From c13784724ba3826e6cc3faeb85571cf30776592d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 6 Sep 2010 16:39:44 +0000
Subject: [PATCH] JAL-591

---
 src/jalview/gui/Desktop.java               |   11 +
 src/jalview/gui/WsJobParameters.java       |   18 +-
 src/jalview/gui/WsParamSetManager.java     |  298 ++++++++++++++++++++++++++++
 src/jalview/ws/jws2/JabaParamStore.java    |  201 +++++++++++++------
 src/jalview/ws/jws2/JabaPreset.java        |    2 +-
 src/jalview/ws/jws2/Jws2Discoverer.java    |   47 +++--
 src/jalview/ws/jws2/MsaWSClient.java       |    2 +-
 src/jalview/ws/params/ParamDatastoreI.java |   45 ++++-
 src/jalview/ws/params/ParamManager.java    |   23 ++-
 9 files changed, 554 insertions(+), 93 deletions(-)
 create mode 100644 src/jalview/gui/WsParamSetManager.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 53fa463..8531e04 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -19,6 +19,7 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.io.*;
+import jalview.ws.params.ParamManager;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
@@ -2200,4 +2201,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }).start();    
   }
 
+  public static WsParamSetManager wsparamManager = null;
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager==null)
+    {
+      wsparamManager = new WsParamSetManager();
+    }
+    return wsparamManager;
+  }
+
 }
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 58c9646..1d56b69 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -389,11 +389,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     if (isUserPreset)
     {
       String curname = ((String) setName.getSelectedItem()).trim();
-      if (curname.length() > 0 && !curname.equals(lastParmSet))
-      {
-        _deleteUserPreset(lastParmSet);
-      }
-      _storeCurrentPreset(curname);
+      _updatePreset(lastParmSet, curname);
       lastParmSet = curname;
       isUserPreset = true;
       initArgSetModified();
@@ -401,6 +397,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
   }
 
+
   private void _deleteUserPreset(String lastParmSet2)
   {
     paramStore.deletePreset(lastParmSet2);
@@ -1466,7 +1463,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
             }
             {
               System.out.println("Testing opts dupes for "
-                      + lastserv.getHost() + " : "
+                      + lastserv.getUri() + " : "
                       + lastserv.getActionText() + ":" + pr.getName());
               List<Option> rg = lastserv.getRunnerConfig().getOptions();
               for (Option o : rg)
@@ -1806,6 +1803,10 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
     }
   }
+  private void _renameExistingPreset(String oldName, String curSetName2)
+  {
+    paramStore.updatePreset(oldName, curSetName2, setDescr.getText(), getJobParams());
+  }
 
   /**
    * store current settings as given name. You should then reset gui.
@@ -1816,6 +1817,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
   {
     paramStore.storePreset(curSetName2, setDescr.getText(), getJobParams());
   }
+  private void _updatePreset(String lastParmSet2, String curname)
+  {
+    paramStore.updatePreset(lastParmSet2, curname, setDescr.getText(), getJobParams());
+    
+  }
 
