMenuItem("Sort alignment by tree");
+        sortMenuItem.setVisible(false);
+        menu.add(sortMenuItem);
+      }
+
+    }
+    aptxFrame.validate();
   }
 
   @Override
-  public ExternalTreePanelI getTreePanel()
+  public ExternalTreePanel getTreePanel()
   {
-    ExternalTreePanelI aptxPanel = new AptxTreePanel(
-            aptxApp.getMainPanel().getCurrentTreePanel());
+    ExternalTreePanel aptxPanel = new AptxTreePanel(
+            aptxFrame.getMainPanel().getCurrentTreePanel());
     return aptxPanel;
   }
-}
+
+  @Override
+  public void switchTreePanel(int panelIndex)
+  {
+    aptxFrame.getMainPanel().getTabbedPane().getTabComponentAt(panelIndex);
+
+  }
+
+  @Override
+  public ExternalTreeI getTree()
+  {
+    return new Tree(
+            aptxFrame.getMainPanel().getCurrentTreePanel().getPhylogeny());
+  }
+
+  @Override
+  public void checkMultipleTrees()
+  {
+    aptxFrame.activateSaveAllIfNeeded();
+
+  }
+
+  @Override
+  public int getNumberOfTrees()
+  {
+    return aptxFrame.getMainPanel().getTabbedPane().getTabCount();
+  }
+
+  @Override
+  public ExternalTreeControlsI getTreeControls()
+  {
+    return new AptxControlPanel(aptxFrame.getMainPanel().getControlPanel());
+  }
+}
\ No newline at end of file
diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index dfc4387..e8fa7d0 100644
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -2,14 +2,17 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
 import jalview.ext.treeviewer.ExternalTreeBuilderI;
+import jalview.ext.treeviewer.ExternalTreeFrame;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
 import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.Desktop;
 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;
@@ -19,15 +22,8 @@ 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;
-import org.forester.archaeopteryx.MainFrame;
 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
 import org.forester.archaeopteryx.webservices.WebserviceUtil;
 import org.forester.io.parsers.PhylogenyParser;
@@ -39,7 +35,6 @@ import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.util.ForesterUtil;
 
@@ -52,7 +47,7 @@ import org.forester.util.ForesterUtil;
  */
 public final class AptxInit
 {
-  private final static Configuration APTX_CONFIG = new Configuration(
+  public final static Configuration APTX_CONFIG = new Configuration(
           "_aptx_jalview_configuration_file",
             false, false, false);
 
@@ -71,19 +66,19 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
-  private static Map<MainFrame, JalviewBinding> activeAptx = new HashMap<>();
+  private static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> activeAptx = new HashMap<>();
 
 
 
-  public static MainFrame createInstanceFromCalculation(
+  public static ExternalTreeFrame createInstanceFromCalculation(
           final TreeBuilder calculatedTree)
   {
-    ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
+    ExternalTreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
             calculatedTree);
 
-    Phylogeny aptxTree = aptxTreeBuilder.buildTree();
+    ExternalTreeI aptxTree = aptxTreeBuilder.buildTree();
 
-    MainFrame aptxApp = createAptxFrame(aptxTree,
+    ExternalTreeFrame aptxApp = createAptxFrame(aptxTree,
             calculatedTree.getAvport(), null);
             
     return aptxApp;
@@ -98,7 +93,8 @@ public final class AptxInit
    * @throws IOException
    * @throws FileNotFoundException
    */
-  public static MainFrame[] createInstancesFromFile(String filePath,
+  public static ExternalTreeFrame[] createInstancesFromFile(
+          String filePath,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException
   {
@@ -116,7 +112,8 @@ public final class AptxInit
       Desktop.instance.startLoading(filePath);
     }
     boolean nhx_or_nexus = false;
-    final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType(
+    final PhylogenyParser parser = ParserUtils
+            .createParserDependingOnFileType(
             treeFile, VALIDATE_PHYLOXML_XSD);
     if (parser instanceof NHXParser)
     {
@@ -143,21 +140,24 @@ public final class AptxInit
                                        JvOptionPane.WARNING_MESSAGE );
       }
     }
-    Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser, treeFile);
-    MainFrame[] aptxFrames = new MainFrame[trees.length];
+    Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser,
+            treeFile);
+    ExternalTreeFrame[] aptxFrames = new ExternalTreeFrame[trees.length];
 
 
     for (int i = 0; i < trees.length; i++)
       {
-      Phylogeny tree = trees[i];
+      Phylogeny aptxPhylogeny = trees[i];
 
       if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
       {
-        PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
+        PhylogenyMethods.transferInternalNodeNamesToConfidence(aptxPhylogeny,
+                "");
       }
       String treeTitle = treeFile.getName() + "[" + i + "]";
-      tree.setName(treeTitle);
-      aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+      aptxPhylogeny.setName(treeTitle);
+      Tree aptxTree = new Tree(aptxPhylogeny);
+      aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
 
     }
     if (Desktop.instance != null)
@@ -168,7 +168,7 @@ public final class AptxInit
     }
 
 
-  public static MainFrame[] createInstancesFromUrl(URL treeUrl,
+  public static ExternalTreeFrame[] createInstancesFromUrl(URL treeUrl,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException, RuntimeException
   {
@@ -183,11 +183,12 @@ public final class AptxInit
              REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
             TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
 
-    MainFrame[] aptxFrames = new MainFrame[trees.length];
+    ExternalTreeFrame[] aptxFrames = new ExternalTreeFrame[trees.length];
     for (int i = 0; i < trees.length; i++)
     {
-      Phylogeny tree = trees[i];
-      aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+      Phylogeny aptxTree = trees[i];
+      Tree jalviewTree = new Tree(aptxTree);
+      aptxFrames[i] = createAptxFrame(jalviewTree, viewport, treeTitle);
     }
 
