From 150bdda45255ff291d4ed3c75bcab837a50c2ac4 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 6 Feb 2009 14:56:21 +0000
Subject: [PATCH] fix occasional nullpointer ref when seq ID retrieval doesn't
 resolve to a sequence object

---
 src/jalview/analysis/CrossRef.java |   59 +++++++++++++++++++-----------------
 1 file changed, 32 insertions(+), 27 deletions(-)

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 8bc844b..ffda7f2 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -104,36 +104,41 @@ public class CrossRef
     Vector refs = new Vector();
     for (int s = 0; s < seqs.length; s++)
     {
-      SequenceI dss = seqs[s];
-      while (dss.getDatasetSequence() != null)
+      if (seqs[s] != null)
       {
-        dss = dss.getDatasetSequence();
-      }
-      DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
-      for (int r = 0; rfs != null && r < rfs.length; r++)
-      {
-        if (!refs.contains(rfs[r].getSource()))
+
+        SequenceI dss = seqs[s];
+        while (dss.getDatasetSequence() != null)
         {
-          refs.addElement(rfs[r].getSource());
+          dss = dss.getDatasetSequence();
         }
-      }
-      if (dataset != null)
-      {
-        // search for references to this sequence's direct references.
-        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
-        Vector rseqs = new Vector();
-        CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
-                null); // don't need to specify codon frame for mapping here
-        Enumeration lr = rseqs.elements();
-        while (lr.hasMoreElements())
+        DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
+        for (int r = 0; rfs != null && r < rfs.length; r++)
         {
-          SequenceI rs = (SequenceI) lr.nextElement();
-          DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
-          for (int r = 0; rfs != null && r < rfs.length; r++)
+          if (!refs.contains(rfs[r].getSource()))
           {
-            if (!refs.contains(rfs[r].getSource()))
+            refs.addElement(rfs[r].getSource());
+          }
+        }
+        if (dataset != null)
+        {
+          // search for references to this sequence's direct references.
+          DBRefEntry[] lrfs = CrossRef
+                  .findXDbRefs(!dna, seqs[s].getDBRef());
+          Vector rseqs = new Vector();
+          CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
+                  null); // don't need to specify codon frame for mapping here
+          Enumeration lr = rseqs.elements();
+          while (lr.hasMoreElements())
+          {
+            SequenceI rs = (SequenceI) lr.nextElement();
+            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
+            for (int r = 0; rfs != null && r < rfs.length; r++)
             {
-              refs.addElement(rfs[r].getSource());
+              if (!refs.contains(rfs[r].getSource()))
+              {
+                refs.addElement(rfs[r].getSource());
+              }
             }
           }
         }
@@ -326,9 +331,9 @@ public class CrossRef
             try
             {
               retrieved = sftch.getSequences(xrfs); // problem here is we don't
-                                                    // know which of xrfs
-                                                    // resulted in which
-                                                    // retrieved element
+              // know which of xrfs
+              // resulted in which
+              // retrieved element
             } catch (Exception e)
             {
               System.err
-- 
1.7.10.2