JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / ext / archaeopteryx / Tree.java

diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
index 884a359..616ea4b 100644 (file)
--- a/src/jalview/ext/archaeopteryx/Tree.java
+++ b/src/jalview/ext/archaeopteryx/Tree.java
@@ -1,30 +1,55 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
+import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.io.writers.PhylogenyWriter;
 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;
 
+
+  public Tree()
+  {
+    tree = new Phylogeny();
+  }
+
   public Tree(Phylogeny aptxTree)
   {
     tree = aptxTree;
+    wrapAllTreeNodes();
+
   }
 
-  @Override
-  public Phylogeny getOriginalTree()
+  private void wrapAllTreeNodes()
   {
-    return tree;
+    for (Iterator<PhylogenyNode> iterator = tree
+            .iteratorPostorder(); iterator.hasNext();)
+    {
+      PhylogenyNode foresterNode = iterator.next();
+      TreeNodeI treeNode = TreeNode
+              .getUniqueWrapper(foresterNode);
 
+    }
   }
 
   @Override
-  public ExternalTreeNodeI getRoot()
+  public TreeNodeI getRoot()
   {
-    ExternalTreeNodeI root = new TreeNode(tree.getRoot());
+    TreeNodeI root = TreeNode.getUniqueWrapper(tree.getRoot());
     return root;
   }
 
@@ -36,9 +61,9 @@ public class Tree implements ExternalTreeI
   }
 
   @Override
-  public ExternalTreeNodeI getNodeWithName(String name)
+  public TreeNodeI getNodeWithName(String name)
   {
-    return new TreeNode(tree.getNode(name));
+    return TreeNode.getUniqueWrapper(tree.getNode(name));
 
   }
 
@@ -47,4 +72,125 @@ 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(TreeNodeI rootNode)
+  {
+    PhylogenyNode treeRoot = TreeNode.unwrapNode(rootNode);
+    tree.setRoot(treeRoot);
+    wrapAllTreeNodes();
+
+  }
+
+  @Override
+  public double getMaximumLength(boolean adjustForCollapsedSubtrees)
+  {
+    return tree.calculateHeight(adjustForCollapsedSubtrees);
+  }
+
+  @Override
+  public Iterator<TreeNodeI> iterateInPreOrder()
+  {
+    Iterator<TreeNodeI> iter = new TreeIterator(
+            tree.iteratorPreorder());
+    return iter;
+  }
+
+  @Override
+  public Iterator<TreeNodeI> iterateInLevelOrder()
+  {
+    Iterator<TreeNodeI> iter = new TreeIterator(
+            tree.iteratorLevelOrder());
+    return iter;
+  }
+
+  @Override
+  public Iterator<TreeNodeI> iterateInPostOrder()
+  {
+    Iterator<TreeNodeI> iter = new TreeIterator(
+            tree.iteratorPostorder());
+    return iter;
+  }
+
+  @Override
+  public TreeNodeI getFurthestNode()
+  {
+    PhylogenyNode furthestNode = PhylogenyMethods
+            .calculateNodeWithMaxDistanceToRoot(tree);
+    return TreeNode.getUniqueWrapper(furthestNode);
+  }
+
+  @Override
+  public TreeFrameI createTreeViewerFromTree(String instanceTitle)
+  {
+    return new AptxFrame(Archaeopteryx.createApplication(tree,
+            AptxInit.APTX_CONFIG,
+            instanceTitle));
+  }
+
+  @Override
+  public List<SequenceI> getNodeSequences()
+  {
+    List<SequenceI> treeSeqs = new ArrayList<>();
+    Iterator<TreeNodeI> iter = iterateInPreOrder();
+    while (iter.hasNext())
+    {
+
+      SequenceI nodeSeq = iter.next().getSequence();
+      if (nodeSeq != null)
+      {
+        treeSeqs.add(nodeSeq);
+      }
+    }
+    return treeSeqs;
+  }
+
+  @Override
+  public TreeNodeI[] getAllNodes()
+  {
+    TreeNodeI[] treeNodes = new TreeNodeI[tree.getNodeCount()];
+    Iterator<TreeNodeI> iter = iterateInPreOrder();
+    int i = 0;
+    while (iter.hasNext())
+    {
+      treeNodes[i++] = iter.next();
+    }
+    return treeNodes;
+  }
+
+  @Override
+  public void outputAsFile(File outputFile) throws IOException
+  {
+    PhylogenyWriter treeWriter = new PhylogenyWriter();
+    treeWriter.toPhyloXML(tree, 0, outputFile);
+
+
+  }
+
 }