     if (Desktop.instance != null)
@@ -206,7 +207,7 @@ public final class AptxInit
    * @param viewport
    * @return
    */
-  public static MainFrame[] createInstancesFromDb(
+  public static ExternalTreeFrame[] createInstancesFromDb(
           PhylogeniesWebserviceClient treeDbClient, String identifier,
           AlignmentViewport viewport)
   {
@@ -238,7 +239,7 @@ public final class AptxInit
                           { identifier }),
                   MessageManager.getString("label.invalid_url"),
                   JvOptionPane.ERROR_MESSAGE);
-          return new MainFrame[0];
+          return new ExternalTreeFrame[0];
         }
         identifier = id + "";
       }
@@ -357,20 +358,21 @@ public final class AptxInit
       }
       if ((trees != null) && (trees.length > 0))
       {
-        for (final Phylogeny phylogeny : trees)
+        for (final Phylogeny aptxTree : trees)
         {
-          if (!phylogeny.isEmpty())
+          if (!aptxTree.isEmpty())
           {
             if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
             {
-              phylogeny.setRerootable(false);
-              phylogeny.setRooted(true);
+              aptxTree.setRerootable(false);
+              aptxTree.setRooted(true);
             }
             if (treeDbClient.getProcessingInstructions() != null)
             {
               try
               {
-                WebserviceUtil.processInstructions(treeDbClient, phylogeny);
+                WebserviceUtil.processInstructions(treeDbClient,
+                        aptxTree);
               } catch (final PhyloXmlDataFormatException e)
               {
                 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -382,7 +384,7 @@ public final class AptxInit
             {
               try
               {
-                PhylogenyMethods.transferNodeNameToField(phylogeny,
+                PhylogenyMethods.transferNodeNameToField(aptxTree,
                         treeDbClient.getNodeField(), false);
               } catch (final PhyloXmlDataFormatException e)
               {
@@ -391,44 +393,47 @@ public final class AptxInit
                         JvOptionPane.ERROR_MESSAGE);
               }
             }
-            phylogeny.setIdentifier(
+            aptxTree.setIdentifier(
                     new Identifier(identifier, treeDbClient.getName()));
             // _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
-            // _main_frame.getMenuBarOfMainFrame()
+            // _main_frame.getMenuBarOfExternalTreeFrameI()
             // .add(_main_frame.getHelpMenu());
-            // _main_frame.getMainPanel().addPhylogenyInNewTab(phylogeny,
+            // _main_frame.getMainPanel().addExternalTreeIInNewTab(ExternalTreeI,
             // _main_frame.getConfiguration(),
             // new File(url.getFile()).getName(), url.toString());
 
-            MainFrame aptxApp = createAptxFrame(phylogeny, viewport,
+            Tree jalviewTree = new Tree(aptxTree);
+
+            ExternalTreeFrame aptxApp = createAptxFrame(jalviewTree,
+                    viewport,
                     url.getFile());
             String my_name_for_file = "";
-            if (!ForesterUtil.isEmpty(phylogeny.getName()))
+            if (!ForesterUtil.isEmpty(jalviewTree.getTreeName()))
             {
-              my_name_for_file = new String(phylogeny.getName())
+              my_name_for_file = new String(jalviewTree.getTreeName())
                       .replaceAll(" ", "_");
             }
-            else if (phylogeny.getIdentifier() != null)
+            else if (aptxTree.getIdentifier() != null)
             {
               final StringBuffer sb = new StringBuffer();
               if (!ForesterUtil
-                      .isEmpty(phylogeny.getIdentifier().getProvider()))
+                      .isEmpty(aptxTree.getIdentifier().getProvider()))
               {
-                sb.append(phylogeny.getIdentifier().getProvider());
+                sb.append(aptxTree.getIdentifier().getProvider());
                 sb.append("_");
               }
-              sb.append(phylogeny.getIdentifier().getValue());
+              sb.append(aptxTree.getIdentifier().getValue());
               my_name_for_file = new String(
                       sb.toString().replaceAll(" ", "_"));
             }
-            aptxApp.getMainPanel().getCurrentTreePanel()
+            aptxApp.getTreePanel()
                     .setTreeFile(new File(my_name_for_file));
-            AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
-                    phylogeny, aptxApp.getMainPanel().getControlPanel(),
-                    APTX_CONFIG);
-            // _main_frame.getMainPanel().getControlPanel().showWhole();
+            // AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
+            // aptxTree, aptxApp.getMainPanel().getControlPanel(),
+            // APTX_CONFIG);
+            aptxApp.getTreeControls().displayEntireTree();
 
-            aptxApp.activateSaveAllIfNeeded();
+            aptxApp.checkMultipleTrees();
           }
         }
       }
@@ -472,8 +477,8 @@ public final class AptxInit
 
 
 
-  public static MainFrame createAptxFrame(
-          final Phylogeny aptxTree,
+  public static ExternalTreeFrame createAptxFrame(
+          final ExternalTreeI aptxTree,
           final AlignmentViewport jalviewAlignport, String treeTitle)
   {
     if (APTX_CONFIG == null || APTX_CONFIG.isCouldReadConfigFile() == false)
@@ -493,11 +498,9 @@ public final class AptxInit
       }
 
     }
-    MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
-            APTX_CONFIG, treeTitle);
+    ExternalTreeFrame aptxApp = aptxTree.createInstanceFromTree(treeTitle);
 
-    adaptAptxGui(aptxApp);
-    LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
+    ExternalLoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
     bindAptxNodes.associateLeavesToSequences();
 
@@ -506,15 +509,16 @@ public final class AptxInit
             bindAptxNodes.getNodesWithAlignment());
     bindTreeViewFrameToJalview(aptxApp);
 
+    // adaptAptxGui(aptxApp); //moved to AptxFrame
     return aptxApp;
   }
 
 
-  public static ExternalTreeViewerBindingI<?> bindNodesToJalviewSequences(
-          final MainFrame aptxApp,
+  public static ExternalTreeViewerBindingI bindNodesToJalviewSequences(
+          final ExternalTreeFrame aptxApp,
           final AlignmentViewport jalviewAlignViewport,
-          final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
-          final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+          final Map<SequenceI, ExternalTreeNodeI> alignMappedToNodes,
+          final Map<ExternalTreeNodeI, SequenceI> nodesMappedToAlign)
   {
     JalviewBinding treeBinding = new JalviewBinding(aptxApp,
             jalviewAlignViewport,
@@ -524,8 +528,8 @@ public final class AptxInit
   }
 
 
-  public static MainFrame bindTreeViewFrameToJalview(
-          final MainFrame aptxApp)
+  public static ExternalTreeFrame bindTreeViewFrameToJalview(
+          final ExternalTreeFrame aptxApp)
   {
     int width = 400;
     int height = 550;
@@ -533,8 +537,7 @@ public final class AptxInit
     // aptxApp.setFont(Desktop.instance.getFont());
     // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
     String frameTitle = MessageManager.getString("label.aptx_title");
-    File treeFile = aptxApp.getMainPanel().getCurrentTreePanel()
-            .getTreeFile();
+    File treeFile = aptxApp.getTreePanel().getTreeFile();
     if (treeFile != null)
     {
       frameTitle += MessageManager.formatMessage("label.aptx_title_append",
@@ -547,59 +550,9 @@ 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()
+  public static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> getAllAptxFrames()
   {
     return activeAptx;
   }
diff --git a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
index 74d89d2..54bcff1 100644
--- a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
@@ -2,9 +2,10 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.DataConversions;
 import jalview.ext.forester.ForesterMatrix;
 import jalview.ext.treeviewer.ExternalTreeBuilderI;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
@@ -14,8 +15,6 @@ import java.util.Map;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.NodeData;
-import org.forester.phylogeny.data.Sequence;
 
 /**
  * Class for converting trees made in Jalview (through TreeBuilder) to trees
@@ -28,7 +27,7 @@ import org.forester.phylogeny.data.Sequence;
  *
  */
 public class AptxTreeBuilder
-        implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
+        implements ExternalTreeBuilderI
 {
   protected final SequenceI[] sequences;
 
