JAL-1479 refactored SequenceI interface - changed getDBRef() to getDBRefs() since...

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d531fea..b708ec1 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -400,7 +400,7 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(),
+                      sequence.getDBRefs(),
                       new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
@@ -524,7 +524,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[] { dbSource });
+              entry.getDBRefs(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -591,8 +591,8 @@ public class DBRefFetcher implements Runnable
         // no existing references
         // TODO: test for legacy where uniprot or EMBL refs exist but no
         // mappings are made (but content matches retrieved set)
-        boolean updateRefFrame = sequence.getDBRef() == null
-                || sequence.getDBRef().length == 0;
+        boolean updateRefFrame = sequence.getDBRefs() == null
+                || sequence.getDBRefs().length == 0;
         // TODO:
         // verify sequence against the entry sequence
 
@@ -737,7 +737,7 @@ public class DBRefFetcher implements Runnable
     for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
     {
       nseq.addElement(sequencesArray[i]);
-      DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+      DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
       jalview.datamodel.Mapping map = null;
       for (int r = 0; (dbr != null) && r < dbr.length; r++)
       {