From 961d720adf23c1206d8110f6b2d00f072872155a Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 31 Aug 2012 11:16:58 +0100
Subject: [PATCH] JAL-1064 patch for NPE when registerd database names do not
 resolve to one or more proxies

---
 src/jalview/ws/DBRefFetcher.java                |    5 ++++-
 src/jalview/ws/seqfetcher/ASequenceFetcher.java |   10 +++++-----
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 1886172..5413a30 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -153,7 +153,10 @@ public class DBRefFetcher implements Runnable
       }
       List<DbSourceProxy> srces=new ArrayList<DbSourceProxy>();
       for (String ddb:defdb) {
-        srces.addAll(sfetcher.getSourceProxy(ddb));
+        List<DbSourceProxy> srcesfordb=sfetcher.getSourceProxy(ddb);
+        if (srcesfordb!=null) {
+          srces.addAll(srcesfordb);
+        }
       }
       
       // append the selected sequence sources to the default dbs
diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index d4501d8..09a7a95 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -262,10 +262,10 @@ public class ASequenceFetcher
   public List<DbSourceProxy> getSourceProxy(String db)
   {
     List<DbSourceProxy> dbs;
-    Collection<DbSourceProxy> dblist = FETCHABLEDBS.get(db).values();
-    if (dblist.size()>1)
-    {
-      DbSourceProxy[] l=dblist.toArray(new DbSourceProxy[0]);
+    Map<String,DbSourceProxy> dblist = FETCHABLEDBS.get(db);
+    if (dblist==null) {return new ArrayList<DbSourceProxy>();};
+    if (dblist.size()>1) {
+      DbSourceProxy[] l=dblist.values().toArray(new DbSourceProxy[0]);
       int i=0;
       String[] nm=new String[l.length];
       for (DbSourceProxy s:l)
@@ -279,7 +279,7 @@ public class ASequenceFetcher
         dbs.add(l[i]);
       }
     } else {
-      dbs = new ArrayList<DbSourceProxy>(dblist);
+      dbs = new ArrayList<DbSourceProxy>(dblist.values());
     }
     return dbs;
   }
-- 
1.7.10.2