JAL-1953 -External from all interfaces names

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 058cc72..9f9b774 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -29,8 +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.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
 import jalview.util.QuickSort;
 
 import java.util.ArrayList;
@@ -72,7 +72,7 @@ public class AlignmentSorter
 
   static TreeModel lastTree = null;
 
-  static ExternalTreeI lastExternalTree = null;
+  static TreeI lastExternalTree = null;
 
   static boolean sortTreeAscending = true;
 
@@ -468,16 +468,16 @@ public class AlignmentSorter
 
 
 
-  private static List<SequenceI> getOrderByTree(ExternalTreeI aptxTree,
-          Map<ExternalTreeNodeI, SequenceI> nodesWithBoundSeqs)
+  private static List<SequenceI> getOrderByTree(TreeI aptxTree,
+          Map<TreeNodeI, SequenceI> nodesWithBoundSeqs)
   {
     List<SequenceI> seqsByTreeOrder = new ArrayList<>();
     if (!aptxTree.isEmpty())
     {
-      for (final Iterator<ExternalTreeNodeI> iter = aptxTree
+      for (final Iterator<TreeNodeI> iter = aptxTree
               .iterateInPreOrder(); iter.hasNext();)
       {
-        ExternalTreeNodeI treeNode = iter.next();
+        TreeNodeI treeNode = iter.next();
         seqsByTreeOrder.add(nodesWithBoundSeqs.get(treeNode));
       }
 
@@ -530,17 +530,17 @@ public class AlignmentSorter
    *          tree which has
    */
   public static void sortByTree(AlignmentI align,
-          Map<ExternalTreeNodeI, SequenceI> nodesBoundToSequences,
-          ExternalTreeI externalTreeI) throws IllegalArgumentException
+          Map<TreeNodeI, SequenceI> nodesBoundToSequences,
+          TreeI treeI) throws IllegalArgumentException
   {
-    List<SequenceI> tmp = getOrderByTree(externalTreeI, nodesBoundToSequences);
+    List<SequenceI> tmp = getOrderByTree(treeI, nodesBoundToSequences);
 
     if (!tmp.isEmpty())
     {
-      if (lastExternalTree != externalTreeI)
+      if (lastExternalTree != treeI)
       {
         sortTreeAscending = true;
-        lastExternalTree = externalTreeI;
+        lastExternalTree = treeI;
       }
       else
       {

diff --git a/src/jalview/ext/archaeopteryx/AptxControlPanel.java b/src/jalview/ext/archaeopteryx/AptxControlPanel.java
index facbe01..2744908 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxControlPanel.java
+++ b/src/jalview/ext/archaeopteryx/AptxControlPanel.java
@@ -1,10 +1,10 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeControlsI;
+import jalview.ext.treeviewer.TreeControlsI;
 
 import org.forester.archaeopteryx.ControlPanel;
 
-public class AptxControlPanel implements ExternalTreeControlsI
+public class AptxControlPanel implements TreeControlsI
 {
   ControlPanel aptxCp;
 

diff --git a/src/jalview/ext/archaeopteryx/AptxFrame.java b/src/jalview/ext/archaeopteryx/AptxFrame.java
index 9a47836..e050425 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxFrame.java
+++ b/src/jalview/ext/archaeopteryx/AptxFrame.java
@@ -1,10 +1,10 @@
 package jalview.ext.archaeopteryx;
 
 import jalview.bin.Cache;
-import jalview.ext.treeviewer.ExternalTreeControlsI;
-import jalview.ext.treeviewer.ExternalTreeFrame;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreePanel;
+import jalview.ext.treeviewer.TreeControlsI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreePanelI;
 import jalview.gui.Desktop;
 import jalview.gui.EPSOptions;
 import jalview.io.JalviewFileChooser;
@@ -38,13 +38,13 @@ import org.forester.archaeopteryx.MainFrame;
 import org.forester.phylogeny.Phylogeny;
 import org.jibble.epsgraphics.EpsGraphics2D;
 
-public class AptxFrame implements ExternalTreeFrame
+public class AptxFrame implements TreeFrameI
 {
   private final MainFrame aptxFrame;
 
-  private ExternalTreePanel aptxPanel;
+  private TreePanelI aptxPanel;
 
-  private ExternalTreeControlsI aptxControls;
+  private TreeControlsI aptxControls;
 
 
   public AptxFrame(Phylogeny tree, Configuration aptxConfig,
@@ -228,13 +228,13 @@ public class AptxFrame implements ExternalTreeFrame
     }
   }
   @Override
-  public ExternalTreePanel getTreePanel()
+  public TreePanelI getTreePanel()
   {
     return aptxPanel;
   }
 
   @Override
-  public ExternalTreeI getTree()
+  public TreeI getTree()
   {
     return aptxPanel.getTree();
   }
@@ -253,7 +253,7 @@ public class AptxFrame implements ExternalTreeFrame
   }
 
   @Override
-  public ExternalTreeControlsI getTreeControls()
+  public TreeControlsI getTreeControls()
   {
     return aptxControls;
   }

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index 49c3162..5752e51 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -3,12 +3,12 @@ package jalview.ext.archaeopteryx;
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
 import jalview.ext.forester.UtilityMethods;
-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.ext.treeviewer.LoadedTreeAssociationI;
+import jalview.ext.treeviewer.TreeBuilderI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
 import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
@@ -74,20 +74,20 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
-  private static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> activeAptx = new HashMap<>();
+  private static Map<TreeFrameI, TreeViewerBindingI> activeAptx = new HashMap<>();
 
 
 
 
-  public static ExternalTreeFrame createInstanceFromCalculation(
+  public static TreeFrameI createInstanceFromCalculation(
           final TreeBuilder calculatedTree)
   {
-    ExternalTreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
+    TreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
             calculatedTree);
 
-    ExternalTreeI aptxTree = aptxTreeBuilder.buildTree();
+    TreeI aptxTree = aptxTreeBuilder.buildTree();
 
