JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 47130a3..8fa118d 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -20,7 +20,7 @@
  */
 package jalview.ws.jws2;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -58,7 +58,7 @@ public class MsaWSClient extends Jws2Client
 
   public MsaWSClient(Jws2Instance sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -68,7 +68,7 @@ public class MsaWSClient extends Jws2Client
 
   public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -95,7 +95,7 @@ public class MsaWSClient extends Jws2Client
   public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
           List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     super(_alignFrame, preset, arguments);
@@ -138,7 +138,7 @@ public class MsaWSClient extends Jws2Client
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
   {
     // if (!locateWebService())
     // {
@@ -216,6 +216,7 @@ public class MsaWSClient extends Jws2Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
@@ -263,6 +264,7 @@ public class MsaWSClient extends Jws2Client
 
       method.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
@@ -288,6 +290,7 @@ public class MsaWSClient extends Jws2Client
 
         method.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             AlignmentView msa = alignFrame.gatherSequencesForAlignment();
@@ -335,17 +338,20 @@ public class MsaWSClient extends Jws2Client
               }
 
             });
-            methodR.setToolTipText(JvSwingUtils.wrapTooltip(
-                    true,
-                    "<p><strong>"
-                            + (preset.isModifiable() ? MessageManager
-                                    .getString("label.user_preset")
-                                    : MessageManager
-                                            .getString("label.service_preset"))
-                            + "</strong><br/>" + preset.getDescription()
-                            + "</p>"));
+            String tooltip = JvSwingUtils
+                    .wrapTooltip(
+                            true,
+                            "<strong>"
+                                    + (preset.isModifiable() ? MessageManager
+                                            .getString("label.user_preset")
+                                            : MessageManager
+                                                    .getString("label.service_preset"))
+                                    + "</strong><br/>"
+                                    + preset.getDescription());
+            methodR.setToolTipText(tooltip);
             methodR.addActionListener(new ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 AlignmentView msa = alignFrame