Merge branch 'develop' into features/JAL-892varnaToProject

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 6a871ee..4c8f3ce 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -20,16 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-import java.io.File;
-import java.io.FileReader;
-import java.io.Reader;
-import java.util.Vector;
-
-import org.exolab.castor.xml.Unmarshaller;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -42,6 +32,15 @@ import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
+import java.io.File;
+import java.io.FileReader;
+import java.io.Reader;
+import java.util.Vector;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
 /**
  * @author JimP
  * 
@@ -156,7 +155,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     {
       queries = queries.toUpperCase().replaceAll(
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
-      Alignment al = null;
+      AlignmentI al = null;
       EBIFetchClient ebi = new EBIFetchClient();
       // uniprotxml parameter required since december 2007
       // uniprotkb dbname changed introduced december 2008
@@ -245,7 +244,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * @param entries
    *          a list of n uniprot entries to be analysed.
    */
-  public void addUniprotXrefs(Alignment al, Vector<UniprotEntry> entries)
+  public void addUniprotXrefs(AlignmentI al, Vector<UniprotEntry> entries)
   {
     final String dbVersion = getDbVersion();