From 29f633ca27df2db2790b81b1ca346d6692d4936c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 25 Jul 2007 17:16:54 +0000
Subject: [PATCH] better vamsas tree io (for when there are no nodemappings)

---
 src/jalview/io/vamsas/Tree.java |   23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 12c471e..82f4f07 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,5 +1,6 @@
 package jalview.io.vamsas;
 
+import java.io.IOException;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
@@ -60,7 +61,7 @@ public class Tree extends DatastoreItem
         {
           inputData = (AlignmentView) idata[0];
         }
-        ntree = new jalview.io.NewickFile(tree.getNewick(0).getContent());
+        ntree = getNtree();
         title = tree.getNewick(0).getTitle();
         if (title==null || title.length()==0)
         {
@@ -74,6 +75,10 @@ public class Tree extends DatastoreItem
       }
     }
   }
+  private NewickFile getNtree() throws IOException
+  {
+    return new jalview.io.NewickFile(tree.getNewick(0).getContent());
+  }
   public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2)
   {
     super(datastore);
@@ -402,5 +407,21 @@ public class Tree extends DatastoreItem
   {
     return inputData;
   }
+  public boolean isValidTree()
+  {
+    try {
+      ntree.parse();
+      if (ntree.getTree()!=null)
+      {
+        ntree = getNtree();
+      }
+        return true;
+    }
+    catch (Exception e)
+    {
+      Cache.log.debug("Failed to parse newick tree string",e);
+    }
+    return false;
+  }
 
 }
-- 
1.7.10.2