JAL-2629 hmmsearch # of new sequences now only displayed when specified

[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 54e0e04..b04030d 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -47,8 +47,8 @@ import javax.swing.event.MenuListener;
  * @author JimP
  * 
  */
-public class RestClient extends WSClient implements WSClientI,
-        WSMenuEntryProviderI
+public class RestClient extends WSClient
+        implements WSClientI, WSMenuEntryProviderI
 {
   RestServiceDescription service;
 
@@ -96,9 +96,9 @@ 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)
@@ -107,8 +107,8 @@ public class RestClient extends WSClient implements WSClientI,
     }
     if (!headless)
     {
-      wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
-              + WebServiceReference, true);
+      wsInfo = new WebserviceInfo(WebServiceJobTitle,
+              WebServiceName + "\n" + WebServiceReference, true);
       wsInfo.setRenderAsHtml(true);
     }
 
@@ -141,9 +141,9 @@ 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()
     {
 
@@ -258,40 +258,42 @@ public class RestClient extends WSClient implements WSClientI,
         {
           // intersect groups with selected region
           _input = new AlignmentView(av.getAlignment(),
-                  av.getColumnSelection(), av.getSelectionGroup(),
-                  av.hasHiddenColumns(), true, true);
+                  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") : ""),
+                  "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.hasHiddenColumns(), false, true);
+                  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") : ""),
+                "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.hasHiddenColumns(), true, true);
+                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") : ""),
+                "label.select_visible_region_of", new String[]
+                { (av.hasHiddenColumns()
+                        ? MessageManager.getString("label.visible")
+                        : ""),
                     af.getTitle() });
       }
     }
@@ -299,13 +301,16 @@ public class RestClient extends WSClient implements WSClientI,
     {
       // standard alignment view without selection present
       _input = new AlignmentView(av.getAlignment(),
-              av.getColumnSelection(), null, av.hasHiddenColumns(), false,
-              true);
+              av.getAlignment().getHiddenColumns(), null,
+              av.hasHiddenColumns(), false, true);
       viewTitle = ""
-              + (av.hasHiddenColumns() ? (new StringBuffer(" ")
-                      .append(MessageManager
-                              .getString("label.visible_region_of"))
-                      .toString()) : "") + af.getTitle();
+              + (av.hasHiddenColumns()
+                      ? (new StringBuffer(" ")
+                              .append(MessageManager
+                                      .getString("label.visible_region_of"))
+                              .toString())
+                      : "")
+              + af.getTitle();
     }
 
     RestJobThread jobsthread = new RestJobThread(this);
@@ -323,15 +328,13 @@ public class RestClient extends WSClient implements WSClientI,
     else
     {
       // TODO: try to tell the user why the job couldn't be started.
-      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"),
-                      JvOptionPane.WARNING_MESSAGE);
+      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"),
+              JvOptionPane.WARNING_MESSAGE);
     }
   }
 
@@ -375,8 +378,8 @@ public class RestClient extends WSClient implements WSClientI,
         }
       } catch (Exception ex)
       {
-        System.err
-                .println("Serious - RSBS descriptions in user preferences are corrupt!");
+        System.err.println(
+                "Serious - RSBS descriptions in user preferences are corrupt!");
         ex.printStackTrace();
       }