X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestClient.java;h=27f5271097e0645777f97d8aa24e6ce9a4d21936;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=41713f1df551f4027c2230d46617722145332933;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 41713f1..27f5271 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,6 +26,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.gui.WebserviceInfo;
 import jalview.io.packed.DataProvider.JvDataType;
 import jalview.util.MessageManager;
@@ -40,7 +41,6 @@ import java.util.Vector;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
@@ -97,7 +97,9 @@ public class RestClient extends WSClient implements WSClientI,
 
   public void setWebserviceInfo(boolean headless)
   {
-    WebServiceJobTitle = MessageManager.formatMessage("label.webservice_job_title", new String[]{service.details.Action,service.details.Name});
+    WebServiceJobTitle = MessageManager.formatMessage(
+            "label.webservice_job_title", new String[] {
+                service.details.Action, service.details.Name });
     WebServiceName = service.details.Name;
     WebServiceReference = "No reference - go to url for more info";
     if (service.details.description != null)
@@ -140,7 +142,9 @@ public class RestClient extends WSClient implements WSClientI,
           final AlignFrame alignFrame)
   {
     JMenuItem submit = new JMenuItem(service.details.Name);
-    submit.setToolTipText(MessageManager.formatMessage("label.rest_client_submit", new String[]{service.details.Action,service.details.Name}));
+    submit.setToolTipText(MessageManager.formatMessage(
+            "label.rest_client_submit", new String[] {
+                service.details.Action, service.details.Name }));
     submit.addActionListener(new ActionListener()
     {
 
@@ -255,36 +259,58 @@ public class RestClient extends WSClient implements WSClientI,
         {
           // intersect groups with selected region
           _input = new AlignmentView(av.getAlignment(),
-                  av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+                  .getHiddenColumns(), av.getSelectionGroup(),
                   av.hasHiddenColumns(), true, true);
-          viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+          viewTitle = MessageManager.formatMessage(
+                  "label.select_visible_region_of",
+                  new String[] {
+                      (av.hasHiddenColumns() ? MessageManager
+                              .getString("label.visible") : ""),
+                      af.getTitle() });
         }
         else
         {
           // use selected region to partition alignment
           _input = new AlignmentView(av.getAlignment(),
-                  av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+                  .getHiddenColumns(), av.getSelectionGroup(),
                   av.hasHiddenColumns(), false, true);
         }
-        viewTitle = MessageManager.formatMessage("label.select_unselect_visible_regions_from", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+        viewTitle = MessageManager.formatMessage(
+                "label.select_unselect_visible_regions_from",
+                new String[] {
+                    (av.hasHiddenColumns() ? MessageManager
+                            .getString("label.visible") : ""),
+                    af.getTitle() });
       }
       else
       {
         // just take selected region intersection
         _input = new AlignmentView(av.getAlignment(),
-                av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+                .getHiddenColumns(), av.getSelectionGroup(),
                 av.hasHiddenColumns(), true, true);
-        viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+        viewTitle = MessageManager.formatMessage(
+                "label.select_visible_region_of",
+                new String[] {
+                    (av.hasHiddenColumns() ? MessageManager
+                            .getString("label.visible") : ""),
+                    af.getTitle() });
       }
     }
     else
     {
       // standard alignment view without selection present
       _input = new AlignmentView(av.getAlignment(),
-              av.getColumnSelection(), null, av.hasHiddenColumns(), false,
+ av.getAlignment()
+              .getHiddenColumns(), null, av.hasHiddenColumns(), false,
               true);
-      viewTitle = "" + (av.hasHiddenColumns() ? (new StringBuffer(" ").append(MessageManager.getString("label.visible_region_of")).toString()) : "")
-              + af.getTitle();
+      viewTitle = ""
+              + (av.hasHiddenColumns() ? (new StringBuffer(" ")
+                      .append(MessageManager
+                              .getString("label.visible_region_of"))
+                      .toString()) : "") + af.getTitle();
     }
 
     RestJobThread jobsthread = new RestJobThread(this);
@@ -302,19 +328,22 @@ public class RestClient extends WSClient implements WSClientI,
     else
     {
       // TODO: try to tell the user why the job couldn't be started.
-      JOptionPane
+      JvOptionPane
               .showMessageDialog(
                       Desktop.desktop,
                       (jobsthread.hasWarnings() ? jobsthread.getWarnings()
-                              : MessageManager.getString("label.job_couldnt_be_started_check_input")),
-                      MessageManager.getString("label.unable_start_web_service_analysis"),
-                      JOptionPane.WARNING_MESSAGE);
+                              : MessageManager
+                                      .getString("label.job_couldnt_be_started_check_input")),
+                      MessageManager
+                              .getString("label.unable_start_web_service_analysis"),
+                      JvOptionPane.WARNING_MESSAGE);
     }
   }
 
   public static RestClient makeShmmrRestClient()
   {
-    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager.getString("label.multiharmony");
+    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
+            .getString("label.multiharmony");
     Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
     jalview.ws.rest.params.JobConstant toolp;
     // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
@@ -407,33 +436,6 @@ public class RestClient extends WSClient implements WSClientI,
     return lst;
   }
 
-  public static void main(String args[])
-  {
-    try
-    {
-      RestClient[] clients = getRestClients();
-      System.out.println("Got " + clients.length + " clients.");
-      int i = 0;
-      Vector<String> urls = new Vector<String>();
-      for (RestClient cl : clients)
-      {
-        System.out.println("" + (++i) + ": " + cl.service.toString());
-        urls.add(cl.service.toString());
-      }
-      setRsbsServices(urls);
-      if (clients.length != getRestClients().length)
-      {
-        System.err
-                .println("Failed. Differing numbers of clients when stringified and parsed again.");
-      }
-
-    } catch (Throwable x)
-    {
-      System.err.println("Failed. Unexpected exception.");
-      x.printStackTrace();
-    }
-  }
-
   public String getAction()
   {
     return service.details.Action;