X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=a3cd23d147802bb7dd271258a2f00ca9d582562d;hb=7d6575e94bed92bc06043d432576e3a39e8a8e75;hp=72382393811ab4b8a7e97b6bcae75726958dec0c;hpb=792a03fc1994671ae23e7263cefd51c9b0da53cb;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7238239..a3cd23d 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -20,21 +20,23 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * Functions for cross-referencing sequence databases. user must first specify
  * if cross-referencing from protein or dna (set dna==true)
@@ -329,7 +331,7 @@ public class CrossRef
               for (int rs = 0; rs < retrieved.length; rs++)
               {
                 // TODO: examine each sequence for 'redundancy'
-                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
+                DBRefEntry[] dbr = retrieved[rs]
                         .getDBRef();
                 if (dbr != null && dbr.length > 0)
                 {
@@ -337,7 +339,7 @@ public class CrossRef
                   {
                     // find any entry where we should put in the sequence being
                     // cross-referenced into the map
-                    jalview.datamodel.Mapping map = dbr[di].getMap();
+                    Mapping map = dbr[di].getMap();
                     if (map != null)
                     {
                       if (map.getTo() != null && map.getMap() != null)
@@ -492,7 +494,7 @@ public class CrossRef
             // check if this is the correct sequence type
             {
               typer[0] = nxt;
-              boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+              boolean isDna = Comparison.isNucleotide(typer);
               if ((direct && isDna == dna) || (!direct && isDna != dna))
               {
                 // skip this sequence because it is same molecule type
@@ -504,12 +506,12 @@ public class CrossRef
             DBRefEntry[] poss = nxt.getDBRef(), cands = null;
             if (direct)
             {
-              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+              cands = DBRefUtils.searchRefs(poss, xrf);
             }
             else
             {
               poss = CrossRef.findXDbRefs(dna, poss); //
-              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+              cands = DBRefUtils.searchRefs(poss, xrf);
             }
             if (cands != null)
             {