@@ -38,13 +37,13 @@ public class AptxTreeBuilder
   
   public String treeTitle;
 
-  private final Phylogeny aptxTree;
+  private final ExternalTreeI aptxTree;
 
-  private PhylogenyNode rootNode;
+  private ExternalTreeNodeI rootNode;
 
-  private final Map<SequenceI, PhylogenyNode> alignmentWithNodes;
+  private final Map<SequenceI, ExternalTreeNodeI> alignmentWithNodes;
 
-  private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;
+  private final Map<ExternalTreeNodeI, SequenceI> nodesWithAlignment;
 
   public AptxTreeBuilder(final TreeBuilder calculatedTree)
   {
@@ -53,8 +52,8 @@ public class AptxTreeBuilder
     distances = ForesterMatrix.convertJalviewToForester(
             jalviewTree.getDistances(), sequences);
 
-    aptxTree = new Phylogeny();
-    rootNode = new PhylogenyNode();
+    aptxTree = new Tree(new Phylogeny());
+    rootNode = new TreeNode(new PhylogenyNode());
 
     int amountOfSequences = distances.getSize();
     alignmentWithNodes = new HashMap<>(amountOfSequences);
@@ -64,7 +63,7 @@ public class AptxTreeBuilder
   }
 
   @Override
-  public Phylogeny buildTree(final PhylogenyNode treeRoot)
+  public ExternalTreeI buildTree(final ExternalTreeNodeI treeRoot)
   {
 
     if (treeRoot != null)
@@ -80,17 +79,16 @@ public class AptxTreeBuilder
 
 
   @Override
-  public Phylogeny buildTree()
+  public ExternalTreeI buildTree()
   {
 
     for (SequenceI sequence : sequences)
     {
-      Sequence seq = DataConversions
-              .createForesterSequence(sequence, true);
-      PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
 
-      NodeData nodeData = sequenceNode.getNodeData();
-      nodeData.setSequence(seq);
+      ExternalTreeNodeI sequenceNode = new TreeNode(
+              new PhylogenyNode(sequence.getName()));
+
+      sequenceNode.setSequence(sequence);
 
       MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
               sequenceNode, sequence);
@@ -103,29 +101,25 @@ public class AptxTreeBuilder
     aptxTree.setRoot(rootNode);
 
     treeTitle = generateTreeName();
-    aptxTree.setName(treeTitle);
+    aptxTree.setTreeName(treeTitle);
 
     return aptxTree;
 
   }
 
   @Override
-  public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
+  public Map<SequenceI, ExternalTreeNodeI> getAlignmentBoundNodes()
   {
     return alignmentWithNodes;
   }
 
   @Override
-  public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
+  public Map<ExternalTreeNodeI, SequenceI> getNodesBoundAlignment()
   {
     return nodesWithAlignment;
   }
 
-  private Phylogeny clusterNodes()
-  {
-    return aptxTree;
 
-  }
   /**
    * Formats a localised title for the tree panel, like
    * <p>
@@ -165,6 +159,8 @@ public class AptxTreeBuilder
       return ttl;
     }
   }
+
+
   
 
 }
diff --git a/src/jalview/ext/archaeopteryx/AptxTreePanel.java b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
index 631ff15..94e0f91 100644
--- a/src/jalview/ext/archaeopteryx/AptxTreePanel.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
@@ -1,8 +1,13 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreePanelI;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.ExternalTreePanel;
 
-public class AptxTreePanel implements ExternalTreePanelI
+import java.io.File;
+import java.util.Set;
+
+public class AptxTreePanel extends ExternalTreePanel
 {
   private final org.forester.archaeopteryx.TreePanel treeView;
 
@@ -11,4 +16,41 @@ public class AptxTreePanel implements ExternalTreePanelI
     treeView = aptxTreePanel;
 
   }
+
+  @Override
+  public void setTreeFile(File file)
+  {
+    treeView.setTreeFile(file);
+  }
+
+  @Override
+  public ExternalTreeI getTree()
+  {
+    return new Tree(treeView.getPhylogeny());
+  }
+
+  @Override
+  public File getTreeFile()
+  {
+    return treeView.getTreeFile();
+  }
+
+  @Override
+  public ExternalTreeNodeI findNode(int x, int y)
+  {
+    return new TreeNode(treeView.findNode(x, y));
+  }
+
+  @Override
+  public void setMatchingNodes(Set<Long> hashSet)
+  {
+    treeView.setFoundNodes0(hashSet);
+
+  }
+
+  @Override
+  public Set<Long> getMatchingNodes()
+  {
+    return treeView.getFoundNodes0();
+  }
 }
diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index 88b2d15..510becf 100644
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -9,6 +9,10 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalTreeFrame;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.ExternalTreePanel;
 import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
@@ -34,19 +38,10 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import javax.swing.JTabbedPane;
 import javax.swing.SwingUtilities;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
-import org.forester.archaeopteryx.MainFrame;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.BranchColor;
-
 /**
  * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
  * it originates from, meaning that selecting sequences in the tree viewer also
@@ -56,23 +51,21 @@ import org.forester.phylogeny.data.BranchColor;
  *
  */
 public final class JalviewBinding
-        implements ExternalTreeViewerBindingI<PhylogenyNode>
+        implements ExternalTreeViewerBindingI
 {
-  private final MainFrame aptxFrame;
+  private final ExternalTreeFrame aptxFrame;
 
-  private org.forester.archaeopteryx.TreePanel treeView;
+  private ExternalTreePanel treeView;
 
   private AlignmentViewport parentAvport;
 
-  private final JTabbedPane treeTabs;
-
   private final StructureSelectionManager ssm;
 
   private AlignmentPanel[] associatedPanels;
 
-  private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
+  private Map<SequenceI, ExternalTreeNodeI> sequencesBoundToNodes;
 
-  private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
+  private Map<ExternalTreeNodeI, SequenceI> nodesBoundToSequences;
 
   private float rootX;
 
@@ -97,13 +90,13 @@ public final class JalviewBinding
    *          map with tree nodes and matching sequences used to calculate the
    *          tree as key, value pair respectively.
    */
-  public JalviewBinding(final MainFrame archaeopteryx,
+  public JalviewBinding(final ExternalTreeFrame archaeopteryx,
           final AlignmentViewport jalviewAlignmentViewport,
-          final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
-          final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+          final Map<SequenceI, ExternalTreeNodeI> alignMappedToNodes,
+          final Map<ExternalTreeNodeI, SequenceI> nodesMappedToAlign)
   {
 
-    if (archaeopteryx.getMainPanel().getTabbedPane().getTabCount() > 1)
+    if (archaeopteryx.getNumberOfTrees() > 1)
     {
       JvOptionPane.showMessageDialog(Desktop.desktop,
               MessageManager.getString("label.tabs_detected_archaeopteryx"),
@@ -118,8 +111,7 @@ public final class JalviewBinding
     sequencesBoundToNodes = alignMappedToNodes;
     nodesBoundToSequences = nodesMappedToAlign;
 