-    ExternalTreeFrame aptxApp = createAptxFrame(aptxTree,
+    TreeFrameI aptxApp = createAptxFrame(aptxTree,
             calculatedTree.getAvport(), null);
             
     return aptxApp;
@@ -103,13 +103,13 @@ public final class AptxInit
    * @throws IOException
    * @throws FileNotFoundException
    */
-  public static ExternalTreeFrame[] createInstancesFromFile(
+  public static TreeFrameI[] createInstancesFromFile(
           String filePath,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException
   {
     File treeFile = new File(filePath);
-    ExternalTreeFrame[] aptxFrames = null;
+    TreeFrameI[] aptxFrames = null;
     if (UtilityMethods.canForesterReadFile(treeFile))
     {
 
@@ -148,7 +148,7 @@ public final class AptxInit
     }
     Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser,
             treeFile);
-      aptxFrames = new ExternalTreeFrame[trees.length];
+      aptxFrames = new TreeFrameI[trees.length];
 
 
     for (int i = 0; i < trees.length; i++)
@@ -174,7 +174,7 @@ public final class AptxInit
     }
 
 
-  public static ExternalTreeFrame[] createInstancesFromUrl(URL treeUrl,
+  public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException, RuntimeException
   {
@@ -189,7 +189,7 @@ public final class AptxInit
              REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
             TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
 
-    ExternalTreeFrame[] aptxFrames = new ExternalTreeFrame[trees.length];
+    TreeFrameI[] aptxFrames = new TreeFrameI[trees.length];
     for (int i = 0; i < trees.length; i++)
     {
       Phylogeny aptxTree = trees[i];
@@ -212,14 +212,14 @@ public final class AptxInit
    * @param viewport
    * @return
    */
-  public static ExternalTreeFrame[] createInstancesFromDb(
+  public static TreeFrameI[] createInstancesFromDb(
           PhylogeniesWebserviceClient treeDbClient, String identifier,
           AlignmentViewport viewport)
   {
 
     URL url = null;
     Phylogeny[] trees = null;
-    ExternalTreeFrame[] aptxFrames = null;
+    TreeFrameI[] aptxFrames = null;
 
     if ((identifier != null) && (identifier.trim().length() > 0))
     {
@@ -245,7 +245,7 @@ public final class AptxInit
                           { identifier }),
                   MessageManager.getString("label.invalid_url"),
                   JvOptionPane.ERROR_MESSAGE);
-          return new ExternalTreeFrame[0];
+          return new TreeFrameI[0];
         }
         identifier = id + "";
       }
@@ -323,7 +323,7 @@ public final class AptxInit
         // _main_frame.getMainPanel().setWaitCursor();
         // }
         trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
-        aptxFrames = new ExternalTreeFrame[trees.length];
+        aptxFrames = new TreeFrameI[trees.length];
       } catch (final MalformedURLException e)
       {
         exception = true;
@@ -411,7 +411,7 @@ public final class AptxInit
             // new File(url.getFile()).getName(), url.toString());
 
 
-            ExternalTreeFrame aptxApp = createAptxFrame(aptxTree,
+            TreeFrameI aptxApp = createAptxFrame(aptxTree,
                     viewport,
                     url.getFile());
             String my_name_for_file = "";
@@ -483,14 +483,14 @@ public final class AptxInit
 
 
 
-  public static ExternalTreeFrame createAptxFrame(ExternalTreeI aptxTree,
+  public static TreeFrameI createAptxFrame(TreeI aptxTree,
           AlignmentViewport jalviewAlignport, String treeTitle)
   {
     validateConfig(APTX_CONFIG);
-    ExternalTreeFrame aptxApp = aptxTree
+    TreeFrameI aptxApp = aptxTree
             .createTreeViewerFromTree(treeTitle);
-    ExternalTreeI jalviewTree = aptxApp.getTree();
-    ExternalLoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+    TreeI jalviewTree = aptxApp.getTree();
+    LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(),
             jalviewTree);
     bindAptxNodes.associateLeavesToSequences();
@@ -505,15 +505,15 @@ public final class AptxInit
   }
 
 
-  protected static ExternalTreeFrame createAptxFrame(
+  protected static TreeFrameI createAptxFrame(
           final Phylogeny aptxTree,
           final AlignmentViewport jalviewAlignport, String treeTitle)
   {
     validateConfig(APTX_CONFIG);
-    ExternalTreeFrame aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
+    TreeFrameI aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
             treeTitle);
-    ExternalTreeI jalviewTree = aptxApp.getTree();
-    ExternalLoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+    TreeI jalviewTree = aptxApp.getTree();
+    LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(),
             jalviewTree);
     bindAptxNodes.associateLeavesToSequences();
@@ -528,13 +528,13 @@ public final class AptxInit
   }
 
 
-  protected static ExternalTreeViewerBindingI bindNodesToJalviewSequences(
-          final ExternalTreeFrame aptxApp,
+  protected static TreeViewerBindingI bindNodesToJalviewSequences(
+          final TreeFrameI aptxApp,
           final AlignmentViewport jalviewAlignViewport,
-          final Map<SequenceI, ExternalTreeNodeI> alignMappedToNodes,
-          final Map<ExternalTreeNodeI, SequenceI> nodesMappedToAlign)
+          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
   {
-    ExternalTreeViewerBindingI treeBinding = new JalviewBinding(aptxApp,
+    TreeViewerBindingI treeBinding = new JalviewBinding(aptxApp,
             jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
     activeAptx.put(aptxApp, treeBinding);
@@ -542,8 +542,8 @@ public final class AptxInit
   }
 
 
-  protected static ExternalTreeFrame bindTreeViewFrameToJalview(
-          final ExternalTreeFrame aptxApp)
+  protected static TreeFrameI bindTreeViewFrameToJalview(
+          final TreeFrameI aptxApp)
   {
     int width = 400;
     int height = 550;
@@ -588,7 +588,7 @@ public final class AptxInit
 
 
 
