JAL-2738 copy to spikes/mungo

[jalview.git] / src / jalview / ws / jws1 / MsaWSClient.java

diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index 5ea553e..4a09625 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -78,10 +78,12 @@ public class MsaWSClient extends WS1Client
     alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
-      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
-              .formatMessage("label.service_called_is_not_msa_service",
-                      new String[] { sh.getName() }), MessageManager
-              .getString("label.internal_jalview_error"),
+      JvOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.formatMessage(
+                      "label.service_called_is_not_msa_service",
+                      new String[]
+                      { sh.getName() }),
+              MessageManager.getString("label.internal_jalview_error"),
               JvOptionPane.WARNING_MESSAGE);
 
       return;
@@ -90,9 +92,9 @@ public class MsaWSClient extends WS1Client
     if ((wsInfo = setWebService(sh)) == null)
     {
       JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
-              .formatMessage("label.msa_service_is_unknown",
-                      new String[] { sh.getName() }), MessageManager
-              .getString("label.internal_jalview_error"),
+              .formatMessage("label.msa_service_is_unknown", new String[]
+              { sh.getName() }),
+              MessageManager.getString("label.internal_jalview_error"),
               JvOptionPane.WARNING_MESSAGE);
 
       return;
@@ -120,9 +122,8 @@ public class MsaWSClient extends WS1Client
     String jobtitle = WebServiceName.toLowerCase();
     if (jobtitle.endsWith("alignment"))
     {
-      if (submitGaps
-              && (!jobtitle.endsWith("realignment") || jobtitle
-                      .indexOf("profile") == -1))
+      if (submitGaps && (!jobtitle.endsWith("realignment")
+              || jobtitle.indexOf("profile") == -1))
       {
         int pos = jobtitle.indexOf("alignment");
         jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
@@ -213,9 +214,10 @@ public class MsaWSClient extends WS1Client
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-        new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
-                .getTitle(), msa, false, true, alignFrame.getViewport()
-                .getAlignment().getDataset(), alignFrame);
+        new jalview.ws.jws1.MsaWSClient(serviceHandle,
+                alignFrame.getTitle(), msa, false, true,
+                alignFrame.getViewport().getAlignment().getDataset(),
+                alignFrame);
 
       }
 
@@ -224,8 +226,8 @@ public class MsaWSClient extends WS1Client
     if (canSubmitGaps())
     {
       // We know that ClustalWS can accept partial alignments for refinement.
-      final JMenuItem methodR = new JMenuItem(serviceHandle.getName()
-              + " Realign");
+      final JMenuItem methodR = new JMenuItem(
+              serviceHandle.getName() + " Realign");
       methodR.setToolTipText(WsURL);
       methodR.addActionListener(new ActionListener()
       {
@@ -233,9 +235,10 @@ public class MsaWSClient extends WS1Client
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
-                  .getTitle(), msa, true, true, alignFrame.getViewport()
-                  .getAlignment().getDataset(), alignFrame);
+          new jalview.ws.jws1.MsaWSClient(serviceHandle,
+                  alignFrame.getTitle(), msa, true, true,
+                  alignFrame.getViewport().getAlignment().getDataset(),
+                  alignFrame);
 
         }