-    treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
-    treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
+    treeView = archaeopteryx.getTreePanel();
     ssm = parentAvport.getStructureSelectionManager();
     
     ssm.addSelectionListener(this);
@@ -141,36 +133,36 @@ public final class JalviewBinding
 
     });
 
-    treeTabs.addChangeListener(new ChangeListener()
-    {
-
-      @Override
-      public void stateChanged(ChangeEvent e)
-      {
-
-        SwingUtilities.invokeLater(new Runnable()
-        {
-
-          @Override
-          /**
-           * Resend the selection to the tree view when tabs get switched, this
-           * has to be buried in invokeLater as Forester first resets the tree
-           * view on switching tabs, without invokeLater this would get called
-           * before Forester resets which would nullify the selection.
-           */
-          public void run()
-          {
-            treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
-            parentAvport.sendSelection();
-            // PaintRefresher.Refresh(treeView,
-            // parentAvport.getSequenceSetId());
-
-          }
-        });
-
-      }
-
-    });
+    // treeTabs.addChangeListener(new ChangeListener()
+    // {
+    //
+    // @Override
+    // public void stateChanged(ChangeEvent e)
+    // {
+    //
+    // SwingUtilities.invokeLater(new Runnable()
+    // {
+    //
+    // @Override
+    // /**
+    // * Resend the selection to the tree view when tabs get switched, this
+    // * has to be buried in invokeLater as Forester first resets the tree
+    // * view on switching tabs, without invokeLater this would get called
+    // * before Forester resets which would nullify the selection.
+    // */
+    // public void run()
+    // {
+    // treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
+    // parentAvport.sendSelection();
+    // // PaintRefresher.Refresh(treeView,
+    // // parentAvport.getSequenceSetId());
+    //
+    // }
+    // });
+    //
+    // }
+    //
+    // });
 
   }
 
@@ -192,7 +184,8 @@ public final class JalviewBinding
        */
       public void run()
       {
-        final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
+        final ExternalTreeNodeI node = treeView.findNode(e.getX(),
+                e.getY());
         if (node != null)
         {
           if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
@@ -249,26 +242,27 @@ public final class JalviewBinding
     if (source == parentAvport) // check if source is alignment from where the
     // tree originates
     {
-      treeView.setFoundNodes0(
+      treeView.setMatchingNodes(
               new HashSet<Long>(seqsel.getSequences().size()));
 
 
       for (SequenceI selectedSequence : seqsel.getSequences())
       {
-        PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
+        ExternalTreeNodeI matchingNode = sequencesBoundToNodes
+                .get(selectedSequence);
         if (matchingNode != null)
         {
-          treeView.getFoundNodes0().add(matchingNode.getId());
+          treeView.getMatchingNodes().add(matchingNode.getId());
 
 
-          if (!matchingNode.getBranchData().isHasBranchColor())
-          {
-            // Color foundNodesColour = treeView.getTreeColorSet()
-            // .getFoundColor0();
-            // matchingNode.getBranchData()
-            // .setBranchColor(new BranchColor(foundNodesColour));
-
-          }
+          // if (!matchingNode.getBranchData().isHasBranchColor())
+          // {
+          // // Color foundNodesColour = treeView.getTreeColorSet()
+          // // .getFoundColor0();
+          // // matchingNode.getBranchData()
+          // // .setBranchColor(new BranchColor(foundNodesColour));
+          //
+          // }
 
         }
 
@@ -285,14 +279,13 @@ public final class JalviewBinding
    */
   public void partitionTree(final int x)
   {
-    Phylogeny tree = treeView.getPhylogeny();
+    ExternalTreeI tree = treeView.getTree();
 
     if (!tree.isEmpty())
     {
       // should be calculated on each partition as the tree can theoretically
       // change in the meantime
-      PhylogenyNode furthestNode = PhylogenyMethods
-              .calculateNodeWithMaxDistanceToRoot(tree);
+      ExternalTreeNodeI furthestNode = tree.getFurthestNode();
       furthestNodeX = furthestNode.getXcoord();
       rootX = tree.getRoot().getXcoord();
 
@@ -300,7 +293,8 @@ public final class JalviewBinding
       if (furthestNodeX != rootX && !(x > furthestNodeX))
       {
         float threshold = (x - rootX) / (furthestNodeX - rootX);
-        List<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
+        List<ExternalTreeNodeI> foundNodes = getNodesAboveThreshold(
+                threshold,
                 tree.getRoot());
 
       }
@@ -309,11 +303,11 @@ public final class JalviewBinding
 
   }
 
-  public List<PhylogenyNode> getNodesAboveThreshold(double threshold,
-          PhylogenyNode node)
+  public List<ExternalTreeNodeI> getNodesAboveThreshold(double threshold,
+          ExternalTreeNodeI node)
   {
 
-    List<PhylogenyNode> nodesAboveThreshold = new ArrayList<>();
+    List<ExternalTreeNodeI> nodesAboveThreshold = new ArrayList<>();
 
     parentAvport.setSelectionGroup(null);
     parentAvport.getAlignment().deleteAllGroups();
@@ -341,15 +335,14 @@ public final class JalviewBinding
    * @param node
    * @return
    */
-  private List<PhylogenyNode> colourNodesAboveThreshold(
-          List<PhylogenyNode> nodeList, double threshold,
-          PhylogenyNode node)
+  private List<ExternalTreeNodeI> colourNodesAboveThreshold(
+          List<ExternalTreeNodeI> nodeList, double threshold,
+          ExternalTreeNodeI node)
   {
 
-    for (PhylogenyNode childNode : node.getDescendants())
+    for (ExternalTreeNodeI childNode : node.getDirectChildren())
     {
-      childNode.getBranchData()
-              .setBranchColor(new BranchColor(Color.black));
+      childNode.setBranchColor(Color.black);
       float nodeCutoff = (childNode.getXcoord() - rootX)
               / (furthestNodeX - rootX);
 
@@ -359,8 +352,7 @@ public final class JalviewBinding
 
         Color randomColour = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
-        childNode.getBranchData()
-                .setBranchColor(new BranchColor(randomColour));
+        childNode.setBranchColor(randomColour);
 
         List<SequenceI> groupSeqs = new ArrayList<>();
         SequenceI seq = nodesBoundToSequences.get(childNode);
@@ -370,10 +362,10 @@ public final class JalviewBinding
           parentAvport.setSequenceColour(seq, randomColour);
         }
 
-        List<PhylogenyNode> descendantNodes = PhylogenyMethods
-                .getAllDescendants(childNode);
+        List<ExternalTreeNodeI> descendantNodes = childNode
+                .getAllDescendants();
         // .forEach instead?
-        for (PhylogenyNode descNode : descendantNodes)
+        for (ExternalTreeNodeI descNode : descendantNodes)
         {
           seq = nodesBoundToSequences.get(descNode);
           if (seq != null)
@@ -382,8 +374,7 @@ public final class JalviewBinding
             parentAvport.setSequenceColour(seq, randomColour);
           }
 