-  public static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> getAllAptxFrames()
+  public static Map<TreeFrameI, TreeViewerBindingI> getAllAptxFrames()
   {
     return activeAptx;
   }

diff --git a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
index c6f7898..9dff141 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
@@ -3,9 +3,9 @@ package jalview.ext.archaeopteryx;
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
 import jalview.ext.forester.ForesterMatrix;
-import jalview.ext.treeviewer.ExternalTreeBuilderI;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.TreeBuilderI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
@@ -27,7 +27,7 @@ import org.forester.phylogeny.PhylogenyNode;
  *
  */
 public class AptxTreeBuilder
-        implements ExternalTreeBuilderI
+        implements TreeBuilderI
 {
   protected final SequenceI[] sequences;
 
@@ -37,13 +37,13 @@ public class AptxTreeBuilder
   
   public String treeTitle;
 
-  private final ExternalTreeI aptxTree;
+  private final TreeI aptxTree;
 
-  private ExternalTreeNodeI rootNode;
+  private TreeNodeI rootNode;
 
-  private final Map<SequenceI, ExternalTreeNodeI> alignmentWithNodes;
+  private final Map<SequenceI, TreeNodeI> alignmentWithNodes;
 
-  private final Map<ExternalTreeNodeI, SequenceI> nodesWithAlignment;
+  private final Map<TreeNodeI, SequenceI> nodesWithAlignment;
 
   public AptxTreeBuilder(final TreeBuilder calculatedTree)
   {
@@ -63,7 +63,7 @@ public class AptxTreeBuilder
   }
 
   @Override
-  public ExternalTreeI buildTree(final ExternalTreeNodeI treeRoot)
+  public TreeI buildTree(final TreeNodeI treeRoot)
   {
 
     if (treeRoot != null)
@@ -79,13 +79,13 @@ public class AptxTreeBuilder
 
 
   @Override
-  public ExternalTreeI buildTree()
+  public TreeI buildTree()
   {
 
     for (SequenceI sequence : sequences)
     {
 
-      ExternalTreeNodeI sequenceNode = TreeNode
+      TreeNodeI sequenceNode = TreeNode
               .getUniqueWrapper(
               new PhylogenyNode(sequence.getName()));
 
@@ -109,13 +109,13 @@ public class AptxTreeBuilder
   }
 
   @Override
-  public Map<SequenceI, ExternalTreeNodeI> getAlignmentBoundNodes()
+  public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes()
   {
     return alignmentWithNodes;
   }
 
   @Override
-  public Map<ExternalTreeNodeI, SequenceI> getNodesBoundAlignment()
+  public Map<TreeNodeI, SequenceI> getNodesBoundAlignment()
   {
     return nodesWithAlignment;
   }

diff --git a/src/jalview/ext/archaeopteryx/AptxTreePanel.java b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
index 5693b0f..70fc9e1 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxTreePanel.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
@@ -1,8 +1,8 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
-import jalview.ext.treeviewer.ExternalTreePanel;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+import jalview.ext.treeviewer.TreePanelI;
 import jalview.gui.PaintRefresher;
 
 import java.awt.Event;
@@ -16,11 +16,11 @@ import java.util.Set;
 
 import javax.accessibility.AccessibleContext;
 
-public class AptxTreePanel implements ExternalTreePanel
+public class AptxTreePanel implements TreePanelI
 {
   private final org.forester.archaeopteryx.TreePanel treeView;
 
-  private final ExternalTreeI tree;
+  private final TreeI tree;
 
   private String sequenceSetId;
 
@@ -33,7 +33,7 @@ public class AptxTreePanel implements ExternalTreePanel
 
   protected AptxTreePanel(
           org.forester.archaeopteryx.TreePanel aptxTreePanel,
-          ExternalTreeI aptxTree)
+          TreeI aptxTree)
   {
     treeView = aptxTreePanel;
     tree = aptxTree;
@@ -47,7 +47,7 @@ public class AptxTreePanel implements ExternalTreePanel
   }
 
   @Override
-  public ExternalTreeI getTree()
+  public TreeI getTree()
   {
     return tree;
   }
@@ -59,7 +59,7 @@ public class AptxTreePanel implements ExternalTreePanel
   }
 
   @Override
-  public ExternalTreeNodeI findNode(int x, int y)
+  public TreeNodeI findNode(int x, int y)
   {
     return TreeNode.getUniqueWrapper(treeView.findNode(x, y));
   }

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index 772a7d8..6ad0b60 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -9,11 +9,11 @@ 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.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+import jalview.ext.treeviewer.TreePanelI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
 import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
@@ -53,11 +53,11 @@ import javax.swing.event.InternalFrameEvent;
  *
  */
 public final class JalviewBinding
-        implements ExternalTreeViewerBindingI
+        implements TreeViewerBindingI
 {
-  private final ExternalTreeFrame aptxFrame;
+  private final TreeFrameI aptxFrame;
 
-  private ExternalTreePanel treeView;
+  private TreePanelI treeView;
 
   private AlignmentViewport parentAvport;
 
@@ -65,9 +65,9 @@ public final class JalviewBinding
 
   private AlignmentPanel[] associatedPanels;
 
-  private Map<SequenceI, ExternalTreeNodeI> sequencesBoundToNodes;
+  private Map<SequenceI, TreeNodeI> sequencesBoundToNodes;
 
-  private Map<ExternalTreeNodeI, SequenceI> nodesBoundToSequences;
+  private Map<TreeNodeI, SequenceI> nodesBoundToSequences;
 
   private float rootX;
 
@@ -92,10 +92,10 @@ public final class JalviewBinding
    *          map with tree nodes and matching sequences used to calculate the
    *          tree as key, value pair respectively.
    */
-  public JalviewBinding(final ExternalTreeFrame archaeopteryx,
+  public JalviewBinding(final TreeFrameI archaeopteryx,
           final AlignmentViewport jalviewAlignmentViewport,
-          final Map<SequenceI, ExternalTreeNodeI> alignMappedToNodes,
-          final Map<ExternalTreeNodeI, SequenceI> nodesMappedToAlign)
+          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
   {
 
     if (archaeopteryx.getNumberOfTrees() > 1)
@@ -200,7 +200,7 @@ public final class JalviewBinding
 
       Rectangle visibleView = treeView.getVisibleArea();
 
