Merge branch 'kjvdh/features/PhylogenyViewer' of

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

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
similarity index 94%
rename from src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
rename to src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
index f010450..7b03d5c 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
@@ -2,8 +2,9 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterDataConversions;
+import jalview.ext.forester.DataConversions;
 import jalview.ext.forester.ForesterMatrix;
+import jalview.ext.treeviewer.ExternalTreeBuilderI;
 import jalview.util.MessageManager;
 
 import java.util.HashMap;
@@ -25,7 +26,7 @@ import org.forester.phylogeny.data.Sequence;
  * @author kjvanderheide
  *
  */
-public class ArchaeopteryxTreeBuilder
+public class AptxTreeBuilder
         implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
 {
   protected final SequenceI[] sequences;
@@ -44,7 +45,7 @@ public class ArchaeopteryxTreeBuilder
 
   private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;
 
-  public ArchaeopteryxTreeBuilder(final TreeBuilder calculatedTree)
+  public AptxTreeBuilder(final TreeBuilder calculatedTree)
   {
     jalviewTree = calculatedTree;
     sequences = jalviewTree.getSequences();
@@ -83,7 +84,7 @@ public class ArchaeopteryxTreeBuilder
 
     for (SequenceI sequence : sequences)
     {
-      Sequence seq = ForesterDataConversions
+      Sequence seq = DataConversions
               .createForesterSequence(sequence, true);
       PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());