/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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;
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
*
{
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
name.append(n);
}
- if (entry.getProtein() != null
- && entry.getProtein().getName() != null)
+ if (entry.getProtein() != null && entry.getProtein().getName() != null)
{
for (String nm : entry.getProtein().getName())
{
* @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();