X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEBIFetchClient.java;h=5b21bfe092515f97283c01493969dcf18073d963;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=3c6e5f9050109f86badd33815603eada6e06b6e4;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 3c6e5f9..5b21bfe 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -16,166 +16,160 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.io;
 
-import org.apache.axis.client.*;
-
-import java.io.*;
-
-import javax.activation.DataHandler;
 import org.apache.axis.AxisFault;
+import org.apache.axis.client.*;
 import org.apache.axis.encoding.XMLType;
-import javax.xml.rpc.ParameterMode;
-import javax.xml.namespace.QName;
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
 import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;
+import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
 
+import java.io.*;
 
-public class EBIFetchClient
-{
-  Call call;
-  String format = "default";
-  String style = "raw";
-
-  public EBIFetchClient()
-  {
-    try{
-      call = (Call)new Service().createCall();
-      call.setTargetEndpointAddress(new java.net.URL(
-          "http://www.ebi.ac.uk/ws/services/Dbfetch"));
-    }catch(Exception ex){}
-  }
-
-
-  public String []  getSupportedDBs()
-  {
-       try{
-
-         call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
-         call.setReturnType(XMLType.SOAP_ARRAY);
-         return (String[]) call.invoke(new Object[]{});
-
-       }catch(Exception ex){return null;}
-  }
+import javax.activation.DataHandler;
 
-  public String [] getSupportedFormats()
-  {
-      try{
-        call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
-        call.setReturnType(XMLType.SOAP_ARRAY);
-        return (String[]) call.invoke(new Object[] {});
+import javax.xml.namespace.QName;
+import javax.xml.rpc.ParameterMode;
 
-      }catch(Exception ex){ return null; }
-   }
 
-   public String [] getSupportedStyles()
-   {
-        try{
-          call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
-          call.setReturnType(XMLType.SOAP_ARRAY);
-          return (String[]) call.invoke(new Object[] {});
+public class EBIFetchClient {
+    Call call;
+    String format = "default";
+    String style = "raw";
 
-         }catch(Exception ex){return null;}
+    public EBIFetchClient() {
+        try {
+            call = (Call) new Service().createCall();
+            call.setTargetEndpointAddress(new java.net.URL(
+                    "http://www.ebi.ac.uk/ws/services/Dbfetch"));
+        } catch (Exception ex) {
+        }
     }
 
-    public String [] fetchData(String ids, String f, String s)
-    {
-      // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;
-      // max 50 ids can be added at one time
-      try{
-        call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
-        call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
-        call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
-        call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
-        call.setReturnType(XMLType.SOAP_ARRAY);
-
-        if (f != null)
-          format = f;
-
-        if (s != null)
-          style = s;
-
-        return (String[]) call.invoke(new Object[] {ids, format, style});
-
-      }catch(Exception ex){return null;}
+    public String[] getSupportedDBs() {
+        try {
+            call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
+            call.setReturnType(XMLType.SOAP_ARRAY);
 
+            return (String[]) call.invoke(new Object[] {  });
+        } catch (Exception ex) {
+            return null;
+        }
     }
 
-    public String fetchDataFile(String arg, String f, String s)
-    {
-
-      if (f != null)
-        format = f;
+    public String[] getSupportedFormats() {
+        try {
+            call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
+            call.setReturnType(XMLType.SOAP_ARRAY);
 
-      if (s != null)
-        style = s;
-
-
-      call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));
-      call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
-
-      QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");
-      call.registerTypeMapping(javax.activation.DataSource.class,
-                               qnameAttachment,
-                               JAFDataHandlerSerializerFactory.class,
-                               JAFDataHandlerDeserializerFactory.class);
+            return (String[]) call.invoke(new Object[] {  });
+        } catch (Exception ex) {
+            return null;
+        }
+    }
 
-      call.setReturnType(qnameAttachment);
+    public String[] getSupportedStyles() {
+        try {
+            call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
+            call.setReturnType(XMLType.SOAP_ARRAY);
 
