From 94d4877b3d5988c15178a770bd0ebacedd4a9c40 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 15 Dec 2017 14:54:12 +0000
Subject: [PATCH] JAL-1953 removed deprecated interfaces

---
 src/jalview/ext/archaeopteryx/AptxFrame.java     |   27 ------------
 src/jalview/ext/archaeopteryx/AptxTreePanel.java |   14 ------
 src/jalview/ext/archaeopteryx/Tree.java          |   50 ----------------------
 src/jalview/ext/archaeopteryx/TreeNode.java      |   39 -----------------
 4 files changed, 130 deletions(-)
 delete mode 100644 src/jalview/ext/archaeopteryx/AptxFrame.java
 delete mode 100644 src/jalview/ext/archaeopteryx/AptxTreePanel.java
 delete mode 100644 src/jalview/ext/archaeopteryx/Tree.java
 delete mode 100644 src/jalview/ext/archaeopteryx/TreeNode.java

diff --git a/src/jalview/ext/archaeopteryx/AptxFrame.java b/src/jalview/ext/archaeopteryx/AptxFrame.java
deleted file mode 100644
index d5d2b11..0000000
--- a/src/jalview/ext/archaeopteryx/AptxFrame.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.ext.treeviewer.ExternalTreePanelI;
-import jalview.ext.treeviewer.ExternalTreeViewerFrameI;
-
-import org.forester.archaeopteryx.MainFrame;
-
-public class AptxFrame implements ExternalTreeViewerFrameI
-{
-  private final MainFrame aptxApp;
-
-  public AptxFrame(MainFrame aptx)
-  {
-    aptxApp = aptx;
-
-
-
-  }
-
-  @Override
-  public ExternalTreePanelI getTreePanel()
-  {
-    ExternalTreePanelI aptxPanel = new AptxTreePanel(
-            aptxApp.getMainPanel().getCurrentTreePanel());
-    return aptxPanel;
-  }
-}
diff --git a/src/jalview/ext/archaeopteryx/AptxTreePanel.java b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
deleted file mode 100644
index 631ff15..0000000
--- a/src/jalview/ext/archaeopteryx/AptxTreePanel.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.ext.treeviewer.ExternalTreePanelI;
-
-public class AptxTreePanel implements ExternalTreePanelI
-{
-  private final org.forester.archaeopteryx.TreePanel treeView;
-
-  public AptxTreePanel(org.forester.archaeopteryx.TreePanel aptxTreePanel)
-  {
-    treeView = aptxTreePanel;
-
-  }
-}
diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
deleted file mode 100644
index 884a359..0000000
--- a/src/jalview/ext/archaeopteryx/Tree.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
-
-import org.forester.phylogeny.Phylogeny;
-
-public class Tree implements ExternalTreeI
-{
-  private final Phylogeny tree;
-
-  public Tree(Phylogeny aptxTree)
-  {
-    tree = aptxTree;
-  }
-
-  @Override
-  public Phylogeny getOriginalTree()
-  {
-    return tree;
-
-  }
-
-  @Override
-  public ExternalTreeNodeI getRoot()
-  {
-    ExternalTreeNodeI root = new TreeNode(tree.getRoot());
-    return root;
-  }
-
-  @Override
-  public void setTreeName(String name)
-  {
-    tree.setName(name);
-
-  }
-
-  @Override
-  public ExternalTreeNodeI getNodeWithName(String name)
-  {
-    return new TreeNode(tree.getNode(name));
-
-  }
-
-  @Override
-  public String[] getAllLeafNames()
-  {
-    return tree.getAllExternalNodeNames();
-  }
-}
diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
deleted file mode 100644
index b2e33d4..0000000
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.ext.treeviewer.ExternalTreeNodeI;
-
-import java.util.List;
-
-import org.forester.phylogeny.PhylogenyNode;
-
-public class TreeNode implements ExternalTreeNodeI
-{
-  private final PhylogenyNode node;
-
-  public TreeNode(PhylogenyNode aptxNode)
-  {
-    node = aptxNode;
-  }
-
-  @Override
-  public PhylogenyNode getOriginalNode()
-  {
-    return node;
-  }
-
-  @Override
-  public String getNodeName()
-  {
-    return node.getName();
-  }
-
-  @Override
-  public List<ExternalTreeNodeI> getChildren()
-  {
-    // return node.getDescendants();
-    return null;
-
-  }
-
-
-}
-- 
1.7.10.2