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 03918a8..27f5271 100644 (file)
--- 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 2.9.0b1)
- * Copyright (C) 2015 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;
 
@@ -259,7 +259,8 @@ 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",
@@ -272,7 +273,8 @@ public class RestClient extends WSClient implements WSClientI,
         {
           // 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(
@@ -286,7 +288,8 @@ public class RestClient extends WSClient implements WSClientI,
       {
         // 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",
@@ -300,7 +303,8 @@ public class RestClient extends WSClient implements WSClientI,
     {
       // 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(" ")
@@ -324,7 +328,7 @@ 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()
@@ -332,7 +336,7 @@ public class RestClient extends WSClient implements WSClientI,
                                       .getString("label.job_couldnt_be_started_check_input")),
                       MessageManager
                               .getString("label.unable_start_web_service_analysis"),
-                      JOptionPane.WARNING_MESSAGE);
+                      JvOptionPane.WARNING_MESSAGE);
     }
   }