-          descNode.getBranchData()
-                  .setBranchColor(new BranchColor(randomColour));
+          descNode.setBranchColor(randomColour);
         }
 
         if (groupSeqs != null)
@@ -493,7 +484,7 @@ public final class JalviewBinding
    * does)
    */
   @Override
-  public void showNodeSelectionOnAlign(final PhylogenyNode node)
+  public void showNodeSelectionOnAlign(final ExternalTreeNodeI node)
   {
 
       if (node.isInternal())
@@ -514,13 +505,13 @@ public final class JalviewBinding
 
 
   @Override
-  public void showMatchingSequence(final PhylogenyNode nodeToMatch)
+  public void showMatchingSequence(final ExternalTreeNodeI nodeToMatch)
   {
     SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
     if (matchingSequence != null)
     {
       long nodeId = nodeToMatch.getId();
-      addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
+      addOrRemoveInSet(treeView.getMatchingNodes(), nodeId);
       treeSelectionChanged(matchingSequence);
       parentAvport.sendSelection();
 
@@ -528,15 +519,14 @@ public final class JalviewBinding
   }
 
   @Override
-  public void showMatchingChildSequences(final PhylogenyNode parentNode)
+  public void showMatchingChildSequences(final ExternalTreeNodeI parentNode)
   {
     // redundancy here, Forester already iterates through tree to get all
     // descendants
-    List<PhylogenyNode> childNodes = PhylogenyMethods
-            .getAllDescendants(parentNode);
+    List<ExternalTreeNodeI> childNodes = parentNode.getAllDescendants();
 
 
-    for (PhylogenyNode childNode : childNodes)
+    for (ExternalTreeNodeI childNode : childNodes)
     {
       // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
 
@@ -544,7 +534,7 @@ public final class JalviewBinding
       if (matchingSequence != null)
       {
         long nodeId = childNode.getId();
-        addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
+        addOrRemoveInSet(treeView.getMatchingNodes(), nodeId);
 
         treeSelectionChanged(matchingSequence);
 
@@ -642,6 +632,7 @@ public final class JalviewBinding
 
   }
 
+  @Override
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
     // TODO: move to alignment view controller
@@ -652,7 +643,7 @@ public final class JalviewBinding
     {
     AlignmentSorter.sortByTree(viewport.getAlignment(),
             nodesBoundToSequences,
-              treeView.getPhylogeny());
+              treeView.getTree());
       CommandI undo;
       undo = new OrderCommand("Tree Sort", oldOrder,
               viewport.getAlignment());
diff --git a/src/jalview/ext/archaeopteryx/LoadedTreeSequenceAssociation.java b/src/jalview/ext/archaeopteryx/LoadedTreeSequenceAssociation.java
index 86f27d1..f05ba45 100644
--- a/src/jalview/ext/archaeopteryx/LoadedTreeSequenceAssociation.java
+++ b/src/jalview/ext/archaeopteryx/LoadedTreeSequenceAssociation.java
@@ -2,30 +2,29 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.DataConversions;
 import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
+import jalview.ext.treeviewer.ExternalTreeI;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
 import jalview.util.MappingUtils;
 
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.Map;
 
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 
 public class LoadedTreeSequenceAssociation
         implements ExternalLoadedTreeAssociationI
 {
   SequenceI[] alignSequences;
 
-  Phylogeny tree;
+  ExternalTreeI tree;
 
-  Map<SequenceI, PhylogenyNode> alignmentWithNodes;
+  Map<SequenceI, ExternalTreeNodeI> alignmentWithNodes;
 
-  Map<PhylogenyNode, SequenceI> nodesWithAlignment;
+  Map<ExternalTreeNodeI, SequenceI> nodesWithAlignment;
 
   public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
-          Phylogeny aptxTree)
+          ExternalTreeI aptxTree)
   {
     alignSequences = alignmentSequences;
     tree = aptxTree;
@@ -56,18 +55,18 @@ public class LoadedTreeSequenceAssociation
 
     if (!tree.isEmpty())
     {
-      for (final PhylogenyNodeIterator iter = tree.iteratorPreorder(); iter
+      for (final Iterator<ExternalTreeNodeI> iter = tree
+              .iterateInPreOrder(); iter
               .hasNext();)
       {
-        PhylogenyNode treeNode = iter.next();
-        nodeSequenceName = treeNode.getName();
+        ExternalTreeNodeI treeNode = iter.next();
+        nodeSequenceName = treeNode.getNodeName();
 
         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
         if (nodeSequence != null)
         {
-          org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
-                  .createForesterSequence(nodeSequence, true);
-          treeNode.getNodeData().setSequence(foresterNodeSeq);
+
+          treeNode.setSequence(nodeSequence);
 
           MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
                   nodeSequence, treeNode);
@@ -84,78 +83,16 @@ public class LoadedTreeSequenceAssociation
 
 
 
-  public Map<SequenceI, PhylogenyNode> getAlignmentWithNodes()
+  public Map<SequenceI, ExternalTreeNodeI> getAlignmentWithNodes()
   {
     return alignmentWithNodes;
   }
 
-  public Map<PhylogenyNode, SequenceI> getNodesWithAlignment()
+  public Map<ExternalTreeNodeI, SequenceI> getNodesWithAlignment()
   {
     return nodesWithAlignment;
   }
 
-  // {
-  // SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-  //
-  // List<PhylogenyNode> leaves = aptxTree.getExternalNodes();
-  //
-  // int namesleft = seqs.length;
-  // SequenceI nodeSequence;
-  // String nodeSequenceName;
-  // List<SequenceI> one2many = new ArrayList<>();
-  // int countOne2Many = 0;
-  //
-  // for (PhylogenyNode treeNode : leaves)
-  // {
-  // nodeSequenceName = treeNode.getName();
-  // nodeSequence = null;
-  //
-  // if (namesleft > -1)
-  // {
-  // nodeSequence = algnIds.findIdMatch(nodeSequenceName);
-  // }
-  //
-  // if (nodeSequence != null)
-  // {
-  // org.forester.phylogeny.data.Sequence foresterNodeSeq =
-  // ForesterDataConversions.createForesterSequence(nodeSequence, true);
-  //
-  // treeNode.getNodeData().setSequence(foresterNodeSeq);
-  // if (one2many.contains(nodeSequence))
-  // {
-  // countOne2Many++;
-  // if (jalview.bin.Cache.log.isDebugEnabled())
-  // {
-  // jalview.bin.Cache.log.debug("One 2 many relationship for"
-  // +nodeSequence.getName());
-  // }
-  // }
-  // else
-  // {
-  // one2many.add(nodeSequence);
-  // namesleft--;
-  // }
-  // }
-  // else
-  // {
-  // treeNode.setCollapse(true); // collapse nodes that couldn't be connected
-  // // to a sequence
-  //
-  //
-  // // treeNode.setElement( new Sequence(nodeSequenceName,
-  // "THISISAPLACEHOLDER"));
-  // // treeNode.setPlaceholder(true);
-  // }
-  // }
-  // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many > 0)
-  // {
-  // jalview.bin.Cache.log.debug("There were " + countOne2Many
-  // + "alignment sequence ids (out of" + one2many.size()
-  // + " unique ids) linked to two or more leaves.");
-  // }
-  // one2many.clear();
-  //
-  // }
 
