JAL-3066 JAL-3070 pull up non-jabaws specific service descriptor components for annot...

[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 9efe4c3..997913e 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -1,37 +1,40 @@
 /*
- * 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
+ * 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.
+ * 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/>.
+ * 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.api.ServiceWithParameters;
 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
  * 
@@ -40,16 +43,16 @@ import jalview.ws.params.WsParamSetI;
  */
 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
 {
-  Jws2Instance service;
+  ServiceWithParameters service;
 
-  public AAConSettings(boolean autoUpdate, Jws2Instance service,
+  public AAConSettings(boolean autoUpdate, ServiceWithParameters service2,
           WsParamSetI preset, List<ArgumentI> jobArgset)
   {
     super(preset, jobArgset, autoUpdate);
-    this.service = service;
+    this.service = service2;
   }
 
-  public Jws2Instance getService()
+  public ServiceWithParameters getService()
   {
     return service;
   }
@@ -74,7 +77,8 @@ 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<>(),
+              newargs = new ArrayList<>();
       oldargs.addAll(preset.getArguments());
       // need to compare parameters
       for (ArgumentI newparg : pr.getArguments())
@@ -91,23 +95,25 @@ 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);
   }
 
+  @Override
   public String getWsParamFile()
   {
     List<Option> opts = null;
@@ -138,13 +144,12 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
   @Override
   public String getServiceURI()
   {
-    return service.getServiceTypeURI();
+    return service.getNameURI();
   }
 
   @Override
   public String[] getServiceURLs()
   {
-    return new String[]
-    { service.getUri() };
+    return new String[] { service.getUri() };
   }
 }