X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=d204b999b97be9c8136292b83b8540e48a863570;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=f7773d883e3207c08b3cfda1e0eace6a13756943;hpb=977dee6b8ae7d8eec93fe0e895993aae12d99372;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index f7773d8..d204b99 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,28 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.dbsources;
 
 import java.io.File;
 import java.io.FileReader;
-import java.io.IOException;
 import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.Vector;
 
 import org.exolab.castor.xml.Unmarshaller;
@@ -38,9 +38,6 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 import jalview.datamodel.UniprotFile;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.ws.DBRefFetcher;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
@@ -76,7 +73,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    */
   public Regex getAccessionValidator()
   {
-    return null;
+    return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
   }
 
   /*
@@ -101,22 +98,27 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
 
   private EBIFetchClient ebi = null;
 
+  private static org.exolab.castor.mapping.Mapping map;
+
   public Vector getUniprotEntries(File file)
   {
     UniprotFile uni = new UniprotFile();
     try
     {
-      // 1. Load the mapping information from the file
-      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(
-              uni.getClass().getClassLoader());
-      java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
-      map.loadMapping(url);
+      if (map == null)
+      {
+        // 1. Load the mapping information from the file
+        map = new org.exolab.castor.mapping.Mapping(uni.getClass()
+                .getClassLoader());
+        java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
+        map.loadMapping(url);
+      }
 
       // 2. Unmarshal the data
       Unmarshaller unmar = new Unmarshaller(uni);
       unmar.setIgnoreExtraElements(true);
       unmar.setMapping(map);
-      if (file!=null)
+      if (file != null)
       {
         uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
       }
@@ -138,11 +140,14 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     startQuery();
     try
     {
+      queries = queries.toUpperCase().replaceAll(
+              "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       Alignment al = null;
       ebi = new EBIFetchClient();
       StringBuffer result = new StringBuffer();
       // uniprotxml parameter required since december 2007
-      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml",
+      // uniprotkb dbname changed introduced december 2008
+      File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
               null);
       Vector entries = getUniprotEntries(file);
 
@@ -206,10 +211,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   /**
    * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
    * 
-   * @param al -
-   *                a sequence of n sequences
+   * @param al
+   *          - a sequence of n sequences
    * @param entries
-   *                a seuqence of n uniprot entries to be analysed.
+   *          a seuqence of n uniprot entries to be analysed.
    */
   public void addUniprotXrefs(Alignment al, Vector entries)
   {
@@ -275,7 +280,9 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    */
   public boolean isValidReference(String accession)
   {
-    return true;
+    // TODO: make the following a standard validator
+    return (accession == null || accession.length() < 2) ? false
+            : getAccessionValidator().search(accession);
   }
 
   /**
@@ -290,4 +297,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return "Uniprot"; // getDbSource();
   }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }