JAL-2794 reorganized node select code, added subtree selection support

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

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index 640c3ec..21a4e30 100644 (file)
--- 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;
 
@@ -68,7 +78,7 @@ 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);