-      for (ExternalTreeNodeI node : treeView.getTree().getRoot()
+      for (TreeNodeI node : treeView.getTree().getRoot()
               .getAllDescendants())
       {
         if (!(node.getXcoord() > visibleView.getMinX()
@@ -231,7 +231,7 @@ public final class JalviewBinding
        */
       public void run()
       {
-        final ExternalTreeNodeI node = treeView.findNode(e.getX(),
+        final TreeNodeI node = treeView.findNode(e.getX(),
                 e.getY());
         if (node != null)
         {
@@ -296,7 +296,7 @@ public final class JalviewBinding
 
       for (SequenceI selectedSequence : seqsel.getSequences())
       {
-        ExternalTreeNodeI matchingNode = sequencesBoundToNodes
+        TreeNodeI matchingNode = sequencesBoundToNodes
                 .get(selectedSequence);
         if (matchingNode != null)
         {
@@ -327,13 +327,13 @@ public final class JalviewBinding
    */
   public void partitionTree(final int x)
   {
-    ExternalTreeI tree = treeView.getTree();
+    TreeI tree = treeView.getTree();
 
     if (!tree.isEmpty())
     {
       // should be calculated on each partition as the tree can theoretically
       // change in the meantime
-      ExternalTreeNodeI furthestNode = tree.getFurthestNode();
+      TreeNodeI furthestNode = tree.getFurthestNode();
       furthestNodeX = furthestNode.getXcoord();
       rootX = tree.getRoot().getXcoord();
 
@@ -341,7 +341,7 @@ public final class JalviewBinding
       if (furthestNodeX != rootX && !(x > furthestNodeX))
       {
         float threshold = (x - rootX) / (furthestNodeX - rootX);
-        List<ExternalTreeNodeI> foundNodes = getNodesAboveThreshold(
+        List<TreeNodeI> foundNodes = getNodesAboveThreshold(
                 threshold,
                 tree.getRoot());
 
@@ -351,11 +351,11 @@ public final class JalviewBinding
 
   }
 
-  public List<ExternalTreeNodeI> getNodesAboveThreshold(double threshold,
-          ExternalTreeNodeI node)
+  public List<TreeNodeI> getNodesAboveThreshold(double threshold,
+          TreeNodeI node)
   {
 
-    List<ExternalTreeNodeI> nodesAboveThreshold = new ArrayList<>();
+    List<TreeNodeI> nodesAboveThreshold = new ArrayList<>();
 
     parentAvport.setSelectionGroup(null);
     parentAvport.getAlignment().deleteAllGroups();
@@ -383,12 +383,12 @@ public final class JalviewBinding
    * @param node
    * @return
    */
-  private List<ExternalTreeNodeI> colourNodesAboveThreshold(
-          List<ExternalTreeNodeI> nodeList, double threshold,
-          ExternalTreeNodeI node)
+  private List<TreeNodeI> colourNodesAboveThreshold(
+          List<TreeNodeI> nodeList, double threshold,
+          TreeNodeI node)
   {
 
-    for (ExternalTreeNodeI childNode : node.getDirectChildren())
+    for (TreeNodeI childNode : node.getDirectChildren())
     {
       childNode.setBranchColor(Color.black);
       float nodeCutoff = (childNode.getXcoord() - rootX)
@@ -410,10 +410,10 @@ public final class JalviewBinding
           parentAvport.setSequenceColour(seq, randomColour);
         }
 
-        List<ExternalTreeNodeI> descendantNodes = childNode
+        List<TreeNodeI> descendantNodes = childNode
                 .getAllDescendants();
         // .forEach instead?
-        for (ExternalTreeNodeI descNode : descendantNodes)
+        for (TreeNodeI descNode : descendantNodes)
         {
           seq = nodesBoundToSequences.get(descNode);
           if (seq != null)
@@ -532,7 +532,7 @@ public final class JalviewBinding
    * does)
    */
   @Override
-  public void showNodeSelectionOnAlign(final ExternalTreeNodeI node)
+  public void showNodeSelectionOnAlign(final TreeNodeI node)
   {
 
       if (node.isInternal())
@@ -553,7 +553,7 @@ public final class JalviewBinding
 
 
   @Override
-  public void showMatchingSequence(final ExternalTreeNodeI nodeToMatch)
+  public void showMatchingSequence(final TreeNodeI nodeToMatch)
   {
     SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
     if (matchingSequence != null)
@@ -567,14 +567,14 @@ public final class JalviewBinding
   }
 
   @Override
-  public void showMatchingChildSequences(final ExternalTreeNodeI parentNode)
+  public void showMatchingChildSequences(final TreeNodeI parentNode)
   {
     // redundancy here, Forester already iterates through tree to get all
     // descendants
-    List<ExternalTreeNodeI> childNodes = parentNode.getAllDescendants();
+    List<TreeNodeI> childNodes = parentNode.getAllDescendants();
 
 
-    for (ExternalTreeNodeI childNode : childNodes)
+    for (TreeNodeI childNode : childNodes)
     {
       // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
 

diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
index 93091b7..12dd8c7 100644 (file)
--- a/src/jalview/ext/archaeopteryx/Tree.java
+++ b/src/jalview/ext/archaeopteryx/Tree.java
@@ -1,8 +1,8 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeFrame;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
 
 import java.util.Iterator;
 
@@ -11,7 +11,7 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class Tree implements ExternalTreeI
+public class Tree implements TreeI
 {
   private final Phylogeny tree;
 
@@ -32,16 +32,16 @@ public class Tree implements ExternalTreeI
             .iteratorPostorder(); iterator.hasNext();)
     {
       PhylogenyNode foresterNode = iterator.next();
-      ExternalTreeNodeI treeNode = TreeNode
+      TreeNodeI treeNode = TreeNode
               .getUniqueWrapper(foresterNode);
 
     }
   }
 
   @Override
-  public ExternalTreeNodeI getRoot()
+  public TreeNodeI getRoot()
   {
-    ExternalTreeNodeI root = TreeNode.getUniqueWrapper(tree.getRoot());
+    TreeNodeI root = TreeNode.getUniqueWrapper(tree.getRoot());
     return root;
   }
 