-      try{
-        Object ret = call.invoke(new Object[]
-                                 {arg, format, style});
+            return (String[]) call.invoke(new Object[] {  });
+        } catch (Exception ex) {
+            return null;
+        }
+    }
 
-        if (null == ret)
-        {
-          System.err.println("Received null ");
-          throw new AxisFault("", "Received null", null, null);
+    public String[] fetchData(String ids, String f, String s) {
+        // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;
+        // max 50 ids can be added at one time
+        try {
+            call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
+            call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
+            call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
+            call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
+            call.setReturnType(XMLType.SOAP_ARRAY);
+
+            if (f != null) {
+                format = f;
+            }
+
+            if (s != null) {
+                style = s;
+            }
+
+            return (String[]) call.invoke(new Object[] { ids, format, style });
+        } catch (Exception ex) {
+            return null;
         }
-        if (ret instanceof String)
-        {
-          System.err.println("Received problem response from server: " + ret);
-          throw new AxisFault("", (String) ret, null, null);
+    }
+
+    public String fetchDataFile(String arg, String f, String s) {
+        if (f != null) {
+            format = f;
         }
-        if (! (ret instanceof DataHandler))
-        {
-          //The wrong type of object that what was expected.
-          System.err.println("Received problem response from server:" +
-                             ret.getClass().getName());
-          throw new AxisFault("", "Received problem response from server:" +
-                              ret.getClass().getName(), null, null);
 
+        if (s != null) {
+            style = s;
         }
-        //Still here, so far so good.
-        DataHandler rdh = (DataHandler) ret;
 
-        //From here we'll just treat the data resource as file.
-        String receivedfileName = rdh.getName(); //Get the filename.
+        call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));
+        call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
+        call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
+        call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
 
-        if (receivedfileName == null)
-        {
-          System.err.println("Could not get the file name.");
-          throw new AxisFault("", "Could not get the file name.", null, null);
+        QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");
+        call.registerTypeMapping(javax.activation.DataSource.class,
+            qnameAttachment, JAFDataHandlerSerializerFactory.class,
+            JAFDataHandlerDeserializerFactory.class);
+
+        call.setReturnType(qnameAttachment);
+
+        try {
+            Object ret = call.invoke(new Object[] { arg, format, style });
+
+            if (null == ret) {
+                System.err.println("Received null ");
+                throw new AxisFault("", "Received null", null, null);
+            }
+
+            if (ret instanceof String) {
+                System.err.println("Received problem response from server: " +
+                    ret);
+                throw new AxisFault("", (String) ret, null, null);
+            }
+
+            if (!(ret instanceof DataHandler)) {
+                //The wrong type of object that what was expected.
+                System.err.println("Received problem response from server:" +
+                    ret.getClass().getName());
+                throw new AxisFault("",
+                    "Received problem response from server:" +
+                    ret.getClass().getName(), null, null);
+            }
+
+            //Still here, so far so good.
+            DataHandler rdh = (DataHandler) ret;
+
+            //From here we'll just treat the data resource as file.
+            String receivedfileName = rdh.getName(); //Get the filename.
+
+            if (receivedfileName == null) {
+                System.err.println("Could not get the file name.");
+                throw new AxisFault("", "Could not get the file name.", null,
+                    null);
+            }
+
+            if (arg.equalsIgnoreCase("medline")) {
+                return receivedfileName;
+            } else if (arg.equalsIgnoreCase("interpro")) {
+                return receivedfileName;
+            } else {
+                System.err.println(receivedfileName);
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
         }
-        if (arg.equalsIgnoreCase("medline"))
-        {
-          return receivedfileName;
-        }
-        else if (arg.equalsIgnoreCase("interpro"))
-        {
-          return receivedfileName;
-        }
-        else
-          System.err.println(receivedfileName);
-      }catch(Exception ex)
-      {
-        ex.printStackTrace();
-      }
-
-      return "ERROR";
-    }
-
 
+        return "ERROR";
+    }
 }