JAL-2826 added isCollapsed boolean to tree nodes

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

diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
index df572e1..0844171 100644 (file)
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -12,7 +12,6 @@ import java.util.Map;
 
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.BranchColor;
 
 public class TreeNode implements TreeNodeI
 {
@@ -21,16 +20,24 @@ public class TreeNode implements TreeNodeI
   private SequenceI nodeSeq;
 
   private static Map<PhylogenyNode, TreeNodeI> originalNodes = new HashMap<>(
-          500); // prolly make this size dynamic
+          500); // prolly make this size dynamic?
 
   private static Map<TreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
           500);
 
+  /**
+   * Please don't use me directly.
+   * 
+   * @param aptxNode
+   */
   private TreeNode(PhylogenyNode aptxNode)
   {
     node = aptxNode;
+    if (aptxNode.getNodeData().getSequence() != null)
+    {
     nodeSeq = DataConversions
-            .createJalviewSequence(aptxNode.getNodeData().getSequence());
+              .createJalviewSequence(aptxNode);
+    }
     originalNodes.put(aptxNode, this);
     wrappedNodes.put(this, aptxNode);
 
@@ -88,7 +95,6 @@ public class TreeNode implements TreeNodeI
   public SequenceI getSequence()
   {
     return nodeSeq;
-    // ideally this would return a converted node.getNodeData().getSequence()
   }
 
   @Override
@@ -115,7 +121,7 @@ public class TreeNode implements TreeNodeI
   @Override
   public void setBranchColor(Color branchColor)
   {
-    node.getBranchData().setBranchColor(new BranchColor(branchColor));
+    PhylogenyMethods.setBranchColorValue(node, branchColor);
 
   }
 
@@ -241,4 +247,10 @@ public class TreeNode implements TreeNodeI
     return node.getYcoord();
   }
 
+  @Override
+  public boolean isCollapsed()
+  {
+    return node.isCollapse();
+  }
+
 }