JAL-1358 Cleaned up RNAalifoldClient.java. RNA helices colouring bug and parameters...

[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 66ef9a6..896292a 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -19,7 +19,6 @@ package jalview.ws.jws2;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.*;
@@ -28,10 +27,6 @@ import jalview.datamodel.*;
 import jalview.gui.*;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
@@ -58,9 +53,9 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
-          String altitle, jalview.datamodel.AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+          jalview.datamodel.AlignmentView msa, boolean submitGaps,
+          boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -191,7 +186,6 @@ public class MsaWSClient extends Jws2Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
-  
   public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
@@ -261,7 +255,7 @@ public class MsaWSClient extends Jws2Client
         List<WsParamSetI> presets = service.getParamStore().getPresets();
         if (presets != null && presets.size() > 0)
         {
-          JMenu presetlist = new JMenu("Run "+calcName + "with preset");
+          JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 
           for (final WsParamSetI preset : presets)
           {