X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Farchaeopteryx%2FArchaeopteryxTreeConverter.java;h=21a4e30ba2225cdf763aea89a8a2c1f278163c45;hb=4b25259949fbc582a579aa91922cde6f838155ea;hp=58c57288cce6dac57d72c215905bd9c30b557cd0;hpb=6cf0755d3de2f853a2b697230302e3c785694ad3;p=jalview.git

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index 58c5728..21a4e30 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
@@ -15,7 +15,17 @@ import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.Sequence;
 
-public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
+/**
+ * Class for converting trees made in Jalview (through TreeBuilder) to trees
+ * compatible with Forester (Phylogeny objects).
+ * 
+ * Note that this currently demands a 1:1 relationship between tree nodes and
+ * the sequences used for generating them.
+ * 
+ * @author kjvanderheide
+ *
+ */
+public class ArchaeopteryxTreeConverter
 {
   protected final SequenceI[] sequences;
 
@@ -31,6 +41,8 @@ public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
 
   private final Map<SequenceI, PhylogenyNode> alignmentBoundNodes;
 
+  private final Map<PhylogenyNode, SequenceI> nodesBoundAlignment;
+
   public ArchaeopteryxTreeConverter(final TreeBuilder calculatedTree)
   {
     jalviewTree = calculatedTree;
@@ -39,8 +51,8 @@ public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
             jalviewTree.getDistances(), sequences);
     aptxTree = new Phylogeny();
     rootNode = new PhylogenyNode();
-    alignmentBoundNodes = new HashMap<>(
-            distances.getSize());
+    alignmentBoundNodes = new HashMap<>(distances.getSize());
+    nodesBoundAlignment = new HashMap<>(distances.getSize());
 
 
   }
@@ -66,11 +78,12 @@ public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
     for (SequenceI sequence : sequences)
     {
       Sequence seq = ForesterConversions
-              .createForesterSequence(sequence);
+              .createForesterSequence(sequence, true);
       PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
       NodeData nodeData = sequenceNode.getNodeData();
       nodeData.setSequence(seq);
 
+      nodesBoundAlignment.put(sequenceNode, sequence);
       alignmentBoundNodes.put(sequence, sequenceNode);
       rootNode.addAsChild(sequenceNode);
     }
@@ -90,6 +103,11 @@ public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
     return alignmentBoundNodes;
   }
 
+  public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
+  {
+    return nodesBoundAlignment;
+  }
+
   private Phylogeny clusterNodes()
   {
     return aptxTree;