@@ -53,7 +53,7 @@ public class Tree implements ExternalTreeI
   }
 
   @Override
-  public ExternalTreeNodeI getNodeWithName(String name)
+  public TreeNodeI getNodeWithName(String name)
   {
     return TreeNode.getUniqueWrapper(tree.getNode(name));
 
@@ -92,7 +92,7 @@ public class Tree implements ExternalTreeI
   }
 
   @Override
-  public void setRoot(ExternalTreeNodeI rootNode)
+  public void setRoot(TreeNodeI rootNode)
   {
     PhylogenyNode treeRoot = TreeNode.unwrapNode(rootNode);
     tree.setRoot(treeRoot);
@@ -107,31 +107,31 @@ public class Tree implements ExternalTreeI
   }
 
   @Override
-  public Iterator<ExternalTreeNodeI> iterateInPreOrder()
+  public Iterator<TreeNodeI> iterateInPreOrder()
   {
-    Iterator<ExternalTreeNodeI> iter = new TreeIterator(
+    Iterator<TreeNodeI> iter = new TreeIterator(
             tree.iteratorPreorder());
     return iter;
   }
 
   @Override
-  public Iterator<ExternalTreeNodeI> iterateInLevelOrder()
+  public Iterator<TreeNodeI> iterateInLevelOrder()
   {
-    Iterator<ExternalTreeNodeI> iter = new TreeIterator(
+    Iterator<TreeNodeI> iter = new TreeIterator(
             tree.iteratorLevelOrder());
     return iter;
   }
 
   @Override
-  public Iterator<ExternalTreeNodeI> iterateInPostOrder()
+  public Iterator<TreeNodeI> iterateInPostOrder()
   {
-    Iterator<ExternalTreeNodeI> iter = new TreeIterator(
+    Iterator<TreeNodeI> iter = new TreeIterator(
             tree.iteratorPostorder());
     return iter;
   }
 
   @Override
-  public ExternalTreeNodeI getFurthestNode()
+  public TreeNodeI getFurthestNode()
   {
     PhylogenyNode furthestNode = PhylogenyMethods
             .calculateNodeWithMaxDistanceToRoot(tree);
@@ -139,7 +139,7 @@ public class Tree implements ExternalTreeI
   }
 
   @Override
-  public ExternalTreeFrame createTreeViewerFromTree(String instanceTitle)
+  public TreeFrameI createTreeViewerFromTree(String instanceTitle)
   {
     return new AptxFrame(Archaeopteryx.createApplication(tree,
             AptxInit.APTX_CONFIG,

diff --git a/src/jalview/ext/archaeopteryx/TreeIterator.java b/src/jalview/ext/archaeopteryx/TreeIterator.java
index 2d82db2..20c8fc8 100644 (file)
--- a/src/jalview/ext/archaeopteryx/TreeIterator.java
+++ b/src/jalview/ext/archaeopteryx/TreeIterator.java
@@ -1,12 +1,12 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.TreeNodeI;
 
 import java.util.Iterator;
 
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 
-public class TreeIterator implements Iterator<ExternalTreeNodeI>
+public class TreeIterator implements Iterator<TreeNodeI>
 {
   private final PhylogenyNodeIterator iter;
 
@@ -22,9 +22,9 @@ public class TreeIterator implements Iterator<ExternalTreeNodeI>
   }
 
   @Override
-  public ExternalTreeNodeI next()
+  public TreeNodeI next()
   {
-    ExternalTreeNodeI node = TreeNode.getUniqueWrapper(iter.next());
+    TreeNodeI node = TreeNode.getUniqueWrapper(iter.next());
     return node;
   }
 

diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
index e37f89d..07c8d95 100644 (file)
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -1,7 +1,7 @@
 package jalview.ext.archaeopteryx;
 
 import jalview.datamodel.SequenceI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.ext.treeviewer.TreeNodeI;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -13,16 +13,16 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.BranchColor;
 
-public class TreeNode implements ExternalTreeNodeI
+public class TreeNode implements TreeNodeI
 {
   private final PhylogenyNode node;
 
   private SequenceI nodeSeq;
 
-  private static Map<PhylogenyNode, ExternalTreeNodeI> originalNodes = new HashMap<>(
+  private static Map<PhylogenyNode, TreeNodeI> originalNodes = new HashMap<>(
           500); // prolly make this size dynamic
 
-  private static Map<ExternalTreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
+  private static Map<TreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
           500);
 
   private TreeNode(PhylogenyNode aptxNode)
@@ -42,7 +42,7 @@ public class TreeNode implements ExternalTreeNodeI
 
 
   @Override
-  public List<ExternalTreeNodeI> getAllDescendants()
+  public List<TreeNodeI> getAllDescendants()
   {
 
     List<PhylogenyNode> descNodes = PhylogenyMethods
@@ -53,7 +53,7 @@ public class TreeNode implements ExternalTreeNodeI
   }
 
   @Override
-  public List<ExternalTreeNodeI> getExternalDescendants()
+  public List<TreeNodeI> getExternalDescendants()
   {
     List<PhylogenyNode> extDescNodes = node.getAllExternalDescendants();
     return getUniqueWrappers(extDescNodes);
@@ -61,7 +61,7 @@ public class TreeNode implements ExternalTreeNodeI
 
 
   @Override
-  public List<ExternalTreeNodeI> getDirectChildren()
+  public List<TreeNodeI> getDirectChildren()
   {
     List<PhylogenyNode> childNodes = node.getDescendants();
     return getUniqueWrappers(childNodes);
@@ -89,7 +89,7 @@ public class TreeNode implements ExternalTreeNodeI
   }
 
   @Override
-  public void addAsChild(ExternalTreeNodeI childNode)
+  public void addAsChild(TreeNodeI childNode)
   {
     PhylogenyNode aptxNode = unwrapNode(childNode);
 
@@ -122,10 +122,10 @@ public class TreeNode implements ExternalTreeNodeI
     return node.isInternal();
   }
 