 }
 
diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
index 884a359..d06339e 100644
--- a/src/jalview/ext/archaeopteryx/Tree.java
+++ b/src/jalview/ext/archaeopteryx/Tree.java
@@ -1,9 +1,15 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.ext.treeviewer.ExternalTreeFrame;
 import jalview.ext.treeviewer.ExternalTreeI;
 import jalview.ext.treeviewer.ExternalTreeNodeI;
 
+import java.util.Iterator;
+
+import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
 
 public class Tree implements ExternalTreeI
 {
@@ -14,12 +20,6 @@ public class Tree implements ExternalTreeI
     tree = aptxTree;
   }
 
-  @Override
-  public Phylogeny getOriginalTree()
-  {
-    return tree;
-
-  }
 
   @Override
   public ExternalTreeNodeI getRoot()
@@ -47,4 +47,85 @@ public class Tree implements ExternalTreeI
   {
     return tree.getAllExternalNodeNames();
   }
+
+  @Override
+  public void setRerootable(boolean b)
+  {
+    tree.setRerootable(b);
+
+  }
+
+  @Override
+  public void setRooted(boolean b)
+  {
+    tree.setRooted(b);
+
+  }
+
+  @Override
+  public boolean isEmpty()
+  {
+    return tree.isEmpty();
+  }
+
+  @Override
+  public String getTreeName()
+  {
+    return tree.getName();
+  }
+
+  @Override
+  public void setRoot(ExternalTreeNodeI rootNode)
+  {
+    PhylogenyNode treeRoot = new PhylogenyNode(rootNode.getNodeName());
+    // expand this
+    tree.setRoot(treeRoot);
+
+  }
+
+  @Override
+  public double getHeight(boolean adjustForCollapsedSubtrees)
+  {
+    return tree.calculateHeight(adjustForCollapsedSubtrees);
+  }
+
+  @Override
+  public Iterator<ExternalTreeNodeI> iterateInPreOrder()
+  {
+    Iterator<ExternalTreeNodeI> iter = new TreeIterator(
+            tree.iteratorPreorder());
+    return iter;
+  }
+
+  @Override
+  public Iterator<ExternalTreeNodeI> iterateInLevelOrder()
+  {
+    Iterator<ExternalTreeNodeI> iter = new TreeIterator(
+            tree.iteratorLevelOrder());
+    return iter;
+  }
+
+  @Override
+  public Iterator<ExternalTreeNodeI> iterateInPostOrder()
+  {
+    Iterator<ExternalTreeNodeI> iter = new TreeIterator(
+            tree.iteratorPostorder());
+    return iter;
+  }
+
+  @Override
+  public ExternalTreeNodeI getFurthestNode()
+  {
+    PhylogenyNode furthestNode = PhylogenyMethods
+            .calculateNodeWithMaxDistanceToRoot(tree);
+    return new TreeNode(furthestNode);
+  }
+
+  @Override
+  public ExternalTreeFrame createInstanceFromTree(String instanceTitle)
+  {
+    return new AptxFrame(Archaeopteryx.createApplication(tree,
+            AptxInit.APTX_CONFIG,
+            instanceTitle));
+  }
 }
diff --git a/src/jalview/ext/archaeopteryx/TreeIterator.java b/src/jalview/ext/archaeopteryx/TreeIterator.java
new file mode 100644
index 0000000..79e8e49
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/TreeIterator.java
@@ -0,0 +1,31 @@
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.ExternalTreeNodeI;
+
+import java.util.Iterator;
+
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
+public class TreeIterator implements Iterator<ExternalTreeNodeI>
+{
+  private final PhylogenyNodeIterator iter;
+
+  public TreeIterator(PhylogenyNodeIterator aptxIterator)
+  {
+    iter = aptxIterator;
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return iter.hasNext();
+  }
+
+  @Override
+  public ExternalTreeNodeI next()
+  {
+    ExternalTreeNodeI node = new TreeNode(iter.next());
+    return node;
+  }
+
+}
diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
index b2e33d4..78b3981 100644
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -1,39 +1,111 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.datamodel.SequenceI;
+import jalview.ext.forester.DataConversions;
 import jalview.ext.treeviewer.ExternalTreeNodeI;
 
+import java.awt.Color;
 import java.util.List;
 
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.BranchColor;
 
 public class TreeNode implements ExternalTreeNodeI
 {
   private final PhylogenyNode node;
 
+  private SequenceI nodeSeq;
+
   public TreeNode(PhylogenyNode aptxNode)
   {
     node = aptxNode;
+
   }
 
+
   @Override
-  public PhylogenyNode getOriginalNode()
+  public String getNodeName()
   {
-    return node;
+    return node.getName();
   }
 
   @Override
-  public String getNodeName()
+  public List<ExternalTreeNodeI> getAllDescendants()
   {
-    return node.getName();
+    List<PhylogenyNode> descNodes = PhylogenyMethods
+            .getAllDescendants(node);
+    return DataConversions.getConvertedTreeNodes(descNodes);
+
   }
 
   @Override
-  public List<ExternalTreeNodeI> getChildren()
+  public List<ExternalTreeNodeI> getExternalDescendants()
   {
-    // return node.getDescendants();
-    return null;
+    List<PhylogenyNode> extDescNodes = node.getAllExternalDescendants();
+    return DataConversions.getConvertedTreeNodes(extDescNodes);
+  }
 
+
+  @Override
+  public List<ExternalTreeNodeI> getDirectChildren()
+  {
+    List<PhylogenyNode> childNodes = node.getDescendants();
+    return DataConversions.getConvertedTreeNodes(childNodes);
+  }
+
+
+
+  @Override
+  public void setSequence(SequenceI seq)
+  {
+    nodeSeq = seq;
+    org.forester.phylogeny.data.Sequence foresterFormatSeq = DataConversions
+            .createForesterSequence(seq, true);
+    node.getNodeData().setSequence(foresterFormatSeq);
+
+  }
+
+  @Override
+  public SequenceI getSequence()
+  {
+    return nodeSeq;
+    // ideally this would return a converted node.getNodeData().getSequence()
   }
 
+  @Override
+  public void addAsChild(ExternalTreeNodeI childNode)
+  {
+    PhylogenyNode aptxNode = new PhylogenyNode(childNode.getNodeName());
+
+    // expand on this
+    node.addAsChild(aptxNode);
+
+  }
+
+  @Override
+  public long getId()
+  {
+    return node.getId();
+  }
+
+  @Override
+  public float getXcoord()
+  {
+    return node.getXcoord();
+  }
+
+  @Override
+  public void setBranchColor(Color branchColor)
+  {
+    node.getBranchData().setBranchColor(new BranchColor(branchColor));
+
+  }
+
+  @Override
+  public boolean isInternal()
+  {
+    return node.isInternal();
+  }
 
