JAL-3070 pull up generic methods for an automatic alignment analysis web service...

[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 d3ba1a7..fa56874 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -1,35 +1,35 @@
 /*
- * 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 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.WsParamSetI;
 
+import java.util.List;
+
+import compbio.metadata.Option;
+
 /**
  * preferences for running AACon service
  * 
@@ -38,74 +38,13 @@ import jalview.ws.params.WsParamSetI;
  */
 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
 {
-  Jws2Instance 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;
-  }
-
-  public Jws2Instance getService()
-  {
-    return service;
-  }
-
-  public void setService(Jws2Instance service)
-  {
-    this.service = service;
-    if (preset != null)
-    {
-      // migrate preset to new service
-      for (String url : preset.getApplicableUrls())
-      {
-        if (url.equals(service.getUri()))
-        {
-          return;
-        }
-      }
-      WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
-      if (pr instanceof JabaPreset && preset instanceof JabaPreset)
-      {
-        // easy - Presets are identical (we assume)
-        preset = pr;
-        return;
-      }
-      List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
-      oldargs.addAll(preset.getArguments());
-      // need to compare parameters
-      for (ArgumentI newparg : pr.getArguments())
-      {
-        if (!oldargs.remove(newparg))
-        {
-          newargs.add(newparg);
-        }
-      }
-      if (oldargs.size() == 0 && newargs.size() == 0)
-      {
-        // exact match.
-        preset = pr;
-        return;
-      }
-      // Try even harder to migrate arguments.
-      throw new Error("Parameter migration not implemented yet");
-    }
-  }
-
-  public List<Argument> getJobArgset()
-  {
-    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);
+    super(service2, preset, jobArgset, autoUpdate);
   }
 
+  @Override
   public String getWsParamFile()
   {
     List<Option> opts = null;
@@ -132,17 +71,4 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
     }
     return pset.toString();
   }
-
-  @Override
-  public String getServiceURI()
-  {
-    return service.getServiceTypeURI();
-  }
-
-  @Override
-  public String[] getServiceURLs()
-  {
-    return new String[]
-    { service.getUri() };
-  }
 }