-  public static List<ExternalTreeNodeI> getUniqueWrappers(
+  public static List<TreeNodeI> getUniqueWrappers(
           List<PhylogenyNode> aptxNodes)
   {
-    List<ExternalTreeNodeI> wrappedNodes = new ArrayList<>(
+    List<TreeNodeI> wrappedNodes = new ArrayList<>(
             aptxNodes.size());
 
     for (PhylogenyNode aptxNode : aptxNodes)
@@ -143,14 +143,14 @@ public class TreeNode implements ExternalTreeNodeI
    * @param aptxNode
    * @return
    */
-  public static ExternalTreeNodeI getUniqueWrapper(
+  public static TreeNodeI getUniqueWrapper(
           PhylogenyNode aptxNode)
   {
     if (aptxNode == null)
     {
       return null;
     }
-    ExternalTreeNodeI wrappedNode = originalNodes.get(aptxNode);
+    TreeNodeI wrappedNode = originalNodes.get(aptxNode);
     if (wrappedNode == null)
     {
       wrappedNode = new TreeNode(aptxNode);
@@ -168,7 +168,7 @@ public class TreeNode implements ExternalTreeNodeI
    * @param wrappedNode
    * @return
    */
-  protected static PhylogenyNode unwrapNode(ExternalTreeNodeI wrappedNode)
+  protected static PhylogenyNode unwrapNode(TreeNodeI wrappedNode)
   {
     if (wrappedNode == null)
     {

diff --git a/src/jalview/ext/archaeopteryx/TreeParser.java b/src/jalview/ext/archaeopteryx/TreeParser.java
index 79853ed..c16ea12 100644 (file)
--- a/src/jalview/ext/archaeopteryx/TreeParser.java
+++ b/src/jalview/ext/archaeopteryx/TreeParser.java
@@ -1,14 +1,14 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeParserI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeParserI;
 
 import java.io.IOException;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.phylogeny.Phylogeny;
 
-public class TreeParser implements ExternalTreeParserI
+public class TreeParser implements TreeParserI
 {
   private final PhylogenyParser parser;
 
@@ -18,10 +18,10 @@ public class TreeParser implements ExternalTreeParserI
   }
 
   @Override
-  public ExternalTreeI[] parse() throws IOException
+  public TreeI[] parse() throws IOException
   {
     Phylogeny[] foresterTrees = parser.parse();
-    ExternalTreeI[] jalviewTrees = new ExternalTreeI[foresterTrees.length];
+    TreeI[] jalviewTrees = new TreeI[foresterTrees.length];
 
     for (int i = 0; i < foresterTrees.length; i++)
     {

diff --git a/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java b/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
deleted file mode 100644 (file)
index 44ca06e..0000000
--- a/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package jalview.ext.treeviewer;
-
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
-
-/**
- * @author kjvanderheide
- *
- */
-public interface ExternalTreeBuilderI
-{
-  public ExternalTreeI buildTree(ExternalTreeNodeI treeRoot);
-
-  public ExternalTreeI buildTree();
-
-  public Map<SequenceI, ExternalTreeNodeI> getAlignmentBoundNodes();
-
-  public Map<ExternalTreeNodeI, SequenceI> getNodesBoundAlignment();
-
-  public String generateTreeName();
-
-}

diff --git a/src/jalview/ext/treeviewer/ExternalTreeI.java b/src/jalview/ext/treeviewer/ExternalTreeI.java
deleted file mode 100644 (file)
index 820995f..0000000
--- a/src/jalview/ext/treeviewer/ExternalTreeI.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package jalview.ext.treeviewer;
-
-import java.util.Iterator;
-
-public interface ExternalTreeI
-{
-  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();
-
-  ExternalTreeFrame createTreeViewerFromTree(String instanceTitle);
-
-}

diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerConfigI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerConfigI.java
deleted file mode 100644 (file)
index 7617c97..0000000
--- a/src/jalview/ext/treeviewer/ExternalTreeViewerConfigI.java
+++ /dev/null
@@ -1,6 +0,0 @@
-package jalview.ext.treeviewer;
-
-public interface ExternalTreeViewerConfigI
-{
-
-}

diff --git a/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java b/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
similarity index 62%
rename from src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
rename to src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
index 8d35fd7..19cf834 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
+++ b/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
@@ -12,11 +12,11 @@ import java.util.Map;
  *
  * 
  */
-public interface ExternalLoadedTreeAssociationI
+public interface LoadedTreeAssociationI
 {
   public void associateLeavesToSequences();
 
-  public Map<SequenceI, ExternalTreeNodeI> getAlignmentWithNodes();
+  public Map<SequenceI, TreeNodeI> getAlignmentWithNodes();
 
-  public Map<ExternalTreeNodeI, SequenceI> getNodesWithAlignment();
+  public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
 }

diff --git a/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java b/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java
index 05d13e9..4229b50 100644 (file)
--- a/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java
+++ b/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java
@@ -9,18 +9,18 @@ import java.util.Iterator;
 import java.util.Map;
 
 public class LoadedTreeSequenceAssociation
-        implements ExternalLoadedTreeAssociationI
+        implements LoadedTreeAssociationI
 {
   SequenceI[] alignSequences;
 
-  ExternalTreeI tree;
+  TreeI tree;
 
-  Map<SequenceI, ExternalTreeNodeI> alignmentWithNodes;
+  Map<SequenceI, TreeNodeI> alignmentWithNodes;
 
-  Map<ExternalTreeNodeI, SequenceI> nodesWithAlignment;
+  Map<TreeNodeI, SequenceI> nodesWithAlignment;
 
   public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
-          ExternalTreeI extTree)
+          TreeI extTree)
   {
     alignSequences = alignmentSequences;
     tree = extTree;
@@ -49,11 +49,11 @@ public class LoadedTreeSequenceAssociation
 
     if (!tree.isEmpty())
     {
-      for (final Iterator<ExternalTreeNodeI> iter = tree
+      for (final Iterator<TreeNodeI> iter = tree
               .iterateInPreOrder(); iter
               .hasNext();)
       {
-        ExternalTreeNodeI treeNode = iter.next();
+        TreeNodeI treeNode = iter.next();
         nodeSequenceName = treeNode.getNodeName();
 
