JAL-1847 superpose checkbox in structure chooser

[jalview.git] / src / jalview / gui / WsParamSetManager.java

diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index b6a7672..d91775c 100644 (file)
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 import jalview.util.MessageManager;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
@@ -38,8 +39,6 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.StringTokenizer;
 
-import javax.swing.JOptionPane;
-
 /**
  * store and retrieve web service parameter sets.
  * 
@@ -85,8 +84,8 @@ public class WsParamSetManager implements ParamManager
           {
             add = true;
           }
-          add &= (modifiable == p.isModifiable() || unmodifiable == !p
-                  .isModifiable());
+          add &= (modifiable == p.isModifiable()
+                  || unmodifiable == !p.isModifiable());
           add &= name == null || p.getName().equals(name);
 
           if (add)
@@ -98,11 +97,9 @@ public class WsParamSetManager implements ParamManager
         }
       } catch (IOException e)
       {
-        Cache.log
-                .info("Failed to parse parameter file "
-                        + pfile
-                        + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
-                        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]);
@@ -178,18 +175,14 @@ public class WsParamSetManager implements ParamManager
     }
     if (parser == null)
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_cannot_find_marshaller_for_param_set"));
     }
     if (filename == null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "wsparams" },
-              new String[] { "Web Service Parameter File" },
+      JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
               "Web Service Parameter File");
-      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
               .getString("label.choose_filename_for_param_file"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -197,8 +190,8 @@ public class WsParamSetManager implements ParamManager
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         outfile = chooser.getSelectedFile();
-        jalview.bin.Cache
-                .setProperty("LAST_DIRECTORY", outfile.getParent());
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                outfile.getParent());
         filename = outfile.getAbsolutePath();
         if (!filename.endsWith(".wsparams"))
         {
@@ -229,8 +222,8 @@ public class WsParamSetManager implements ParamManager
       paramxml.setVersion("1.0");
       try
       {
-        paramxml.setParameters(parser
-                .generateServiceParameterFile(parameterSet));
+        paramxml.setParameters(
+                parser.generateServiceParameterFile(parameterSet));
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(outfile), "UTF-8"));
         paramxml.marshal(out);
@@ -294,18 +287,18 @@ public class WsParamSetManager implements ParamManager
       File pfile = new File(filename);
       if (pfile.exists() && pfile.canWrite())
       {
-        if (JOptionPane.showConfirmDialog(Desktop.instance,
+        if (JvOptionPane.showConfirmDialog(Desktop.instance,
                 "Delete the preset's file, too ?", "Delete User Preset ?",
-                JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION)
+                JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
         {
           pfile.delete();
         }
       }
     } catch (Exception e)
     {
-      Cache.log
-              .error("Exception when trying to delete webservice user preset: ",
-                      e);
+      Cache.log.error(
+              "Exception when trying to delete webservice user preset: ",
+              e);
     }
   }