   /**
    * last saved name for this user preset
diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
new file mode 100644
index 0000000..77aaf8c
--- /dev/null
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -0,0 +1,298 @@
+package jalview.gui;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+
+import jalview.bin.Cache;
+import jalview.io.JalviewFileChooser;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+
+/**
+ * store and retrieve web service parameter sets.
+ * 
+ * @author JimP
+ * 
+ */
+public class WsParamSetManager implements ParamManager
+{
+  Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<String, ParamDatastoreI>();
+
+  @Override
+  public WsParamSetI[] getParameterSet(String name, String serviceUrl,
+          boolean modifiable, boolean unmodifiable)
+  {
+    String files = Cache.getProperty("WS_PARAM_FILES");
+    if (files == null)
+    {
+      return null;
+    }
+    StringTokenizer st = new StringTokenizer(files, "|");
+    String pfile = null;
+    ArrayList<WsParamSetI> params = new ArrayList<WsParamSetI>();
+    while (st.hasMoreTokens())
+    {
+      pfile = st.nextToken();
+      try
+      {
+        WsParamSetI[] pset = parseParamFile(pfile);
+        for (WsParamSetI p : pset)
+        {
+          boolean add = false;
+          if (serviceUrl != null)
+          {
+            for (String url : p.getApplicableUrls())
+            {
+              if (url.equals(serviceUrl))
+              {
+                add = true;
+              }
+            }
+          }
+          else
+          {
+            add = true;
+          }
+          add &= (modifiable == p.isModifiable() || unmodifiable == !p
+                  .isModifiable());
+          add &= name == null || p.getName().equals(name);
+
+          if (add)
+          {
+
+            params.add(p);
+          }
+
+        }
+      } catch (IOException e)
+      {
+        Cache.log
+                .info("Failed to parse parameter file "
+                        + pfile
+                        + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
+                        e);
+      }
+    }
+    return params.toArray(new WsParamSetI[0]);
+  }
+
+  private WsParamSetI[] parseParamFile(String filename) throws IOException
+  {
+    List<WsParamSetI> psets = new ArrayList<WsParamSetI>();
+    InputStreamReader is = new InputStreamReader(
+            new java.io.FileInputStream(new File(filename)), "UTF-8");
+
+    jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
+
+    org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
+            wspset);
+    unmar.setWhitespacePreserve(true);
+    try
+    {
+      wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
+              .unmarshal(is);
+    } catch (Exception ex)
+    {
+      throw new IOException(ex);
+    }
+    if (wspset != null && wspset.getParameters().length() > 0)
+    {
+      for (String url : wspset.getServiceURL())
+      {
+        ParamDatastoreI parser = paramparsers.get(url);
+        if (parser != null)
+        {
+          WsParamSetI pset = parser.parseServiceParameterFile(
+                  wspset.getName(), wspset.getDescription(),
+                  wspset.getServiceURL(), wspset.getParameters());
+          if (pset != null)
+          {
+            pset.setSourceFile(filename);
+            psets.add(pset);
+            break;
+          }
+        }
+      }
+    }
+
+    return psets.toArray(new WsParamSetI[0]);
+  }
+
+  @Override
+  public void storeParameterSet(WsParamSetI parameterSet)
+  {
+    String filename = parameterSet.getSourceFile();
+    File outfile = null;
+    try
+    {
+      if (filename != null && !((outfile = new File(filename)).canWrite()))
+      {
+        Cache.log.info("Can't write to " + filename
+                + " - Prompting for new file to write to.");
+        filename = null;
+      }
+    } catch (Exception e)
+    {
+      filename = null;
+    }
+
+    ParamDatastoreI parser = null;
+    for (String urls : parameterSet.getApplicableUrls())
+    {
+      if (parser == null)
+      {
+        parser = paramparsers.get(urls);
+      }
+    }
+    if (parser == null)
+    {
+      throw new Error(
+              "Implementation error: Can't find a marshaller for the parameter set");
+    }
+    if (filename == null)
+    {
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+              { "wsparams" }, new String[]
+              { "Web Service Parameter File" },
+              "Web Service Parameter File");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Choose a filename for this parameter file");
+      chooser.setToolTipText("Save");
+      int value = chooser.showOpenDialog(Desktop.instance);
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        outfile = chooser.getSelectedFile();
+        jalview.bin.Cache
+                .setProperty("LAST_DIRECTORY", outfile.getParent());
+        filename = outfile.getAbsolutePath();
+        if (!filename.endsWith(".wsparams"))
+        {
+          filename = filename.concat(".wsparams");
+          outfile = new File(filename);
+        }
+      }
+    }
+    if (outfile != null)
+    {
+      String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+              filename);
+      if (paramFiles.indexOf(filename) == -1)
+      {
+        if (paramFiles.length() > 0)
+        {
+          paramFiles = paramFiles.concat("|");
+        }
+        paramFiles = paramFiles.concat(filename);
+      }
+      jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles);
+
+      jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
+
+      paramxml.setName(parameterSet.getName());
+      paramxml.setDescription(parameterSet.getDescription());
+      paramxml.setServiceURL(parameterSet.getApplicableUrls().clone());
+      paramxml.setVersion("1.0");
+      try
+      {
+        paramxml.setParameters(parser
+                .generateServiceParameterFile(parameterSet));
+        PrintWriter out = new PrintWriter(new OutputStreamWriter(
+                new FileOutputStream(outfile), "UTF-8"));
+        paramxml.marshal(out);
+        out.close();
+        parameterSet.setSourceFile(filename);
+      } catch (Exception e)
+      {
+        Cache.log.error("Couldn't write parameter file to " + outfile, e);
+      }
+    }
+  }
+
+  /*
+   * 
+   * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+   * .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
+   * "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
+   * jalview.io.JalviewFileView());
+   * chooser.setDialogTitle("Load colour scheme");
+   * chooser.setToolTipText("Load");
+   * 
+   * int value = chooser.showOpenDialog(this);
+   * 
+   * if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
+   * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+   * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
+   * "USER_DEFINED_COLOURS", choice.getPath()); if
+   * (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
+   * defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
+   * 
+   * @see
+   * jalview.ws.params.ParamManager#deleteParameterSet(jalview.ws.params.WsParamSetI
+   * )
+   */
+  @Override
+  public void deleteParameterSet(WsParamSetI parameterSet)
+  {
+    String filename = parameterSet.getSourceFile();
+    if (filename == null || filename.trim().length() < 1)
+    {
+      return;
+    }
+    String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+    if (paramFiles.indexOf(filename) > -1)
+    {
+      String nparamFiles = new String();
+      StringTokenizer st = new StringTokenizer(paramFiles, "|");
+      while (st.hasMoreElements())
+      {
+        String fl = st.nextToken();
+        if (!fl.equals(filename))
+        {
+          nparamFiles = nparamFiles.concat("|").concat(fl);
+        }
+      }
+      jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+    }
+
+    try
+    {
+      File pfile = new File(filename);
+      if (pfile.exists() && pfile.canWrite())
+      {
+        if (JOptionPane.showConfirmDialog(Desktop.instance,
+                "Delete the preset's file, too ?", "Delete User Preset ?",
+                JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION)
+        {
+          pfile.delete();
+        }
+      }
+    } catch (Exception e)
+    {
+      Cache.log
+              .error("Exception when trying to delete webservice user preset: ",
+                      e);
+    }
+  }
+
+  @Override
+  public void registerParser(String hosturl, ParamDatastoreI paramdataStore)
+  {
+    paramparsers.put(hosturl, paramdataStore);
+  }
+
+}
diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index 0f7d6fa..bdea5be 100644
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -7,6 +7,7 @@ import java.io.Writer;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.StringTokenizer;
 
