Jalview-JS/JAL-3253-applet more argument parsing

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 74a9ea4..d199963 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -29,6 +29,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.schemes.ResidueProperties;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
@@ -47,6 +48,7 @@ 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;
@@ -79,7 +81,7 @@ public class Uniprot extends DbSourceProxyImpl
 
   private String getDomain()
   {
-    return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+    return Cache.getDefault(Preferences.UNIPROT_DOMAIN, DEFAULT_UNIPROT_DOMAIN);
   }
 
   /*
@@ -178,16 +180,12 @@ public class Uniprot extends DbSourceProxyImpl
   SequenceI uniprotEntryToSequence(Entry entry)
   {
     String id = getUniprotEntryId(entry);
-    String seqString = entry.getSequence().getValue();
-
     /*
-     * for backwards compatibility with Castor processing,
-     * remove any internal spaces
+     * Sequence should not include any whitespace, but JAXB leaves these in
      */
-    if (seqString.indexOf(' ') > -1)
-    {
-      seqString = seqString.replaceAll(" ", "");
-    }
+    String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+            "");
+
     SequenceI sequence = new Sequence(id,
             seqString);
     sequence.setDescription(getUniprotEntryDescription(entry));
@@ -505,7 +503,10 @@ public class Uniprot extends DbSourceProxyImpl
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(is);
       javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-      jalview.xml.binding.uniprot.Uniprot uniprot = (jalview.xml.binding.uniprot.Uniprot) um.unmarshal(streamReader);
+      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();