X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=bc16a0f050cf002f19d27b07e0c3a0f1771a8ec6;hb=ea219b852b0e66a7b025ebfee49030033de23967;hp=789688c72424d116c3b54ab12a82df5a1a20151c;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 789688c..bc16a0f 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -4,11 +4,14 @@
 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;
+
 import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.Alignment;
@@ -19,12 +22,13 @@ import jalview.datamodel.PDBEntry;
 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.DbSourceProxy;
-import jalview.ws.DbSourceProxyImpl;
-import jalview.ws.EBIFetchClient;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * @author JimP
@@ -36,7 +40,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     super();
     addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
     addDbSourceProperty(DBRefSource.PROTSEQDB);
-    addDbSourceProperty(DBRefSource.MULTIACC);
+    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
   }
 
   /*
@@ -81,6 +85,31 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
 
   private EBIFetchClient ebi = null;
 
+  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);
+
+      // 2. Unmarshal the data
+      Unmarshaller unmar = new Unmarshaller(uni);
+      unmar.setIgnoreExtraElements(true);
+      unmar.setMapping(map);
+
+      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+    }
+    catch (Exception e)
+    {
+      System.out.println("Error getUniprotEntries() " + e);
+    }
+
+    return uni.getUniprotEntries();
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -94,9 +123,9 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       Alignment al=null;
       ebi = new EBIFetchClient();
       StringBuffer result=new StringBuffer();
-      File file = ebi.fetchDataAsFile("uniprot:" + queries, "xml", null);
-      DBRefFetcher dbref = new DBRefFetcher();
-      Vector entries = dbref.getUniprotEntries(file);
+      // uniprotxml parameter required since december 2007
+      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
+      Vector entries = getUniprotEntries(file);
 
       if (entries != null)
       {
@@ -175,13 +204,17 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
         onlyPdbEntries.addElement(pdb);
       }
       SequenceI sq = al.getSequenceAt(i);
-      sq = (sq.getDatasetSequence()==null) ? sq : sq.getDatasetSequence();
+      while (sq.getDatasetSequence()!=null)
+      {
+        sq = sq.getDatasetSequence();
+      }
 
       Enumeration en2 = entry.getAccession().elements();
       while (en2.hasMoreElements())
       {
+        // we always add as uniprot if we retrieved from uniprot or uniprot name
         sq.addDBRef(
-                new DBRefEntry(getDbSource(), getDbVersion(), en2.nextElement()
+                new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
                         .toString()));
       }
       sq.setPDBId(onlyPdbEntries);
@@ -214,4 +247,8 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return "P00340";
   }
+  public String getDbName()
+  {
+    return getDbSource();
+  }
 }