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
@@ -21,6 +22,7 @@ import jalview.ws.jws2.dm.JabaParameter;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
 
 public class JabaParamStore implements ParamDatastoreI
@@ -36,56 +38,44 @@ public class JabaParamStore implements ParamDatastoreI
 
   public JabaParamStore(Jws2Instance service)
   {
-    this.service = service;
-    serviceOptions = service.getRunnerConfig();
-    // TODO: discover all the user's locally sored presets for this service and populate the hash table
-    // TODO: for JAL-632
+    this(service, null);
   }
 
-  /**
-   * store the given parameters in the user parameter set database.
-   * 
-   * @param storeSetName
-   *          - lastParmSet
-   * @param descr
-   *          - setDescr.getText()
-   * @param jobParams
-   *          - getJobParams()
-   */
-  private void _storeUserPreset(String storeSetName, String descr,
-          List<Argument> jobParams)
-  {
-    // this is a simple hash store.
-    editedParams.put(storeSetName, new JabaWsParamSet(storeSetName, descr,
-            JabaParamStore.getJwsArgsfromJaba(jobParams)));
-    // writeParam("Saving " + storeSetName + ": ", jobParams);
-  }
+  ParamManager manager;
 
-  private void writeParam(String nm, List<Argument> params)
+  public JabaParamStore(Jws2Instance service, ParamManager manager)
   {
-    for (Argument p : params)
+    this.service = service;
+    serviceOptions = service.getRunnerConfig();
+    this.manager = manager;
+    // discover all the user's locally stored presets for this service and
+    // populate the hash table
+    if (manager != null)
     {
-      System.out.println(nm + ":" + System.identityHashCode(p) + " Name: "
-              + p.getName() + " Value: " + p.getDefaultValue());
+      manager.registerParser(service.getUri(), this);
+      WsParamSetI[] prams = manager.getParameterSet(null, service.getUri(),
+              true, false);
+      if (prams != null)
+      {
+        for (WsParamSetI paramset : prams)
+        {
+          if (paramset instanceof JabaWsParamSet)
+          {
+            editedParams.put(paramset.getName(), (JabaWsParamSet) paramset);
+          }
+          else
+          {
+            System.err
+                    .println("Warning: Ignoring parameter set instance of type "
+                            + paramset.getClass()
+                            + " : Bound but not applicable for service at "
+                            + service.getUri());
+          }
+        }
+      }
     }
   }
 
