X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=19366e0782b01ee0d3af392e1ec73458d5b513b6;hb=d49c33d2fbb65ad7477cb3a538b9e32a68f374a2;hp=8f55080532694eb96e52b2b7c8bd9e178807698c;hpb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 8f55080..19366e0 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -40,6 +40,8 @@ import jalview.ws.ebi.EBIFetchClient;
 import jalview.xml.binding.embl.EntryType;
 import jalview.xml.binding.embl.EntryType.Feature;
 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.jalview.JalviewModel;
+import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.embl.XrefType;
 
 import java.io.File;
@@ -52,9 +54,9 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
-import java.util.regex.Pattern;
 
 import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
 import javax.xml.bind.JAXBException;
 import javax.xml.stream.FactoryConfigurationError;
 import javax.xml.stream.XMLInputFactory;
@@ -68,8 +70,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    */
   private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
 
-  private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
   public EmblXmlSource()
   {
     super();
@@ -85,7 +85,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * @return
    * @throws Exception
    */
-  public AlignmentI getEmblSequenceRecords(String emprefx, String query)
+  protected AlignmentI getEmblSequenceRecords(String emprefx, String query)
           throws Exception
   {
     startQuery();
@@ -118,7 +118,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * @return
    * @throws Exception
    */
-  public AlignmentI getEmblSequenceRecords(String emprefx, String query,
+  protected AlignmentI getEmblSequenceRecords(String emprefx, String query,
           File reply) throws Exception
   {
     List<EntryType> entries = null;
@@ -183,8 +183,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(is);
       javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-      jalview.xml.binding.embl.ROOT root = (jalview.xml.binding.embl.ROOT) um
-              .unmarshal(streamReader);
+      JAXBElement<ROOT> rootElement =  um.unmarshal(streamReader, ROOT.class);
+      ROOT root = rootElement.getValue();
 
       /*
        * document root contains either "entry" or "entrySet"
@@ -244,14 +244,18 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     /*
      * add db references
      */
-    List<XrefType> dbRefs = entry.getXref();
-    if (dbRefs != null)
+    List<XrefType> xrefs = entry.getXref();
+    if (xrefs != null)
     {
-      for (XrefType dbref : dbRefs)
+      for (XrefType xref : xrefs)
       {
-        String acc = dbref.getId();
-        String source = DBRefUtils.getCanonicalName(dbref.getDb());
-        String version = dbref.getSecondaryId();
+        String acc = xref.getId();
+        String source = DBRefUtils.getCanonicalName(xref.getDb());
+        String version = xref.getSecondaryId();
+        if (version == null || "".equals(version))
+        {
+          version = "0";
+        }
         dna.addDBRef(new DBRefEntry(source, version, acc));
       }
     }
@@ -524,10 +528,14 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
          * ensure UniProtKB/Swiss-Prot converted to UNIPROT
          */
         String source = DBRefUtils.getCanonicalName(xref.getDb());
-        DBRefEntry dbref = new DBRefEntry(source, xref.getSecondaryId(),
-                xref.getId());
-        DBRefEntry proteinDbRef = new DBRefEntry(dbref.getSource(),
-                dbref.getVersion(), dbref.getAccessionId());
+        String version = xref.getSecondaryId();
+        if (version == null || "".equals(version))
+        {
+          version = "0";
+        }
+        DBRefEntry dbref = new DBRefEntry(source, version, xref.getId());
+        DBRefEntry proteinDbRef = new DBRefEntry(source, version,
+                dbref.getAccessionId());
         if (source.equals(DBRefSource.UNIPROT))
         {
           String proteinSeqName = DBRefSource.UNIPROT + "|"
@@ -695,19 +703,10 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
     if (!vals.isEmpty())
     {
-      StringBuilder sb = new StringBuilder();
-      boolean first = true;
       for (Entry<String, String> val : vals.entrySet())
       {
-        if (!first)
-        {
-          sb.append(";");
-        }
-        sb.append(val.getKey()).append("=").append(val.getValue());
-        first = false;
         sf.setValue(val.getKey(), val.getValue());
       }
-      sf.setAttributes(sb.toString());
     }
     return sf;
   }