Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 98978d0..b3c0011 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -36,6 +36,7 @@ import java.util.StringTokenizer;
 import com.stevesoft.pat.Regex;
 
 import jalview.bin.Jalview;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
 
@@ -78,7 +79,7 @@ import jalview.util.MessageManager;
  */
 public class NewickFile extends FileParse
 {
-  SequenceNode root;
+  BinaryNode root;
 
   private boolean HasBootstrap = false;
 
@@ -145,7 +146,7 @@ public class NewickFile extends FileParse
    * @param newtree
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree)
+  public NewickFile(BinaryNode newtree)
   {
     root = newtree;
   }
@@ -174,7 +175,7 @@ public class NewickFile extends FileParse
    * @param distances
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances)
   {
     root = newtree;
@@ -194,7 +195,7 @@ public class NewickFile extends FileParse
    * @param rootdistance
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances, boolean rootdistance)
   {
     root = newtree;
@@ -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)
@@ -519,7 +520,7 @@ 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);
@@ -539,7 +540,7 @@ 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);
@@ -578,7 +579,7 @@ 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();
               }
             }
           }
@@ -632,7 +633,7 @@ 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
@@ -679,7 +680,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode getTree()
+  public BinaryNode getTree()
   {
     return root;
   }
@@ -833,7 +834,7 @@ 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)
@@ -850,7 +851,7 @@ 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()))
@@ -865,7 +866,7 @@ public class NewickFile extends FileParse
   }
 
   // Non recursive call deals with root node properties
-  public void print(StringBuffer tf, SequenceNode root)
+  public void print(StringBuffer tf, BinaryNode root)
   {
     if (root != null)
     {
@@ -877,20 +878,20 @@ public class NewickFile extends FileParse
       {
         if (root.isDummy())
         {
-          _print(tf, (SequenceNode) root.right());
-          _print(tf, (SequenceNode) root.left());
+          _print(tf, root.right());
+          _print(tf, root.left());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) root.right());
+          _print(tf, root.right());
 
           if (root.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) root.left());
+          _print(tf, root.left());
           tf.append(")" + printRootField(root));
         }
       }
@@ -898,7 +899,7 @@ public class NewickFile extends FileParse
   }
 
   // Recursive call for non-root nodes
-  public void _print(StringBuffer tf, SequenceNode c)
+  public void _print(StringBuffer tf, BinaryNode c)
   {
     if (c != null)
     {
@@ -910,24 +911,24 @@ public class NewickFile extends FileParse
       {
         if (c.isDummy())
         {
-          _print(tf, (SequenceNode) c.left());
+          _print(tf, c.left());
           if (c.left() != null)
           {
             tf.append(",");
           }
-          _print(tf, (SequenceNode) c.right());
+          _print(tf, c.right());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) c.right());
+          _print(tf, c.right());
 
           if (c.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) c.left());
+          _print(tf, c.left());
           tf.append(")" + printNodeField(c));
         }
       }