-  private JabaWsParamSet _getUserPreset(String setName)
-  {
-    JabaWsParamSet pset = editedParams.get(setName);
-    return pset;
-  }
-
-  /**
-   * remove the given user preset from the preset stash
-   * 
-   * @param setName
-   */
-  private void _deleteUserPreset(String setName)
-  {
-    editedParams.remove(setName);
-  }
-
   @Override
   public List<WsParamSetI> getPresets()
   {
@@ -192,7 +182,12 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (editedParams.containsKey(name))
     {
+      WsParamSetI parameterSet = editedParams.get(name);
       editedParams.remove(name);
+      if (manager != null)
+      {
+        manager.deleteParameterSet(parameterSet);
+      }
       return;
     }
     if (servicePresets.containsKey(name))
@@ -202,45 +197,125 @@ public class JabaParamStore implements ParamDatastoreI
     }
   }
 
-
   @Override
   public void storePreset(String presetName, String text,
           List<ArgumentI> jobParams)
   {
     JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
+    jps.setApplicableUrls(new String[]
+    { service.getUri() });
     editedParams.put(jps.getName(), jps);
+    if (manager != null)
+    {
+      manager.storeParameterSet(jps);
+    }
   }
 
   @Override
-  public boolean readParamSet(WsParamSetI wsp,
-          Reader reader) throws IOException
+  public void updatePreset(String oldName, String presetName, String text,
+          List<ArgumentI> jobParams)
   {
-    if (!(wsp instanceof JabaWsParamSet))
+    JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
+            : getPreset(presetName));
+    if (jps == null)
     {
-      throw new Error("Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+      throw new Error("Implementation error: Can't locate either oldname ("
+              + oldName + ") or presetName (" + presetName
+              + "in the datastore!");
     }
-    List<String> lines=new ArrayList<String>();
-    String line;
-    BufferedReader br = new BufferedReader(reader);
-    while ((line=br.readLine())!=null)
+    jps.setName(presetName);
+    jps.setDescription(text);
+    jps.setArguments(jobParams);
+    jps.setApplicableUrls(new String[]
+    { service.getUri() });
+    if (oldName != null && !oldName.equals(jps.getName()))
     {
-      lines.add(line);
+      editedParams.remove(oldName);
+    }
+    editedParams.put(jps.getName(), jps);
+
+    if (manager != null)
+    {
+      manager.storeParameterSet(jps);
     }
-    ((JabaWsParamSet) wsp).setjabaArguments(ParameterUtils.processParameters(lines, serviceOptions, " "));
-    return true;
+  }
+
+  /**
+   * create a new, empty parameter set for this service
+   * 
+   * @return
+   */
+  WsParamSetI newWsParamSet()
+  {
+    return new JabaWsParamSet();
+  };
+
+  private boolean involves(String[] urls)
+  {
+    boolean found = false;
+    for (String url : urls)
+    {
+      if (service.getUri().equalsIgnoreCase(url))
+      {
+        found = true;
+        break;
+      }
+    }
+    return found;
   }
 
   @Override
-  public boolean writeParamSet(WsParamSetI wsp,
-          Writer writer) throws IOException
+  public WsParamSetI parseServiceParameterFile(String name, String descr,
+          String[] urls, String parameterfile) throws IOException
   {
-            if (!(wsp instanceof JabaWsParamSet))
-            {
-              throw new Error("Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
-            }
-            writer.write(ParameterUtils.writeParameterSet(((JabaWsParamSet)wsp).getjabaArguments(), " ")
-                    .toString());
-            return true;
+    if (!involves(urls))
+    {
+      throw new IOException(
+              "Implementation error: Cannot find service url in the given url set!");
+
+    }
+    JabaWsParamSet wsp = new JabaWsParamSet();
+    wsp.setName(name);
+    wsp.setDescription(descr);
+    wsp.setApplicableUrls(urls.clone());
+
+    List<String> lines = new ArrayList<String>();
+    StringTokenizer st = new StringTokenizer(parameterfile, "\n");
+    while (st.hasMoreTokens())
+    {
+      lines.add(st.nextToken());
+    }
+    wsp.setjabaArguments(ParameterUtils.processParameters(lines,
+            serviceOptions, " "));
+    return wsp;
+  }
+
+  @Override
+  public String generateServiceParameterFile(WsParamSetI pset)
+          throws IOException
+  {
+    if (!involves(pset.getApplicableUrls()))
+    {
+      throw new IOException(
+              "Implementation error: Cannot find service url in the given url set for this service parameter store ("
+                      + service.getUri() + ") !");
+
+    }
+    if (!(pset instanceof JabaWsParamSet))
+    {
+      throw new Error(
+              "Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+    }
+
+    StringBuffer rslt = new StringBuffer();
+    for (String ln : ParameterUtils.writeParameterSet(
+            ((JabaWsParamSet) pset).getjabaArguments(), " "))
+    {
+      rslt.append(ln);
+      rslt.append("\n");
+    }
+    ;
+    return rslt.toString();
   }
 
