From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 9 Jan 2018 17:34:11 +0000 (+0000)
Subject: JAL-2805 Creating jalview sequence now requires the node itself (for the
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=54b89d1e894c6d89adba7c37db1546b629712d38;p=jalview.git

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

diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
index 69077dc..b43e9b4 100644
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -32,7 +32,7 @@ public class TreeNode implements TreeNodeI
     if (aptxNode.getNodeData().getSequence() != null)
     {
     nodeSeq = DataConversions
-              .createJalviewSequence(aptxNode.getNodeData().getSequence());
+              .createJalviewSequence(aptxNode);
     }
     originalNodes.put(aptxNode, this);
     wrappedNodes.put(this, aptxNode);
diff --git a/src/jalview/ext/forester/DataConversions.java b/src/jalview/ext/forester/DataConversions.java
index 4985f5f..c6819a5 100644
--- 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
 {
@@ -42,10 +43,13 @@ 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.deriveSequence();