 }
diff --git a/src/jalview/ext/forester/DataConversions.java b/src/jalview/ext/forester/DataConversions.java
index be97e0e..22c4df0 100644
--- a/src/jalview/ext/forester/DataConversions.java
+++ b/src/jalview/ext/forester/DataConversions.java
@@ -1,10 +1,16 @@
 package jalview.ext.forester;
 
 import jalview.datamodel.SequenceI;
+import jalview.ext.archaeopteryx.TreeNode;
+import jalview.ext.treeviewer.ExternalTreeNodeI;
 import jalview.math.MatrixI;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.phylogeny.PhylogenyNode;
 
 public final class DataConversions
 {
@@ -73,4 +79,15 @@ public final class DataConversions
     return foresterMatrix;
 
   }
+
+  public static List<ExternalTreeNodeI> getConvertedTreeNodes(
+          List<PhylogenyNode> aptxNodes)
+  {
+    List<ExternalTreeNodeI> jalviewNodes = new ArrayList<>();
+    for (PhylogenyNode aptxNode : aptxNodes)
+    {
+      jalviewNodes.add(new TreeNode(aptxNode));
+    }
+    return jalviewNodes;
+  }
 }
diff --git a/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java b/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
index 83ffac6..8d35fd7 100644
--- a/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
+++ b/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
@@ -1,5 +1,9 @@
 package jalview.ext.treeviewer;
 
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
 /**
  * Interface for associating the leaves of a loaded in (not calculated) tree to
  * the alignment sequences in Jalview.
@@ -11,4 +15,8 @@ package jalview.ext.treeviewer;
 public interface ExternalLoadedTreeAssociationI
 {
   public void associateLeavesToSequences();
+
+  public Map<SequenceI, ExternalTreeNodeI> getAlignmentWithNodes();
+
+  public Map<ExternalTreeNodeI, SequenceI> getNodesWithAlignment();
 }
diff --git a/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java b/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
index 8fd1d1d..44ca06e 100644
--- a/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
@@ -5,26 +5,18 @@ import jalview.datamodel.SequenceI;
 import java.util.Map;
 
 /**
- * Note that this will take anything as a Tree or TreeNode object as no
- * assumptions can be made about the inheritance structure of Tree or TreeNode
- * (besides being Objects).
- * 
  * @author kjvanderheide
  *
- * @param <T>
- *          Tree object that the tree viewer requires.
- * @param <N>
- *          Tree node object that the tree viewer requires.
  */
-public interface ExternalTreeBuilderI<T, N>
+public interface ExternalTreeBuilderI
 {
-  public T buildTree(N treeRoot);
+  public ExternalTreeI buildTree(ExternalTreeNodeI treeRoot);
 
-  public T buildTree();
+  public ExternalTreeI buildTree();
 
-  public Map<SequenceI, N> getAlignmentBoundNodes();
+  public Map<SequenceI, ExternalTreeNodeI> getAlignmentBoundNodes();
 
-  public Map<N, SequenceI> getNodesBoundAlignment();
+  public Map<ExternalTreeNodeI, SequenceI> getNodesBoundAlignment();
 
   public String generateTreeName();
 
diff --git a/src/jalview/ext/treeviewer/ExternalTreeControlsI.java b/src/jalview/ext/treeviewer/ExternalTreeControlsI.java
new file mode 100644
index 0000000..e278879
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreeControlsI.java
@@ -0,0 +1,9 @@
+package jalview.ext.treeviewer;
+
+public interface ExternalTreeControlsI
+{
+  public void defaultSettings();
+
+  public void displayEntireTree();
+
+}
diff --git a/src/jalview/ext/treeviewer/ExternalTreeFrame.java b/src/jalview/ext/treeviewer/ExternalTreeFrame.java
new file mode 100644
index 0000000..32c8e51
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreeFrame.java
@@ -0,0 +1,19 @@
+package jalview.ext.treeviewer;
+
+import javax.swing.JInternalFrame;
+
+public abstract class ExternalTreeFrame extends JInternalFrame
+{
+  public abstract ExternalTreePanel getTreePanel();
+
+  public abstract void switchTreePanel(int panelIndex);
+
+  public abstract ExternalTreeI getTree();
+
+  public abstract void checkMultipleTrees();
+
+  public abstract int getNumberOfTrees();
+
+  public abstract ExternalTreeControlsI getTreeControls();
+
+}
diff --git a/src/jalview/ext/treeviewer/ExternalTreeI.java b/src/jalview/ext/treeviewer/ExternalTreeI.java
index 0184227..68e5ff8 100644
--- a/src/jalview/ext/treeviewer/ExternalTreeI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeI.java
@@ -1,15 +1,37 @@
 package jalview.ext.treeviewer;
 
+import java.util.Iterator;
+
 public interface ExternalTreeI
 {
-  public void setTreeName(String name);
-
-  public <T> T getOriginalTree();
-
   public ExternalTreeNodeI getRoot();
 
   public ExternalTreeNodeI getNodeWithName(String name);
 
+  public ExternalTreeNodeI getFurthestNode();
+
   public String[] getAllLeafNames();
 
+  public void setTreeName(String treeTitle);
+
+  public void setRerootable(boolean b);
+
+  public void setRooted(boolean b);
+
+  public boolean isEmpty();
+
+  public String getTreeName();
+
+  public void setRoot(ExternalTreeNodeI rootNode);
+
+  public double getHeight(boolean adjustForCollapsedSubtrees);
+
+  public Iterator<ExternalTreeNodeI> iterateInPreOrder();
+
+  public Iterator<ExternalTreeNodeI> iterateInLevelOrder();
+
+  public Iterator<ExternalTreeNodeI> iterateInPostOrder();
+
+  public ExternalTreeFrame createInstanceFromTree(String instanceTitle);
+
 }
diff --git a/src/jalview/ext/treeviewer/ExternalTreeIteratorI.java b/src/jalview/ext/treeviewer/ExternalTreeIteratorI.java
new file mode 100644
index 0000000..e5a39f6
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreeIteratorI.java
@@ -0,0 +1,6 @@
+package jalview.ext.treeviewer;
+
+public interface ExternalTreeIteratorI
+{
+
+}
diff --git a/src/jalview/ext/treeviewer/ExternalTreeNodeI.java b/src/jalview/ext/treeviewer/ExternalTreeNodeI.java
index 34f45bd..1481b06 100644
--- a/src/jalview/ext/treeviewer/ExternalTreeNodeI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeNodeI.java
@@ -1,12 +1,38 @@
 package jalview.ext.treeviewer;
 
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
 import java.util.List;
 
 public interface ExternalTreeNodeI
 {
-  public <N> N getOriginalNode();
+  final static int nodeCount = 0;
 
   public String getNodeName();
 