 }
diff --git a/src/jalview/ws/jws2/JabaPreset.java b/src/jalview/ws/jws2/JabaPreset.java
index 1f8517e..c8177ba 100644
--- a/src/jalview/ws/jws2/JabaPreset.java
+++ b/src/jalview/ws/jws2/JabaPreset.java
@@ -28,7 +28,7 @@ public class JabaPreset implements WsParamSetI {
   @Override
   public String[] getApplicableUrls()
   {
-    return new String[] { service.getHost()};
+    return new String[] { service.getUri()};
   }
   @Override
   public String getSourceFile()
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index eccbdaf..2ef9cfd 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -23,6 +23,7 @@ import org.apache.log4j.Level;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.ws.WSMenuEntryProviderI;
 import jalview.ws.params.ParamDatastoreI;
 import compbio.data.msa.MsaWS;
@@ -182,7 +183,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
     PresetManager presets = null;
 
-    public JabaParamStore paramStore=null;
+    public JabaParamStore paramStore = null;
 
     /**
      * non thread safe - gets the presets for this service (blocks whilst it
@@ -260,14 +261,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       if (paramStore == null)
       {
-        try {
-        paramStore = new JabaParamStore(this);
+        try
+        {
+          paramStore = new JabaParamStore(this,
+                  (Desktop.instance != null ? Desktop
+                          .getUserParameterStore() : null));
         } catch (Exception ex)
-        {}
-        
+        {
+        }
+
       }
       return paramStore;
     }
+
+    public String getUri()
+    {
+      // this is only valid for Jaba 1.0 - this formula might have to change!
+      return hosturl+"/"+serviceType;
+    }
   };
 
   /**
@@ -307,8 +318,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     // dynamically regenerate service list.
     final JMenu jws2al = new JMenu("JABA Alignment");
-    jws2al.addMenuListener(new MenuListener() {
-      // TODO: future: add menu listener to parent menu - so submenus are populated *before* they are selected.
+    jws2al.addMenuListener(new MenuListener()
+    {
+      // TODO: future: add menu listener to parent menu - so submenus are
+      // populated *before* they are selected.
       @Override
       public void menuSelected(MenuEvent e)
       {
@@ -319,19 +332,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       public void menuDeselected(MenuEvent e)
       {
         // TODO Auto-generated method stub
-        
+
       }
 
       @Override
       public void menuCanceled(MenuEvent e)
       {
         // TODO Auto-generated method stub
-        
+
       }
-      
+
     });
     wsmenu.add(jws2al);
   }
+
   private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
   {
     if (running || services == null || services.size() == 0)
@@ -524,22 +538,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   /**
    * test the given URL with the JabaWS test code
+   * 
    * @param foo
    * @return
    */
   public static boolean testServiceUrl(URL foo)
   {
-    try {
-      compbio.ws.client.WSTester.main(new String[] { "-h="+foo.toString()});
+    try
+    {
+      compbio.ws.client.WSTester.main(new String[]
+      { "-h=" + foo.toString() });
     } catch (Exception e)
     {
       return false;
-    }
-    catch (OutOfMemoryError e)
+    } catch (OutOfMemoryError e)
     {
       return false;
-    }
-    catch (Error e)
+    } catch (Error e)
     {
       return false;
     }
diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 7df3a98..d7b968d 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -151,7 +151,7 @@ public class MsaWSClient extends Jws2Client
     {
       if (sh.paramStore == null)
       {
-        sh.paramStore = new JabaParamStore(sh);
+        sh.paramStore = new JabaParamStore(sh, Desktop.getUserParameterStore());
       }
       WsJobParameters jobParams = new WsJobParameters(sh, preset);
       if (!jobParams.showRunDialog())
diff --git a/src/jalview/ws/params/ParamDatastoreI.java b/src/jalview/ws/params/ParamDatastoreI.java
index 217de90..78ca8fc 100644
--- a/src/jalview/ws/params/ParamDatastoreI.java
+++ b/src/jalview/ws/params/ParamDatastoreI.java
@@ -3,7 +3,7 @@ package jalview.ws.params;
 import java.io.IOException;
 import java.util.List;
 
