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 997913e..fa56874 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -20,19 +20,14 @@
  */
 package jalview.ws.jws2.dm;
 
-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.WsParamSetI;
 
-import java.util.ArrayList;
 import java.util.List;
 
-import compbio.metadata.Argument;
 import compbio.metadata.Option;
 
 /**
@@ -43,74 +38,10 @@ import compbio.metadata.Option;
  */
 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
 {
-  ServiceWithParameters service;
-
   public AAConSettings(boolean autoUpdate, ServiceWithParameters service2,
           WsParamSetI preset, List<ArgumentI> jobArgset)
   {
-    super(preset, jobArgset, autoUpdate);
-    this.service = service2;
-  }
-
-  public ServiceWithParameters 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<>(),
-              newargs = new ArrayList<>();
-      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(MessageManager
-              .getString("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
@@ -140,16 +71,4 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
     }
     return pset.toString();
   }
-
-  @Override
-  public String getServiceURI()
-  {
-    return service.getNameURI();
-  }
-
-  @Override
-  public String[] getServiceURLs()
-  {
-    return new String[] { service.getUri() };
-  }
 }