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 22c4df0..c6819a5 100644 (file)
--- a/src/jalview/ext/forester/DataConversions.java
+++ b/src/jalview/ext/forester/DataConversions.java
@@ -1,13 +1,9 @@
 package jalview.ext.forester;
 
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.ext.archaeopteryx.TreeNode;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
 import jalview.math.MatrixI;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.phylogeny.PhylogenyNode;
@@ -23,14 +19,14 @@ public final class DataConversions
     {
       foresterSeq.setName(jalviewSequence.getDescription());
     }
-    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned); // all tree
-                                                                // sequences
-                                                                // should
-                                                                // be aligned
-                                                                // already
+
+    // all tree sequences should be aligned already
+    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
+
     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
-    if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
-                                     // forester itself?)
+    
+    // add checks for DNA or RNA (infer from forester itself?)
+    if (jalviewSequence.isProtein())
     {
       try
       {
@@ -46,6 +42,20 @@ public final class DataConversions
 
   }
 
+  public static SequenceI createJalviewSequence(
+          PhylogenyNode foresterNode)
+  {
+    String seq = foresterNode.getNodeData().getSequence()
+            .getMolecularSequence();
+    String seqName = foresterNode.getName();
+
+    SequenceI jalviewSeq = new Sequence(foresterNode.getName(), seq, 1,
+            seq.length() + 1);
+    return jalviewSeq.deriveSequence();
+
+
+  }
+
 
   // public static org.forester.phylogeny.data.Accession
   // createForesterAccession(
@@ -80,14 +90,5 @@ public final class DataConversions
 
   }
 
-  public static List<ExternalTreeNodeI> getConvertedTreeNodes(
-          List<PhylogenyNode> aptxNodes)
-  {
-    List<ExternalTreeNodeI> jalviewNodes = new ArrayList<>();
-    for (PhylogenyNode aptxNode : aptxNodes)
-    {
-      jalviewNodes.add(new TreeNode(aptxNode));
-    }
-    return jalviewNodes;
-  }
+
 }