From: jprocter <Jim Procter>
Date: Fri, 19 Jun 2009 09:48:55 +0000 (+0000)
Subject: debug
X-Git-Tag: Release_2_5~257
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0cedccadb3d3c1fd6f3038d8385fdccaa354753e;p=jalview.git

debug
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7002f07..d7a3175 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -286,7 +286,7 @@ public class CrossRef
           // xrefs on this sequence.
           if (dataset != null)
           {
-            found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf);
+            found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
             if (found)
               xrfs[r] = null; // we've recovered seqs for this one.
           }
@@ -512,16 +512,16 @@ public class CrossRef
           }
 
           // look for direct or indirect references in common
-          DBRefEntry[] poss = null, cands = null;
+          DBRefEntry[] poss = nxt.getDBRef(), cands = null;
           if (direct)
           {
-            cands = jalview.util.DBRefUtils.searchRefs(poss = nxt
-                    .getDBRef(), xrf);
+            cands = jalview.util.DBRefUtils.searchRefs(poss , xrf);
           }
           else
           {
-            cands = jalview.util.DBRefUtils.searchRefs(poss = CrossRef
-                    .findXDbRefs(dna, nxt.getDBRef()), xrf);
+            poss = CrossRef
+            .findXDbRefs(dna, poss); // 
+            cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
           }
           if (cands != null)
           {