Merge branch 'kjvdh/features/PhylogenyViewer' of

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

diff --git a/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java b/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
similarity index 91%
rename from src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
rename to src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
index b1dc106..adea693 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
+++ b/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
@@ -2,7 +2,9 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterDataConversions;
+import jalview.ext.forester.DataConversions;
+import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
+import jalview.ext.treeviewer.ExternalTreeBuilderI;
 
 import java.util.HashMap;
 import java.util.List;
@@ -11,7 +13,7 @@ import java.util.Map;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class AptxNodeAssociation
+public class LoadedTreeAssociation
         implements ExternalLoadedTreeAssociationI
 {
   SequenceI[] alignSequences;
@@ -22,7 +24,7 @@ public class AptxNodeAssociation
 
   Map<PhylogenyNode, SequenceI> nodesWithAlignment;
 
-  public AptxNodeAssociation(SequenceI[] alignmentSequences,
+  public LoadedTreeAssociation(SequenceI[] alignmentSequences,
           Phylogeny aptxTree)
   {
     alignSequences = alignmentSequences;
@@ -61,7 +63,7 @@ public class AptxNodeAssociation
       nodeSequence = algnIds.findIdMatch(nodeSequenceName);
       if (nodeSequence != null)
       {
-        org.forester.phylogeny.data.Sequence foresterNodeSeq = ForesterDataConversions
+        org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
                 .createForesterSequence(nodeSequence, true);
         treeNode.getNodeData().setSequence(foresterNodeSeq);
 
@@ -77,6 +79,8 @@ public class AptxNodeAssociation
 
   }
 
+
+
   public Map<SequenceI, PhylogenyNode> getAlignmentWithNodes()
   {
     return alignmentWithNodes;