Merge branch 'develop' into JAL-1705_trialMerge

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index e96d9d7..21fd08d 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -98,7 +98,7 @@ public class CrossRef
         {
           dss = dss.getDatasetSequence();
         }
-        DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
+        DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRefs());
         if (rfs != null)
         {
           for (DBRefEntry ref : rfs)
@@ -112,13 +112,13 @@ public class CrossRef
         if (dataset != null)
         {
           // search for references to this sequence's direct references.
-          DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
+          DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
           List<SequenceI> rseqs = new ArrayList<SequenceI>();
           CrossRef.searchDatasetXrefs(seq, !dna, lrfs, dataset, rseqs,
                   null); // don't need to specify codon frame for mapping here
           for (SequenceI rs : rseqs)
           {
-            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
+            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRefs());
             if (xrs != null)
             {
               for (DBRefEntry ref : xrs)
@@ -170,7 +170,7 @@ public class CrossRef
     Vector cseqs = new Vector();
     for (int s = 0; s < seqs.length; s++)
     {
-      DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
+      DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRefs());
       for (int c = 0; c < cdna.length; c++)
       {
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
@@ -231,12 +231,12 @@ public class CrossRef
         dss = dss.getDatasetSequence();
       }
       boolean found = false;
-      DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
+      DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRefs());
       if ((xrfs == null || xrfs.length == 0) && dataset != null)
       {
         System.out.println("Attempting to find ds Xrefs refs.");
         // FIXME should be dss not seq here?
-        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
+        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
         // less ambiguous would be a 'find primary dbRefEntry' method.
         // filter for desired source xref here
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
@@ -342,7 +342,7 @@ public class CrossRef
               for (int rs = 0; rs < retrieved.length; rs++)
               {
                 // TODO: examine each sequence for 'redundancy'
-                DBRefEntry[] dbr = retrieved[rs].getDBRef();
+                DBRefEntry[] dbr = retrieved[rs].getDBRefs();
                 if (dbr != null && dbr.length > 0)
                 {
                   for (int di = 0; di < dbr.length; di++)
@@ -514,7 +514,7 @@ public class CrossRef
             }
 
             // look for direct or indirect references in common
-            DBRefEntry[] poss = nxt.getDBRef(), cands = null;
+            DBRefEntry[] poss = nxt.getDBRefs(), cands = null;
             if (direct)
             {
               cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);