From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 23 Jun 2016 13:15:05 +0000 (+0100)
Subject: JAL-2110 make indirect xref searches work by not filtering refs on candidates after... 
X-Git-Tag: Release_2_10_0~140^2~5^2~38
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=702c98b00aef5fee4ad1a8bd669854cabe4b104d;p=jalview.git

JAL-2110 make indirect xref searches work by not filtering refs on candidates after selecting them by molecule type (direct==same, indirect==different)
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 1cd6a3d..0011e39 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -827,21 +827,16 @@ public class CrossRef
           // look for direct or indirect references in common
           DBRefEntry[] poss = nxt.getDBRefs();
           List<DBRefEntry> cands = null;
-          /*
-           * TODO does this make any sense?
-           * if 'direct', search the dbrefs for xrf
-           * else, filter the dbrefs by type and then search for xrf
-           * - the result is the same isn't it?
-           */
-          if (direct)
-          {
-            cands = DBRefUtils.searchRefs(poss, xrf);
-          }
-          else
-          {
-            poss = DBRefUtils.selectDbRefs(!fromDna, poss);
-            cands = DBRefUtils.searchRefs(poss, xrf);
-          }
+
+          // todo: indirect specifies we select either direct references to nxt
+          // that match xrf which is indirect to sequenceI, or indirect
+          // references to nxt that match xrf which is direct to sequenceI
+          cands = DBRefUtils.searchRefs(poss, xrf);
+          // else
+          // {
+          // poss = DBRefUtils.selectDbRefs(nxt.isProtein()!fromDna, poss);
+          // cands = DBRefUtils.searchRefs(poss, xrf);
+          // }
           if (!cands.isEmpty())
           {
             if (!rseqs.contains(nxt))