-public interface ParamDatastoreI 
+public interface ParamDatastoreI
 {
 
   public List<WsParamSetI> getPresets();
@@ -17,19 +17,54 @@ public interface ParamDatastoreI
   public void deletePreset(String name);
 
   /**
-   * writes or overwrites the record for a modifiable WsParamSetI entry in the datastore.
+   * writes or overwrites the record for a modifiable WsParamSetI entry with a given name in the
+   * datastore.
+   * 
    * @param presetName
    * @param text
    * @param jobParams
-   * may throw an illegal argument RunTimeException if the presetName overwrites an existing, unmodifiable preset.
+   *          may throw an illegal argument RunTimeException if the presetName
+   *          overwrites an existing, unmodifiable preset.
    */
   public void storePreset(String presetName, String text,
           List<ArgumentI> jobParams);
 
-  public boolean readParamSet(WsParamSetI wsp, java.io.Reader reader)
+  /**
+   * update an existing instance with a new name, descriptive text and parameters.
+   * @param oldName
+   * @param presetName
+   * @param text
+   * @param jobParams
+   */
+  public void updatePreset(String oldName, String presetName, String text,
+           List<ArgumentI> jobParams);
+
+  /**
+   * factory method - builds a service specific parameter object using the given
+   * data
+   * 
+   * @param name
+   * @param description
+   * @param applicable
+   *          URLs
+   * @param parameterfile
+   *          Service specific jalview parameter file (as returned from new
+   *          method)
+   * @return null or valid WsParamSetI object for this service.
+   */
+
+  public WsParamSetI parseServiceParameterFile(String name,
+          String description, String[] serviceURL, String parameters)
           throws IOException;
 
-  public boolean writeParamSet(WsParamSetI wsp, java.io.Writer writer)
+  /**
+   * create the service specific parameter file for this pset object.
+   * 
+   * @param pset
+   * @return string representation of the parameters specified by this set.
+   * @throws IOException
+   */
+  public String generateServiceParameterFile(WsParamSetI pset)
           throws IOException;
 
 }
diff --git a/src/jalview/ws/params/ParamManager.java b/src/jalview/ws/params/ParamManager.java
index 828d76e..39afc8c 100644
--- a/src/jalview/ws/params/ParamManager.java
+++ b/src/jalview/ws/params/ParamManager.java
@@ -1,4 +1,7 @@
 package jalview.ws.params;
+
+import jalview.ws.jws2.dm.JabaWsParamSet;
+
 /**
  * Interface implemented by classes for maintaining user's parameters in a Jalview session
  * @author JimP
@@ -14,7 +17,25 @@ public interface ParamManager
    * @param unmodifiable - if true, return server presets
    * @return null if no parameters found, or one or more parameter sets
    */
-  public abstract WsParamSetI[] getParameterSet(String name, String serviceUrl, boolean modifiable,boolean unmodifiable);
+  public WsParamSetI[] getParameterSet(String name, String serviceUrl, boolean modifiable,boolean unmodifiable);
+  /**
+   * save the given parameter set in the user's parameter set database.
+   * Note: this may result in a modal dialog box being raised.
+   * @param parameterSet
+   */
+  public void storeParameterSet(WsParamSetI parameterSet);
+  /**
+   * delete the specified parameter set from the database.
+   * Note: this may result in a modal dialog box being raised.
+   * @param parameterSet
+   */
+  public void deleteParameterSet(WsParamSetI parameterSet);
+  /**
+   * register a parser for the given host url
+   * @param hosturl
+   * @param jabaParamStore
+   */
+  public void registerParser(String hosturl, ParamDatastoreI paramdataStore);
   
 
 }
-- 
1.7.10.2