         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
@@ -78,13 +78,13 @@ public class LoadedTreeSequenceAssociation
 
 
   @Override
-  public Map<SequenceI, ExternalTreeNodeI> getAlignmentWithNodes()
+  public Map<SequenceI, TreeNodeI> getAlignmentWithNodes()
   {
     return alignmentWithNodes;
   }
 
   @Override
-  public Map<ExternalTreeNodeI, SequenceI> getNodesWithAlignment()
+  public Map<TreeNodeI, SequenceI> getNodesWithAlignment()
   {
     return nodesWithAlignment;
   }

diff --git a/src/jalview/ext/treeviewer/TreeBuilderI.java b/src/jalview/ext/treeviewer/TreeBuilderI.java
new file mode 100644 (file)
index 0000000..37bad36
--- /dev/null
+++ b/src/jalview/ext/treeviewer/TreeBuilderI.java
@@ -0,0 +1,23 @@
+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
+/**
+ * @author kjvanderheide
+ *
+ */
+public interface TreeBuilderI
+{
+  public TreeI buildTree(TreeNodeI treeRoot);
+
+  public TreeI buildTree();
+
+  public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes();
+
+  public Map<TreeNodeI, SequenceI> getNodesBoundAlignment();
+
+  public String generateTreeName();
+
+}

diff --git a/src/jalview/ext/treeviewer/ExternalTreeControlsI.java b/src/jalview/ext/treeviewer/TreeControlsI.java
similarity index 73%
rename from src/jalview/ext/treeviewer/ExternalTreeControlsI.java
rename to src/jalview/ext/treeviewer/TreeControlsI.java
index e278879..9a209e7 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeControlsI.java
+++ b/src/jalview/ext/treeviewer/TreeControlsI.java
@@ -1,6 +1,6 @@
 package jalview.ext.treeviewer;
 
-public interface ExternalTreeControlsI
+public interface TreeControlsI
 {
   public void defaultSettings();
 

diff --git a/src/jalview/ext/treeviewer/ExternalTreeFrame.java b/src/jalview/ext/treeviewer/TreeFrameI.java
similarity index 84%
rename from src/jalview/ext/treeviewer/ExternalTreeFrame.java
rename to src/jalview/ext/treeviewer/TreeFrameI.java
index 48b150e..922c304 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeFrame.java
+++ b/src/jalview/ext/treeviewer/TreeFrameI.java
@@ -10,19 +10,19 @@ import javax.swing.RootPaneContainer;
 import javax.swing.WindowConstants;
 import javax.swing.event.InternalFrameListener;
 
-public interface ExternalTreeFrame
+public interface TreeFrameI
         extends Accessible, WindowConstants, RootPaneContainer,
         ImageObserver, MenuContainer
 {
-  public abstract ExternalTreePanel getTreePanel();
+  public abstract TreePanelI getTreePanel();
 
-  public abstract ExternalTreeI getTree();
+  public abstract TreeI getTree();
 
   public abstract void checkMultipleTrees();
 
   public abstract int getNumberOfTrees();
 
-  public ExternalTreeControlsI getTreeControls();
+  public TreeControlsI getTreeControls();
 
   public void addFrameListener(InternalFrameListener listener);
 

diff --git a/src/jalview/ext/treeviewer/TreeI.java b/src/jalview/ext/treeviewer/TreeI.java
new file mode 100644 (file)
index 0000000..0ebf991
--- /dev/null
+++ b/src/jalview/ext/treeviewer/TreeI.java
@@ -0,0 +1,37 @@
+package jalview.ext.treeviewer;
+
+import java.util.Iterator;
+
+public interface TreeI
+{
+  public TreeNodeI getRoot();
+
+  public TreeNodeI getNodeWithName(String name);
+
+  public TreeNodeI 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(TreeNodeI rootNode);
+
+  public double getHeight(boolean adjustForCollapsedSubtrees);
+
+  public Iterator<TreeNodeI> iterateInPreOrder();
+
+  public Iterator<TreeNodeI> iterateInLevelOrder();
+
+  public Iterator<TreeNodeI> iterateInPostOrder();
+
+  TreeFrameI createTreeViewerFromTree(String instanceTitle);
+
+}

diff --git a/src/jalview/ext/treeviewer/ExternalTreeNodeI.java b/src/jalview/ext/treeviewer/TreeNodeI.java
similarity index 60%
rename from src/jalview/ext/treeviewer/ExternalTreeNodeI.java
rename to src/jalview/ext/treeviewer/TreeNodeI.java
index 85be915..89de82f 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeNodeI.java
+++ b/src/jalview/ext/treeviewer/TreeNodeI.java
@@ -5,22 +5,22 @@ import jalview.datamodel.SequenceI;
 import java.awt.Color;
 import java.util.List;
 
-public interface ExternalTreeNodeI
+public interface TreeNodeI
 {
 
   public String getNodeName();
 
-  public List<ExternalTreeNodeI> getAllDescendants();
+  public List<TreeNodeI> getAllDescendants();
 
-  public List<ExternalTreeNodeI> getExternalDescendants();
+  public List<TreeNodeI> getExternalDescendants();
 
-  public List<ExternalTreeNodeI> getDirectChildren();
+  public List<TreeNodeI> getDirectChildren();
 
   public void setSequence(SequenceI seq);
 
   public SequenceI getSequence();
 
-  public void addAsChild(ExternalTreeNodeI childNode);
+  public void addAsChild(TreeNodeI childNode);
 
   public long getId();
 

diff --git a/src/jalview/ext/treeviewer/ExternalTreePanel.java b/src/jalview/ext/treeviewer/TreePanelI.java
similarity index 87%
rename from src/jalview/ext/treeviewer/ExternalTreePanel.java
rename to src/jalview/ext/treeviewer/TreePanelI.java
index 85ad800..657ef57 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreePanel.java
+++ b/src/jalview/ext/treeviewer/TreePanelI.java
@@ -9,7 +9,7 @@ import java.util.Set;
 
 import javax.accessibility.Accessible;
 
-public interface ExternalTreePanel extends Accessible, MenuContainer
+public interface TreePanelI extends Accessible, MenuContainer
 {
 
