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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index aaf8519..d5f6a5d 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2446,7 +2446,7 @@ public class Jalview2XML
           argList = parmSet.getArguments();
           parmSet = null;
         }
-        AAConSettings settings = new AAConSettings(
+        AutoCalcSetting settings = new AAConSettings(
                 calcIdParam.isAutoUpdate(), service, parmSet, argList);
         av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
                 calcIdParam.isNeedsUpdate());

diff --git a/src/jalview/ws/jws2/Jws2ClientFactory.java b/src/jalview/ws/jws2/Jws2ClientFactory.java
index 6a177dd..2a38b85 100644 (file)
--- a/src/jalview/ws/jws2/Jws2ClientFactory.java
+++ b/src/jalview/ws/jws2/Jws2ClientFactory.java
@@ -5,8 +5,9 @@ import jalview.bin.Cache;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
 import java.awt.event.ActionEvent;
@@ -22,7 +23,7 @@ import javax.swing.event.MenuListener;
 public class Jws2ClientFactory
 {
   static boolean registerAAConWSInstance(final JMenu wsmenu,
-      final Jws2Instance service, final AlignFrame alignFrame)
+          final ServiceWithParameters service, final AlignFrame alignFrame)
   {
     final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null
                                                                         // ; //
@@ -183,7 +184,7 @@ public class Jws2ClientFactory
      * AACon server to use What parameters to use
      */
     // could actually do a class search for this too
-    AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+    AutoCalcSetting fave = alignFrame.getViewport()
             .getCalcIdSettingsFor(aaui.getCalcId());
     if (fave == null)
     {
@@ -201,13 +202,13 @@ public class Jws2ClientFactory
 
   private static void buildCurrentAAConWorkerFor(
           final AlignAnalysisUIText aaui, AlignFrame alignFrame,
-          Jws2Instance service)
+          ServiceWithParameters service)
   {
     /*
      * preferred settings Whether AACon is automatically recalculated Which
      * AACon server to use What parameters to use
      */
-    AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+    AutoCalcSetting fave = alignFrame.getViewport()
             .getCalcIdSettingsFor(aaui.getCalcId());
     if (fave == null)
     {
@@ -226,14 +227,14 @@ public class Jws2ClientFactory
     new SequenceAnnotationWSClient(fave, alignFrame, false);
   }
 
-  private static AAConSettings createDefaultAAConSettings(
+  private static AutoCalcSetting createDefaultAAConSettings(
           AlignAnalysisUIText aaui)
   {
     return createDefaultAAConSettings(aaui, null);
   }
 
-  private static AAConSettings createDefaultAAConSettings(
-          AlignAnalysisUIText aaui, Jws2Instance service)
+  private static AutoCalcSetting createDefaultAAConSettings(
+          AlignAnalysisUIText aaui, ServiceWithParameters service)
   {
     if (service != null)
     {

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index a2038f0..501e93d 100644 (file)
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -26,8 +26,7 @@ import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.api.ServiceWithParameters;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
@@ -153,7 +152,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     }
   }
 
-  public SequenceAnnotationWSClient(AAConSettings fave,
+  public SequenceAnnotationWSClient(AutoCalcSetting fave,
           AlignFrame alignFrame, boolean b)
   {
     super(alignFrame, fave.getPreset(), fave.getArgumentSet());
@@ -172,8 +171,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
           final ServiceWithParameters service,
           final AlignFrame alignFrame)
   {
-    if (service instanceof Jws2Instance
-        && Jws2ClientFactory.registerAAConWSInstance(wsmenu, (Jws2Instance) service, alignFrame))
+    if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
+            service, alignFrame))
     {
       // Alignment dependent analysis calculation WS gui
       return;

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() };
-  }
 }

diff --git a/src/jalview/ws/params/AutoCalcSetting.java b/src/jalview/ws/params/AutoCalcSetting.java
index 29aeef9..55eeb50 100644 (file)
--- a/src/jalview/ws/params/AutoCalcSetting.java
+++ b/src/jalview/ws/params/AutoCalcSetting.java
@@ -20,6 +20,10 @@
  */
 package jalview.ws.params;
 
+import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
+
+import java.util.ArrayList;
 import java.util.List;
 
 public abstract class AutoCalcSetting
@@ -31,9 +35,13 @@ public abstract class AutoCalcSetting
 
   protected List<ArgumentI> jobArgset;
 
-  public AutoCalcSetting(WsParamSetI preset2, List<ArgumentI> jobArgset2,
+  protected ServiceWithParameters service;
+
+  public AutoCalcSetting(ServiceWithParameters service2,
+          WsParamSetI preset2, List<ArgumentI> jobArgset2,
           boolean autoUpdate2)
   {
+    service = service2;
     autoUpdate = autoUpdate2;
     preset = preset2;
     jobArgset = jobArgset2;
@@ -66,20 +74,29 @@ public abstract class AutoCalcSetting
   }
 
   /**
+   * TODO: refactor to ServiceWithParameters ?
    * 
    * @return characteristic URI for this service. The URI should reflect the
    *         type and version of this service, enabling the service client code
    *         to recover the correct client for this calculation.
    */
-  public abstract String getServiceURI();
+  public String getServiceURI()
+  {
+    return service.getNameURI();
+  }
 
   /**
+   * TODO: refactor to ServiceWithParameters ?
+   * 
    * return any concrete service endpoints associated with this calculation.
    * built in services should return a zero length array
    * 
    * @return
    */
-  public abstract String[] getServiceURLs();
+  public String[] getServiceURLs()
+  {
+    return new String[] { service.getUri() };
+  }
 
   /**
    * 
@@ -87,4 +104,61 @@ public abstract class AutoCalcSetting
    */
   public abstract String getWsParamFile();
 
+  public ServiceWithParameters getService()
+  {
+    return service;
+  }
+
+  public void setService(ServiceWithParameters service)
+  {
+    this.service = service;
+    if (preset != null)
+    {
+      // check if we need to migrate preset to a new service URL
+      for (String url : preset.getApplicableUrls())
+      {
+        if (url.equals(service.getUri()))
+        {
+          // preset already verified
+          return;
+        }
+      }
+      WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
+  
+      // TODO: decide of this distinction between preset and args are needed.
+      //
+      // if (pr instanceof JabaPreset && preset instanceof JabaPreset)
+      // {
+      // // easy - Presets are identical (we assume)
+      // preset = pr;
+      // return;
+      // }
+  
+      // this verifies that all arguments in the existing preset are the same as
+      // the parameters for the preset provided by the service parameter store.
+      // ie the LastUsed settings or a predefined preset.
+  
+      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"));
+    }
+  }
+
 }