From 4b268a681aa223713eff460b2be60f1c64a42774 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 6 Dec 2005 12:07:06 +0000
Subject: [PATCH] hasDistances added

---
 src/jalview/analysis/NJTree.java |   30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 0683265..40dfc9b 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -60,6 +60,10 @@ public class NJTree
     Object leaves = null;
     int start;
     int end;
+    boolean hasDistances = true; // normal case for jalview trees
+	boolean hasBootstrap = false; // normal case for jalview trees
+
+    private boolean hasRootDistance = true;
 
     /**
      * Creates a new NJTree object.
@@ -81,6 +85,11 @@ public class NJTree
     public NJTree(SequenceI[] seqs, NewickFile treefile)
     {
         top = treefile.getTree();
+
+        hasDistances = treefile.HasDistances();
+        hasBootstrap = treefile.HasBootstrap();
+        hasRootDistance = treefile.HasRootDistance();
+
         maxheight = findHeight(top);
 
         SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
@@ -1134,6 +1143,27 @@ public class NJTree
     {
         return top;
     }
+    /**
+     *
+     * @return true if tree has real distances
+     */
+    public boolean isHasDistances() {
+      return hasDistances;
+    }
+
+    /**
+     *
+     * @return true if tree has real bootstrap values
+     */
+    public boolean isHasBootstrap() {
+      return hasBootstrap;
+    }
+
+  public boolean isHasRootDistance()
+  {
+    return hasRootDistance;
+  }
+
 }
 
 
-- 
1.7.10.2