*/
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;
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;
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
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
*/
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 );
}
/*
"(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();
String seqString = entry.getSequence().getValue().replaceAll("\\s*",
"");
- SequenceI sequence = new Sequence(id,
- seqString);
+ SequenceI sequence = new Sequence(id, seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
/*
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();