X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FWsParamSetManager.java;h=272e05bacc31af6f32a13d14dfc2c09d36a1342e;hb=0751c58086542f9e0466201b624f84d1efd547bb;hp=ab03d694ea32a6dda5a06024d35bc875c1ded9ff;hpb=7b5c84397cf62677cedfa8800022acacc905302c;p=jalview.git

diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index ab03d69..272e05b 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -27,8 +27,11 @@ import jalview.util.MessageManager;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
+import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.WebServiceParameterSet;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -39,6 +42,12 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
 /**
  * store and retrieve web service parameter sets.
  * 
@@ -61,7 +70,7 @@ public class WsParamSetManager implements ParamManager
     }
     StringTokenizer st = new StringTokenizer(files, "|");
     String pfile = null;
-    ArrayList<WsParamSetI> params = new ArrayList<>();
+    List<WsParamSetI> params = new ArrayList<>();
     while (st.hasMoreTokens())
     {
       pfile = st.nextToken();
@@ -111,31 +120,37 @@ public class WsParamSetManager implements ParamManager
   {
     List<WsParamSetI> psets = new ArrayList<>();
     InputStreamReader is = new InputStreamReader(
-            new java.io.FileInputStream(new File(filename)), "UTF-8");
-
-    jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
+            new FileInputStream(new File(filename)), "UTF-8");
 
-    org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
-            wspset);
-    unmar.setWhitespacePreserve(true);
+    WebServiceParameterSet wspset = null;
     try
     {
-      wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
-              .unmarshal(is);
+      JAXBContext jc = JAXBContext
+              .newInstance("jalview.xml.binding.jalview");
+      javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+      XMLStreamReader streamReader = XMLInputFactory.newInstance()
+              .createXMLStreamReader(is);
+      JAXBElement<WebServiceParameterSet> jbe = um.unmarshal(streamReader,
+              WebServiceParameterSet.class);
+      wspset = jbe.getValue();
     } catch (Exception ex)
     {
       throw new IOException(ex);
     }
+
     if (wspset != null && wspset.getParameters().length() > 0)
     {
-      for (String url : wspset.getServiceURL())
+      List<String> urls = wspset.getServiceURL();
+      final String[] urlArray = urls.toArray(new String[urls.size()]);
+
+      for (String url : urls)
       {
         ParamDatastoreI parser = paramparsers.get(url);
         if (parser != null)
         {
           WsParamSetI pset = parser.parseServiceParameterFile(
                   wspset.getName(), wspset.getDescription(),
-                  wspset.getServiceURL(), wspset.getParameters());
+                  urlArray, wspset.getParameters());
           if (pset != null)
           {
             pset.setSourceFile(filename);
@@ -182,18 +197,19 @@ public class WsParamSetManager implements ParamManager
     }
     if (filename == null)
     {
+      // TODO: JAL-3048 webservice - not required for Jalview-JS
+
       JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
               "Web Service Parameter File");
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
               .getString("label.choose_filename_for_param_file"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
-      int value = chooser.showSaveDialog(Desktop.instance);
+      int value = chooser.showSaveDialog(Desktop.getInstance());
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         outfile = chooser.getSelectedFile();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                outfile.getParent());
+        Cache.setProperty("LAST_DIRECTORY", outfile.getParent());
         filename = outfile.getAbsolutePath();
         if (!filename.endsWith(".wsparams"))
         {
@@ -214,13 +230,17 @@ public class WsParamSetManager implements ParamManager
         }
         paramFiles = paramFiles.concat(filename);
       }
-      jalview.bin.Cache.setProperty(WS_PARAM_FILES, paramFiles);
 
-      jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
+      Cache.setProperty(WS_PARAM_FILES, paramFiles);
+
+      WebServiceParameterSet paramxml = new WebServiceParameterSet();
 
       paramxml.setName(parameterSet.getName());
       paramxml.setDescription(parameterSet.getDescription());
-      paramxml.setServiceURL(parameterSet.getApplicableUrls().clone());
+      for (String url : parameterSet.getApplicableUrls())
+      {
+        paramxml.getServiceURL().add(url);
+      }
       paramxml.setVersion("1.0");
       try
       {
@@ -228,7 +248,12 @@ public class WsParamSetManager implements ParamManager
                 parser.generateServiceParameterFile(parameterSet));
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(outfile), "UTF-8"));
-        paramxml.marshal(out);
+        JAXBContext jaxbContext = JAXBContext
+                .newInstance(WebServiceParameterSet.class);
+        Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+        jaxbMarshaller.marshal(
+                new ObjectFactory().createWebServiceParameterSet(paramxml),
+                out);
         out.close();
         parameterSet.setSourceFile(filename);
       } catch (Exception e)
@@ -289,7 +314,7 @@ public class WsParamSetManager implements ParamManager
       File pfile = new File(filename);
       if (pfile.exists() && pfile.canWrite())
       {
-        if (JvOptionPane.showConfirmDialog(Desktop.instance,
+        if (JvOptionPane.showConfirmDialog(Desktop.getInstance(),
                 "Delete the preset's file, too ?", "Delete User Preset ?",
                 JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
         {