-  public List<ExternalTreeNodeI> getChildren();
+  public List<ExternalTreeNodeI> getAllDescendants();
+
+  public List<ExternalTreeNodeI> getExternalDescendants();
+
+  public List<ExternalTreeNodeI> getDirectChildren();
+
+  public void setSequence(SequenceI seq);
+
+  public SequenceI getSequence();
+
+  public void addAsChild(ExternalTreeNodeI childNode);
+
+  public long getId();
+
+  public float getXcoord();
+
+  public void setBranchColor(Color branchColor);
+
+  public boolean isInternal();
+
+  public static int getTotalNodes()
+  {
+    return nodeCount;
+  }
 }
diff --git a/src/jalview/ext/treeviewer/ExternalTreePanel.java b/src/jalview/ext/treeviewer/ExternalTreePanel.java
new file mode 100644
index 0000000..705117d
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreePanel.java
@@ -0,0 +1,22 @@
+package jalview.ext.treeviewer;
+
+import java.io.File;
+import java.util.Set;
+
+import javax.swing.JPanel;
+
+public abstract class ExternalTreePanel extends JPanel
+{
+
+  public abstract void setTreeFile(File file);
+
+  public abstract File getTreeFile();
+
+  public abstract ExternalTreeI getTree();
+
+  public abstract ExternalTreeNodeI findNode(int x, int y);
+
+  public abstract void setMatchingNodes(Set<Long> matchingNodes);
+
+  public abstract Set<Long> getMatchingNodes();
+}
diff --git a/src/jalview/ext/treeviewer/ExternalTreePanelI.java b/src/jalview/ext/treeviewer/ExternalTreePanelI.java
deleted file mode 100644
index c488683..0000000
--- a/src/jalview/ext/treeviewer/ExternalTreePanelI.java
+++ /dev/null
@@ -1,6 +0,0 @@
-package jalview.ext.treeviewer;
-
-public interface ExternalTreePanelI
-{
-
-}
diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
index 4fc267a..de76b82 100644
--- a/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
@@ -20,7 +20,9 @@
  */
 package jalview.ext.treeviewer;
 
+import jalview.commands.CommandI;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
 import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 
@@ -30,16 +32,13 @@ import java.awt.event.MouseListener;
 /**
  * 
  * Interface for binding a tree viewer to Jalview alignments. Assumes a tree
- * viewer will both want to receive and send selection events. Note that this
- * will take anything as a TreeNode object as no assumptions can be made about
- * the inheritance structure of the TreeNode (besides being an Object).
+ * viewer will both want to receive and send selection events.
  * 
  * @author kjvanderheide
  *
- * @param <N>
- *          Tree node object.
+ * 
  */
-public interface ExternalTreeViewerBindingI<N>
+public interface ExternalTreeViewerBindingI
         extends ActionListener, MouseListener, SelectionListener,
         SelectionSource
 {
@@ -48,14 +47,16 @@ public interface ExternalTreeViewerBindingI<N>
    * corresponding sequence in the Jalview alignment view. If an internal node
    * is selected all child sequences get highlighted as well.
    */
-  public void showNodeSelectionOnAlign(N node);
+  public void showNodeSelectionOnAlign(ExternalTreeNodeI node);
 
   public void treeSelectionChanged(SequenceI sequence);
 
-  public void showMatchingSequence(N nodeToMatch);
+  public void showMatchingSequence(ExternalTreeNodeI nodeToMatch);
 
-  public void showMatchingChildSequences(N parentNode);
+  public void showMatchingChildSequences(ExternalTreeNodeI parentNode);
 
   public void sortByTree_actionPerformed();
 
+  public CommandI sortAlignmentIn(AlignmentPanel alignPanel);
+
 }
diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerConfigI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerConfigI.java
new file mode 100644
index 0000000..7617c97
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreeViewerConfigI.java
@@ -0,0 +1,6 @@
+package jalview.ext.treeviewer;
+
+public interface ExternalTreeViewerConfigI
+{
+
+}
diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerFrameI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerFrameI.java
deleted file mode 100644
index bc1924a..0000000
--- a/src/jalview/ext/treeviewer/ExternalTreeViewerFrameI.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package jalview.ext.treeviewer;
-
-public interface ExternalTreeViewerI
-{
-  public ExternalTreePanelI getTreePanel();
-
-}
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 84e02c7..184ffeb 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -62,9 +62,10 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.AptxInit;
-import jalview.ext.archaeopteryx.JalviewBinding;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
 import jalview.ext.forester.io.TreeParser;
+import jalview.ext.treeviewer.ExternalTreeFrame;
+import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -141,6 +142,7 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -156,7 +158,6 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
-import org.forester.archaeopteryx.MainFrame;
 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
 import org.forester.archaeopteryx.webservices.WebservicesManager;
 
@@ -3764,7 +3765,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .get(viewport.getSequenceSetId());
     List<TreePanel> treePanels = new ArrayList<>();
 
-    Map<MainFrame, JalviewBinding> aptxFrames = AptxInit.getAllAptxFrames();
+    Map<ExternalTreeFrame, ExternalTreeViewerBindingI> aptxFrames = AptxInit
+            .getAllAptxFrames();
 
     for (Component comp : comps)
     {
@@ -3784,19 +3786,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sortByTreeMenu.setVisible(true);
 
-    for (Map.Entry<MainFrame, JalviewBinding> aptxFrameWithBinding : aptxFrames
+    for (Entry<ExternalTreeFrame, ExternalTreeViewerBindingI> aptxFrameWithBinding : aptxFrames
             .entrySet())
     {
-      MainFrame aptxFrame = aptxFrameWithBinding.getKey();
-      JalviewBinding binding = aptxFrameWithBinding.getValue();
+      ExternalTreeFrame aptxFrame = aptxFrameWithBinding.getKey();
+      ExternalTreeViewerBindingI binding = aptxFrameWithBinding.getValue();
 
       // future support for multiple tabs
       // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame
       // .getMainPanel().getTreePanels())
       {
         final JMenuItem item = new JMenuItem(
-                aptxFrame.getMainPanel().getCurrentTreePanel()
-                        .getPhylogeny().getName());
+                aptxFrame.getTree().getTreeName());
 
           item.addActionListener(new ActionListener()
           {
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d40ce8d..3ff0b75 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -43,6 +43,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalTreeI;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
@@ -956,6 +957,7 @@ public abstract class AlignmentViewport
     changeSupport = null;
     ranges = null;
     currentTree = null;
+    currentExtTree = null;
     selectionGroup = null;
     setAlignment(null);
   }
@@ -2879,6 +2881,8 @@ public abstract class AlignmentViewport
 
   protected TreeModel currentTree = null;
 
+  protected ExternalTreeI currentExtTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2949,4 +2953,15 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  public ExternalTreeI getCurrentExtTree()
+  {
+    return currentExtTree;
+  }
+
+  public void setCurrentExtTree(ExternalTreeI externalTree)
+  {
+    currentExtTree = externalTree;
+  }
+
 }