JAL-2418 source formatting

[jalview.git] / src / jalview / ws / jws2 / dm / AAConSettings.java

diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index f226ce1..708787e 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -1,27 +1,46 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws2.dm;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import compbio.metadata.Argument;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-
+import jalview.util.MessageManager;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.JabaPreset;
 import jalview.ws.jws2.ParameterUtils;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Argument;
+import compbio.metadata.Option;
+
 /**
  * preferences for running AACon service
  * 
  * @author jprocter TODO: refactor to a generic 'last job and service run'
  *         container ?
  */
-public class AAConSettings extends jalview.ws.params.AutoCalcSetting 
+public class AAConSettings extends jalview.ws.params.AutoCalcSetting
 {
   Jws2Instance service;
 
@@ -57,7 +76,8 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
         preset = pr;
         return;
       }
-      List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
+      List<ArgumentI> oldargs = new ArrayList<ArgumentI>(),
+              newargs = new ArrayList<ArgumentI>();
       oldargs.addAll(preset.getArguments());
       // need to compare parameters
       for (ArgumentI newparg : pr.getArguments())
@@ -74,41 +94,47 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
         return;
       }
       // Try even harder to migrate arguments.
-      throw new Error("Parameter migration not implemented yet");
+      throw new Error(MessageManager
+              .getString("error.parameter_migration_not_implemented_yet"));
     }
   }
 
   public List<Argument> getJobArgset()
   {
-    return jobArgset==null ? null : JabaParamStore.getJabafromJwsArgs(jobArgset);
+    return jobArgset == null ? null
+            : JabaParamStore.getJabafromJwsArgs(jobArgset);
   }
 
   public void setJobArgset(List<Argument> jobArgset)
   {
     // TODO: test if parameters valid for service
-    this.jobArgset = jobArgset==null ? null : JabaParamStore.getJwsArgsfromJaba(jobArgset);
+    this.jobArgset = jobArgset == null ? null
+            : JabaParamStore.getJwsArgsfromJaba(jobArgset);
   }
 
   public String getWsParamFile()
   {
-    List<Option> opts=null;
-    if (jobArgset!=null)
+    List<Option> opts = null;
+    if (jobArgset != null)
     {
       opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
-    } else {
-      if (preset!=null)
+    }
+    else
+    {
+      if (preset != null)
       {
         opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
       }
     }
-    if (opts==null  || opts.size()==0)
+    if (opts == null || opts.size() == 0)
     {
       return "";
     }
-    StringBuffer pset=new StringBuffer();
-    for (String ps:ParameterUtils.writeParameterSet(opts, " "))
+    StringBuffer pset = new StringBuffer();
+    for (String ps : ParameterUtils.writeParameterSet(opts, " "))
     {
-      pset.append(ps); pset.append("\n");
+      pset.append(ps);
+      pset.append("\n");
     }
     return pset.toString();
   }
@@ -118,6 +144,7 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
   {
     return service.getServiceTypeURI();
   }
+
   @Override
   public String[] getServiceURLs()
   {