Merge branch 'bug/JAL-2634' into develop

[jalview.git] / src / jalview / ws / rest / RestClient.java

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index f9b72e3..27f5271 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -20,23 +20,13 @@
  */
 package jalview.ws.rest;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Hashtable;
-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;
-
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 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;
@@ -44,6 +34,16 @@ import jalview.ws.WSClient;
 import jalview.ws.WSClientI;
 import jalview.ws.WSMenuEntryProviderI;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
 /**
  * @author JimP
  * 
@@ -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");