From: jprocter <Jim Procter>
Date: Fri, 21 Dec 2007 14:55:02 +0000 (+0000)
Subject: bugfixes
X-Git-Tag: Release_2_4~170
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=55bc4c7f64c6dfde45db1b8a783777f7f933f55f

bugfixes
---

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 746a7d0..8c73992 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -67,8 +67,7 @@ public class Sequencemapping extends Rangetype
   }
   private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
   {
-    // TODO Auto-generated method stub
-
+    System.err.println("Conflict in update of sequenceMapping "+sequenceMapping.getVorbaId());
   }
   private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
   {
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index a45c98d..eb4af4a 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -557,6 +557,10 @@ public class Tree extends DatastoreItem
   {
     try
     {
+      if (ntree==null)
+      {
+        return false;
+      }
       ntree.parse();
       if (ntree.getTree() != null)
       {