X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FTDBeacons.java;h=66190ca12d62da6df8d8cc9b30bc8f4a68b812d1;hb=3e912e689b988d1c8fe85f87a9374d7f7a40dbae;hp=345e21758fca362d94c5ea57cd58914bf8416fe5;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/ws/dbsources/TDBeacons.java b/src/jalview/ws/dbsources/TDBeacons.java
index 345e217..66190ca 100644
--- a/src/jalview/ws/dbsources/TDBeacons.java
+++ b/src/jalview/ws/dbsources/TDBeacons.java
@@ -20,7 +20,23 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Locale;
+import java.util.Vector;
+
+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;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
 
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -32,9 +48,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.uniprot.DbReferenceType;
 import jalview.xml.binding.uniprot.Entry;
 import jalview.xml.binding.uniprot.FeatureType;
@@ -42,23 +58,6 @@ import jalview.xml.binding.uniprot.LocationType;
 import jalview.xml.binding.uniprot.PositionType;
 import jalview.xml.binding.uniprot.PropertyType;
 
-import java.io.InputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-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;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * This class queries the Uniprot database for sequence data, unmarshals the
  * returned XML, and converts it to Jalview Sequence records (including attached
@@ -72,9 +71,15 @@ public class TDBeacons extends DbSourceProxyImpl
   private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
 
   private static final String BAR_DELIMITER = "|";
-  
+
   private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/";
 
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_THREEDBEACONS_DOMAIN);
+  }
+
   /**
    * Constructor
    */
@@ -86,7 +91,7 @@ public class TDBeacons extends DbSourceProxyImpl
   private String getDomain()
   {
     return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
-    //return Cache.getDefault("3DB_DOMAIN", DEFAULT_THREEDBEACONS_DOMAIN );
+    // return Cache.getDefault("3DB_DOMAIN", DEFAULT_THREEDBEACONS_DOMAIN );
   }
 
   /*
@@ -148,9 +153,8 @@ public class TDBeacons extends DbSourceProxyImpl
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
 
-      String downloadstring = getDomain() + "/uniprot/" + queries
-              + ".xml";
-//      String downloadstring = getDomain() + queries + ".json";
+      String downloadstring = getDomain() + "/uniprot/" + queries + ".xml";
+      // String downloadstring = getDomain() + queries + ".json";
 
       URL url = new URL(downloadstring);
       URLConnection urlconn = url.openConnection();
@@ -192,8 +196,7 @@ public class TDBeacons extends DbSourceProxyImpl
     String seqString = entry.getSequence().getValue().replaceAll("\\s*",
             "");
 
-    SequenceI sequence = new Sequence(id,
-            seqString);
+    SequenceI sequence = new Sequence(id, seqString);
     sequence.setDescription(getUniprotEntryDescription(entry));
 
     /*
@@ -509,10 +512,12 @@ public class TDBeacons extends DbSourceProxyImpl
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(is);
       javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-      JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = 
-    		  um.unmarshal(streamReader, jalview.xml.binding.uniprot.Uniprot.class);
-      jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement.getValue();
-      
+      JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = um
+              .unmarshal(streamReader,
+                      jalview.xml.binding.uniprot.Uniprot.class);
+      jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement
+              .getValue();
+
       if (uniprot != null && !uniprot.getEntry().isEmpty())
       {
         entries = uniprot.getEntry();