JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

[jalview.git] / src / jalview / ws / jws2 / MsaWSClient.java

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 23c6949..e33b4bd 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -20,16 +20,6 @@
  */
 package jalview.ws.jws2;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
@@ -42,6 +32,15 @@ import javax.swing.ToolTipManager;
 
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -214,9 +213,9 @@ public class MsaWSClient extends Jws2Client
 
   @Override
   public void attachWSMenuEntry(JMenu rmsawsmenu,
-          final Jws2Instance service, final AlignFrame alignFrame)
+          final Jws2Instance service, final AlignFrame af)
   {
-    if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+    if (registerAAConWSInstance(rmsawsmenu, service, af))
     {
       // Alignment dependent analysis calculation WS gui
       return;
@@ -264,14 +263,14 @@ public class MsaWSClient extends Jws2Client
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+          AlignmentView msa = af.gatherSequencesForAlignment();
 
           if (msa != null)
           {
-            new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+            new MsaWSClient(service, af.getTitle(), msa, withGaps,
                     true,
-                    alignFrame.getViewport().getAlignment().getDataset(),
-                    alignFrame);
+                    af.getViewport().getAlignment().getDataset(),
+                    af);
           }
 
         }
@@ -291,13 +290,10 @@ public class MsaWSClient extends Jws2Client
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+            AlignmentView msa = af.gatherSequencesForAlignment();
             if (msa != null)
             {
-              new MsaWSClient(service, null, null, true,
-                      alignFrame.getTitle(), msa, withGaps, true,
-                      alignFrame.getViewport().getAlignment().getDataset(),
-                      alignFrame);
+              startJob(service, af, withGaps, msa);
             }
 
           }
@@ -312,9 +308,9 @@ public class MsaWSClient extends Jws2Client
 
           final int showToolTipFor = ToolTipManager.sharedInstance()
                   .getDismissDelay();
-          for (final WsParamSetI preset : presets)
+          for (final WsParamSetI preSet : presets)
           {
-            final JMenuItem methodR = new JMenuItem(preset.getName());
+            final JMenuItem methodR = new JMenuItem(preSet.getName());
             final int QUICK_TOOLTIP = 1500;
             // JAL-1582 shorten tooltip display time in these menu items as
             // they can obscure other options
@@ -336,27 +332,27 @@ public class MsaWSClient extends Jws2Client
 
             });
             String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
-                    + (preset.isModifiable()
+                    + (preSet.isModifiable()
                             ? MessageManager.getString("label.user_preset")
                             : MessageManager
                                     .getString("label.service_preset"))
-                    + "</strong><br/>" + preset.getDescription());
+                    + "</strong><br/>" + preSet.getDescription());
             methodR.setToolTipText(tooltip);
             methodR.addActionListener(new ActionListener()
             {
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                AlignmentView msa = alignFrame
+                AlignmentView msa = af
                         .gatherSequencesForAlignment();
 
                 if (msa != null)
                 {
-                  MsaWSClient msac = new MsaWSClient(service, preset,
-                          alignFrame.getTitle(), msa, false, true,
-                          alignFrame.getViewport().getAlignment()
+                  MsaWSClient msac = new MsaWSClient(service, preSet,
+                          af.getTitle(), msa, false, true,
+                          af.getViewport().getAlignment()
                                   .getDataset(),
-                          alignFrame);
+                          af);
                 }
 
               }
@@ -378,4 +374,20 @@ public class MsaWSClient extends Jws2Client
       }
     } while (!finished);
   }
+
+  protected void startJob(final Jws2Instance service, final AlignFrame af,
+          final boolean withGaps, AlignmentView msa)
+  {
+    try {
+    new MsaWSClient(service, null, null, true,
+            af.getTitle(), msa, withGaps, true,
+            af.getViewport().getAlignment().getDataset(),
+            af);
+    } catch (Exception e) {
+      JvOptionPane.showMessageDialog(alignFrame, e.getMessage(),
+              MessageManager.getString("label.state_job_error"),
+              JvOptionPane.WARNING_MESSAGE);
+
+    }
+  }
 }