X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=c1fe276676973d08f180c17f30df232d0bb9c61d;hb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;hp=ad8c0f090de983a099e69c82841db784e2a7790a;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ad8c0f0..c1fe276 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -126,8 +126,8 @@ public class DBRefFetcher implements Runnable
       String[] defdb = null, otherdb = sfetcher
               .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
       Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings
-              .getSelectedSources()
-              : new jalview.gui.DasSourceBrowser().getSelectedSources();
+              .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+              .getSelectedSources();
       Enumeration en = dasselsrc.elements();
       while (en.hasMoreElements())
       {
@@ -193,9 +193,7 @@ public class DBRefFetcher implements Runnable
     {
       String[] newsrc = new String[dbSources.length + otherdb.length];
       System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
-      System
-              .arraycopy(otherdb, 0, newsrc, dbSources.length,
-                      otherdb.length);
+      System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
       dbSources = newsrc;
     }
   }
@@ -387,9 +385,7 @@ public class DBRefFetcher implements Runnable
               for (int j = 0; j < uprefs.length; j++)
               {
                 addSeqId(sequence, uprefs[j].getAccessionId());
-                queries
-                        .addElement(uprefs[j].getAccessionId()
-                                .toUpperCase());
+                queries.addElement(uprefs[j].getAccessionId().toUpperCase());
               }
             }
             else
@@ -407,8 +403,9 @@ public class DBRefFetcher implements Runnable
                   try
                   {
                     presp = picrClient
-                            .getUPIForAccession(token, null, picrClient
-                                    .getMappedDatabaseNames(), null, true);
+                            .getUPIForAccession(token, null,
+                                    picrClient.getMappedDatabaseNames(),
+                                    null, true);
                   } catch (Exception e)
                   {
                     System.err.println("Exception with Picr for '" + token
@@ -447,11 +444,10 @@ public class DBRefFetcher implements Runnable
     } // all databases have been queries.
     if (sbuffer.length() > 0)
     {
-      output
-              .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
-                      + "altered, most likely the start/end residue will have been updated.\n"
-                      + "Save your alignment to maintain the updated id.\n\n"
-                      + sbuffer.toString());
+      output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
+              + "altered, most likely the start/end residue will have been updated.\n"
+              + "Save your alignment to maintain the updated id.\n\n"
+              + sbuffer.toString());
       Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
       // The above is the dataset, we must now find out the index
       // of the viewed sequence
@@ -496,9 +492,9 @@ public class DBRefFetcher implements Runnable
       // taking into account all accessionIds and names in the file
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
-      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
-              .getDBRef(), new String[]
-      { dbSource });
+      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
+              entry.getDBRef(), new String[]
+              { dbSource });
       if (entryRefs == null)
       {
         System.err