From 251060eb361feb3286f32cbd70d6ec559c03598d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 30 Mar 2005 13:49:20 +0000
Subject: [PATCH] Fixed a sensible default leaf distance (for files where only
 a few, or no distances are specified).

---
 src/jalview/io/NewickFile.java |   37 ++++++++++++++++++++++++-------------
 1 file changed, 24 insertions(+), 13 deletions(-)

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index d0af8a7..c3fd9374 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -63,15 +63,24 @@ public class NewickFile extends FileParse
     root = new SequenceNode();
     SequenceNode realroot = null;
     SequenceNode c = root;
+
     int d = -1;
     int cp = 0;
     int flen = nf.length();
+
     String Error = null;
     String nodename = null;
-    float distance=-99999;
-    int bootstrap=-99999;
+
+    float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small
+    int DefBootstrap = 0; // @param Default bootstrap for a node
+
+    float distance=DefDistance;
+    int bootstrap=DefBootstrap;
+
     boolean ascending = false; // flag indicating that we are leaving the current node
+
     com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex("[(\\['),;]");
+
     while (majorsyms.searchFrom(nf, cp) && Error==null) {
       int fcp = majorsyms.matchedFrom();
       switch (nf.charAt(fcp)) {
@@ -103,7 +112,7 @@ public class NewickFile extends FileParse
           d++;
           if (c.right() == null)
           {
-            c.setRight(new SequenceNode(null, c, 0, null));
+            c.setRight(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false));
             c = (SequenceNode) c.right();
           }
           else
@@ -115,15 +124,15 @@ public class NewickFile extends FileParse
               tmpn.SetChildren(c.left(), c.right());
               c.setRight(tmpn);
             }
-            c.setLeft(new SequenceNode(null, c, 0, null));
+            c.setLeft(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false));
             c = (SequenceNode) c.left();
           }
           if (realroot==null) {
             realroot = c;
           }
           nodename = null;
-          distance = -99999;
-          bootstrap = -99999;
+          distance = DefDistance;
+          bootstrap = DefBootstrap;
           cp = fcp + 1;
           break;
 
@@ -229,11 +238,12 @@ public class NewickFile extends FileParse
           else
           {
             // Find a place to put the leaf
-            SequenceNode newnode = new SequenceNode(null, c,
-                (HasDistances) ? distance : 0,
-                nodename);
-
-            newnode.setBootstrap(HasBootstrap ? bootstrap : 0);
+            SequenceNode newnode =
+            new SequenceNode(null, c,
+                             nodename,
+                             (HasDistances) ? distance : DefDistance,
+                             (HasBootstrap) ? bootstrap : DefBootstrap,
+                             false);
 
             if (c.right() == null)
             {
@@ -283,8 +293,8 @@ public class NewickFile extends FileParse
           }
           // Reset new node properties to obvious fakes
           nodename = null;
-          distance = -99999;
-          bootstrap = -99999;
+          distance = DefDistance;
+          bootstrap = DefBootstrap;
 
           cp=fcp+1;
       }
@@ -298,6 +308,7 @@ public class NewickFile extends FileParse
     if (!RootHasDistance) {
       root.dist = 0;
     }
+
   }
 
   public NewickFile(SequenceNode newtree) {
-- 
1.7.10.2