 
@@ -17,9 +17,9 @@ public interface ExternalTreePanel extends Accessible, MenuContainer
 
   public abstract File getTreeFile();
 
-  public abstract ExternalTreeI getTree();
+  public abstract TreeI getTree();
 
-  public abstract ExternalTreeNodeI findNode(int x, int y);
+  public abstract TreeNodeI findNode(int x, int y);
 
   public abstract void setMatchingNodes(Set<Long> matchingNodes);
 

diff --git a/src/jalview/ext/treeviewer/ExternalTreeParserI.java b/src/jalview/ext/treeviewer/TreeParserI.java
similarity index 63%
rename from src/jalview/ext/treeviewer/ExternalTreeParserI.java
rename to src/jalview/ext/treeviewer/TreeParserI.java
index 65ff63c..00c8334 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeParserI.java
+++ b/src/jalview/ext/treeviewer/TreeParserI.java
@@ -2,9 +2,9 @@ package jalview.ext.treeviewer;
 
 import java.io.IOException;
 
-public interface ExternalTreeParserI
+public interface TreeParserI
  {
-  public ExternalTreeI[] parse() throws IOException;
+  public TreeI[] parse() throws IOException;
 
   public void setSource(Object source) throws IOException;
 

diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java b/src/jalview/ext/treeviewer/TreeViewerBindingI.java
similarity index 88%
rename from src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
rename to src/jalview/ext/treeviewer/TreeViewerBindingI.java
index de76b82..da999c6 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
+++ b/src/jalview/ext/treeviewer/TreeViewerBindingI.java
@@ -38,7 +38,7 @@ import java.awt.event.MouseListener;
  *
  * 
  */
-public interface ExternalTreeViewerBindingI
+public interface TreeViewerBindingI
         extends ActionListener, MouseListener, SelectionListener,
         SelectionSource
 {
@@ -47,13 +47,13 @@ public interface ExternalTreeViewerBindingI
    * corresponding sequence in the Jalview alignment view. If an internal node
    * is selected all child sequences get highlighted as well.
    */
-  public void showNodeSelectionOnAlign(ExternalTreeNodeI node);
+  public void showNodeSelectionOnAlign(TreeNodeI node);
 
   public void treeSelectionChanged(SequenceI sequence);
 
-  public void showMatchingSequence(ExternalTreeNodeI nodeToMatch);
+  public void showMatchingSequence(TreeNodeI nodeToMatch);
 
-  public void showMatchingChildSequences(ExternalTreeNodeI parentNode);
+  public void showMatchingChildSequences(TreeNodeI parentNode);
 
   public void sortByTree_actionPerformed();
 

diff --git a/src/jalview/ext/treeviewer/TreeViewerConfigI.java b/src/jalview/ext/treeviewer/TreeViewerConfigI.java
new file mode 100644 (file)
index 0000000..29e4895
--- /dev/null
+++ b/src/jalview/ext/treeviewer/TreeViewerConfigI.java
@@ -0,0 +1,6 @@
+package jalview.ext.treeviewer;
+
+public interface TreeViewerConfigI
+{
+
+}

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 184ffeb..579ed09 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,8 +64,8 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.AptxInit;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
 import jalview.ext.forester.io.TreeParser;
-import jalview.ext.treeviewer.ExternalTreeFrame;
-import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -3765,7 +3765,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .get(viewport.getSequenceSetId());
     List<TreePanel> treePanels = new ArrayList<>();
 
-    Map<ExternalTreeFrame, ExternalTreeViewerBindingI> aptxFrames = AptxInit
+    Map<TreeFrameI, TreeViewerBindingI> aptxFrames = AptxInit
             .getAllAptxFrames();
 
     for (Component comp : comps)
@@ -3786,11 +3786,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sortByTreeMenu.setVisible(true);
 
-    for (Entry<ExternalTreeFrame, ExternalTreeViewerBindingI> aptxFrameWithBinding : aptxFrames
+    for (Entry<TreeFrameI, TreeViewerBindingI> aptxFrameWithBinding : aptxFrames
             .entrySet())
     {
-      ExternalTreeFrame aptxFrame = aptxFrameWithBinding.getKey();
-      ExternalTreeViewerBindingI binding = aptxFrameWithBinding.getValue();
+      TreeFrameI aptxFrame = aptxFrameWithBinding.getKey();
+      TreeViewerBindingI binding = aptxFrameWithBinding.getValue();
 
       // future support for multiple tabs
       // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3ff0b75..d79cdce 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -43,7 +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.ext.treeviewer.TreeI;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
@@ -2881,7 +2881,7 @@ public abstract class AlignmentViewport
 
   protected TreeModel currentTree = null;
 
-  protected ExternalTreeI currentExtTree = null;
+  protected TreeI currentExtTree = null;
 
   @Override
   public boolean hasSearchResults()
@@ -2954,12 +2954,12 @@ public abstract class AlignmentViewport
     return currentTree;
   }
 
-  public ExternalTreeI getCurrentExtTree()
+  public TreeI getCurrentExtTree()
   {
     return currentExtTree;
   }
 
-  public void setCurrentExtTree(ExternalTreeI externalTree)
+  public void setCurrentExtTree(TreeI externalTree)
   {
     currentExtTree = externalTree;
   }

diff --git a/test/jalview/ext/archaeopteryx/TreeViewTest.java b/test/jalview/ext/archaeopteryx/TreeViewTest.java
index f0595f2..87c32e4 100644 (file)
--- a/test/jalview/ext/archaeopteryx/TreeViewTest.java
+++ b/test/jalview/ext/archaeopteryx/TreeViewTest.java
@@ -3,7 +3,7 @@ package jalview.ext.archaeopteryx;
 import static org.testng.Assert.assertTrue;
 
 import jalview.bin.Jalview;
-import jalview.ext.treeviewer.ExternalTreeFrame;
+import jalview.ext.treeviewer.TreeFrameI;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 
@@ -14,7 +14,7 @@ public abstract class TreeViewTest
 {
   Jalview jalview;
 
-  ExternalTreeFrame treeView;
+  TreeFrameI treeView;
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()