JAL-2805 Creating jalview sequence now requires the node itself (for the

[jalview.git] / src / jalview / ext / forester / DataConversions.java

diff --git a/src/jalview/ext/forester/DataConversions.java b/src/jalview/ext/forester/DataConversions.java
index 74a94a6..c6819a5 100644 (file)
--- a/src/jalview/ext/forester/DataConversions.java
+++ b/src/jalview/ext/forester/DataConversions.java
@@ -6,6 +6,7 @@ import jalview.math.MatrixI;
 
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.phylogeny.PhylogenyNode;
 
 public final class DataConversions
 {
@@ -42,12 +43,16 @@ public final class DataConversions
   }
 
   public static SequenceI createJalviewSequence(
-          org.forester.phylogeny.data.Sequence foresterSeq)
+          PhylogenyNode foresterNode)
   {
-    String seq = foresterSeq.getMolecularSequence();
-    SequenceI jalviewSeq = new Sequence(foresterSeq.getName(), seq, 1,
+    String seq = foresterNode.getNodeData().getSequence()
+            .getMolecularSequence();
+    String seqName = foresterNode.getName();
+
+    SequenceI jalviewSeq = new Sequence(foresterNode.getName(), seq, 1,
             seq.length() + 1);
-    return jalviewSeq;
+    return jalviewSeq.deriveSequence();
+
 
   }