JAL-4134 - refactor tree calculation code to work with binaryNode base type.

[jalview.git] / src / jalview / io / NewickFile.java

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 027390a..879b7d4 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -28,6 +28,7 @@ package jalview.io;
 
 import java.util.Locale;
 
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
 
@@ -275,8 +276,8 @@ public class NewickFile extends FileParse
 
     root = new SequenceNode();
 
-    SequenceNode realroot = null;
-    SequenceNode c = root;
+    BinaryNode realroot = null;
+    BinaryNode c = root;
 
     int d = -1;
     int cp = 0;
@@ -323,21 +324,21 @@ public class NewickFile extends FileParse
         {
           c.setRight(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.right();
+          c = (BinaryNode) c.right();
         }
         else
         {
           if (c.left() != null)
           {
             // Dummy node for polytomy - keeps c.left free for new node
-            SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
+            BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
             tmpn.SetChildren(c.left(), c.right());
             c.setRight(tmpn);
           }
 
           c.setLeft(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.left();
+          c = (BinaryNode) c.left();
         }
 
         if (realroot == null)
@@ -518,7 +519,7 @@ public class NewickFile extends FileParse
         else
         {
           // Find a place to put the leaf
-          SequenceNode newnode = new SequenceNode(null, c, nodename,
+          BinaryNode newnode = new SequenceNode(null, c, nodename,
                   (HasDistances) ? distance : DefDistance,
                   (HasBootstrap) ? bootstrap : DefBootstrap, false);
           parseNHXNodeProps(c, commentString2);
@@ -538,7 +539,7 @@ public class NewickFile extends FileParse
             {
               // Insert a dummy node for polytomy
               // dummy nodes have distances
-              SequenceNode newdummy = new SequenceNode(null, c, null,
+              BinaryNode newdummy = new SequenceNode(null, c, null,
                       (HasDistances ? 0 : DefDistance), 0, true);
               newdummy.SetChildren(c.left(), newnode);
               c.setLeft(newdummy);
@@ -577,7 +578,7 @@ public class NewickFile extends FileParse
               // Just advance focus, if we need to
               if ((c.left() != null) && (!c.left().isLeaf()))
               {
-                c = (SequenceNode) c.left();
+                c = (BinaryNode) c.left();
               }
             }
           }
@@ -631,7 +632,7 @@ public class NewickFile extends FileParse
    * @param commentString
    * @param commentString2
    */
-  private void parseNHXNodeProps(SequenceNode c, String commentString)
+  private void parseNHXNodeProps(BinaryNode c, String commentString)
   {
     // TODO: store raw comment on the sequenceNode so it can be recovered when
     // tree is output
@@ -832,7 +833,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printNodeField(SequenceNode c)
+  private String printNodeField(BinaryNode c)
   {
     return ((c.getName() == null) ? "" : nodeName(c.getName()))
             + ((HasBootstrap) ? ((c.getBootstrap() > -1)
@@ -849,7 +850,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printRootField(SequenceNode root)
+  private String printRootField(BinaryNode root)
   {
     return (printRootInfo)
             ? (((root.getName() == null) ? "" : nodeName(root.getName()))