JAL-1953 removed deprecated interfaces

diff --git a/src/jalview/ext/archaeopteryx/AptxFrame.java b/src/jalview/ext/archaeopteryx/AptxFrame.java
deleted file mode 100644 (file)
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 (file)
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 (file)
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 (file)
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;
-
-  }
-
-
-}