Merge remote-tracking branch 'origin/features/JAL-1705_ensembl' into

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 207d2bc..09d33c8 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -54,8 +54,6 @@ import javax.swing.JTextArea;
 import javax.swing.SwingConstants;
 import javax.swing.tree.DefaultMutableTreeNode;
 
-import com.stevesoft.pat.Regex;
-
 public class SequenceFetcher extends JPanel implements Runnable
 {
   JLabel dbeg = new JLabel();
@@ -518,6 +516,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       resetDialog();
       return;
     }
+    // TODO: Refactor to GUI independent code and write tests.
     // indicate if successive sources should be merged into one alignment.
     boolean addToLast = false;
     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
@@ -639,23 +638,9 @@ public class SequenceFetcher extends JPanel implements Runnable
                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
                 dbr.setSource(proxy.getDbSource());
                 dbr.setVersion(null);
-                if (proxy.getAccessionValidator() != null)
-                {
-                  Regex vgr = proxy.getAccessionValidator();
-                  vgr.search(q);
-                  if (vgr.numSubs() > 0)
-                  {
-                    dbr.setAccessionId(vgr.stringMatched(1));
-                  }
-                  else
-                  {
-                    dbr.setAccessionId(vgr.stringMatched());
-                  }
-                }
-                else
-                {
-                  dbr.setAccessionId(q);
-                }
+                String accId = DBRefUtils.processQueryToAccessionFor(proxy,
+                        q);
+                dbr.setAccessionId(accId);
                 boolean rfound = false;
                 for (int r = 0; r < rs.length; r++)
                 {