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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5a5df3b..0ca7ddc 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -102,9 +102,9 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
@@ -4422,7 +4422,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     if (jws2servs.hasServices())
                     {
                       jws2servs.attachWSMenuEntry(webService, me);
-                      for (Jws2Instance sv : jws2servs.getServices())
+                      for (ServiceWithParameters sv : jws2servs.getServices())
                       {
                         if (sv.getName().toLowerCase().contains("jpred"))
                         {

diff --git a/src/jalview/ws/api/ServiceWithParameters.java b/src/jalview/ws/api/ServiceWithParameters.java
index cf82708..d345869 100644 (file)
--- a/src/jalview/ws/api/ServiceWithParameters.java
+++ b/src/jalview/ws/api/ServiceWithParameters.java
@@ -5,6 +5,8 @@ import jalview.ws.params.ParamManager;
 public abstract class ServiceWithParameters extends UIinfo
 {
 
+  protected jalview.ws.uimodel.AlignAnalysisUIText aaui;
+
   public ServiceWithParameters(String serviceType, String action,
           String name, String description, String hosturl)
   {
@@ -13,4 +15,68 @@ public abstract class ServiceWithParameters extends UIinfo
 
   public abstract void initParamStore(ParamManager userParameterStore);
 
+  public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
+  {
+    return aaui;
+  }
+
+  public void setAlignAnalysisUI(
+          jalview.ws.uimodel.AlignAnalysisUIText aaui)
+  {
+    this.aaui = aaui;
+  }
+
+  public boolean isInteractiveUpdate()
+  {
+    return aaui != null && aaui.isAA();
+  }
+  // config flags for SeqAnnotationServiceCalcWorker
+
+  public boolean isProteinService()
+  {
+    return aaui == null ? true : aaui.isPr();
+  }
+
+  public boolean isNucleotideService()
+  {
+    return aaui == null ? false : aaui.isNa();
+  }
+
+  public boolean isNeedsAlignedSequences()
+  {
+    return aaui == null ? false : aaui.isNeedsAlignedSeqs();
+  }
+
+  public boolean isAlignmentAnalysis()
+  {
+    return aaui == null ? false : aaui.isAA();
+  }
+
+  public boolean isFilterSymbols()
+  {
+    return aaui != null ? aaui.isFilterSymbols() : true;
+  }
+
+  public int getMinimumInputSequences()
+  {
+    return aaui != null ? aaui.getMinimumSequences() : 1;
+  }
+
+  public String getNameURI()
+  {
+    return "java:" + getName();
+  }
+
+  public String getUri()
+  {
+    // TODO verify that service parameter sets in projects are consistent with
+    // Jalview 2.10.4
+    // this is only valid for Jaba 1.0 - this formula might have to change!
+    return getHostURL()
+            + (getHostURL().lastIndexOf("/") == (getHostURL().length() - 1)
+                    ? ""
+                    : "/")
+            + getName();
+  }
+
 }

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index e4ff459..2a05228 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -26,6 +26,7 @@ import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ParamDatastoreI;
 
@@ -439,7 +440,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                 MessageManager.getString("label.switch_server")));
         hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
                 MessageManager.getString("label.choose_jabaws_server")));
-        for (final Jws2Instance sv : alternates.get(service.getName()))
+        for (final ServiceWithParameters sv : alternates.get(service.getName()))
         {
           JMenuItem itm;
           hitm.add(itm = new JMenuItem(sv.getHostURL()));
@@ -604,7 +605,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   System.out.println("Changesupport: There are now "
                           + getDiscoverer().services.size() + " services");
                   int i = 1;
-                  for (Jws2Instance instance : getDiscoverer().services)
+                  for (ServiceWithParameters instance : getDiscoverer().services)
                   {
                     System.out.println("Service " + i++ + " "
                             + instance.getClass() + "@"
@@ -1029,7 +1030,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   }
 
   public void setPreferredServiceFor(AlignFrame af, String serviceName,
-          String serviceAction, Jws2Instance selectedServer)
+          String serviceAction, ServiceWithParameters selectedServer)
   {
     // TODO: pull out and generalise for the selectedServer's attributes
     String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
@@ -1048,7 +1049,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   }
 
   public void setPreferredServiceFor(String serviceType,
-          String serviceAction, Jws2Instance selectedServer)
+          String serviceAction, ServiceWithParameters selectedServer)
   {
     setPreferredServiceFor(null, serviceType, serviceAction,
             selectedServer);

diff --git a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index e92a338..6ecc01f 100644 (file)
--- a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
+++ b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@ -38,12 +38,13 @@ import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 import jalview.workers.AlignCalcWorker;
 import jalview.ws.api.CancellableI;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
 import jalview.ws.api.JobId;
 import jalview.ws.api.SequenceAnnotationServiceI;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.api.WSAnnotationCalcManagerI;
 import jalview.ws.gui.AnnotationWsJob;
 import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
@@ -56,7 +57,7 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
         implements WSAnnotationCalcManagerI
 {
 
-  protected Jws2Instance service;
+  protected ServiceWithParameters service;
 
   protected WsParamSetI preset;
 
@@ -157,7 +158,8 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
     super(alignViewport, alignPanel);
   }
 
-  public SeqAnnotationServiceCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+  public SeqAnnotationServiceCalcWorker(ServiceWithParameters service,
+          AlignFrame alignFrame,
           WsParamSetI preset, List<ArgumentI> paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);
@@ -169,7 +171,7 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
     this.service = service;
     try
     {
-      annotService = (jalview.ws.api.SequenceAnnotationServiceI) service
+      annotService = (jalview.ws.api.SequenceAnnotationServiceI) ((JalviewServiceEndpointProviderI) service)
               .getEndpoint();
     } catch (ClassCastException cce)
     {

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index bf5dc23..7163974 100644 (file)
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -62,7 +62,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
   // dan think. Do I need to change this method to run RNAalifold through the
   // GUI
 
-  public void initSequenceAnnotationWSClient(final Jws2Instance sh,
+  public void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
     // dan changed! dan test. comment out if conditional

diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index 5cc8f66..997913e 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -21,6 +21,7 @@
 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;
@@ -42,16 +43,16 @@ import compbio.metadata.Option;
  */
 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;
   }

diff --git a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
index 8acf64f..e7f3022 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
+++ b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
@@ -8,9 +8,9 @@ import jalview.util.MessageManager;
 import jalview.ws.api.JobId;
 import jalview.ws.api.SequenceAnnotationServiceI;
 import jalview.ws.gui.AnnotationWsJob;
-import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
@@ -50,7 +50,8 @@ public abstract class JabawsAnnotationInstance
    */
   public String getCalcId()
   {
-    return our.aaui == null ? null : our.aaui.getCalcId();
+    return our.getAlignAnalysisUI() == null ? null
+            : our.getAlignAnalysisUI().getCalcId();
   }
 
   @Override

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 194b315..9f2d4ae 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -186,18 +186,6 @@ public class Jws2Instance extends ServiceWithParameters
     return paramStore;
   }
 
-  public String getUri()
-  {
-    // TODO verify that service parameter sets in projects are consistent with
-    // Jalview 2.10.4
-    // this is only valid for Jaba 1.0 - this formula might have to change!
-    return getHostURL()
-            + (getHostURL().lastIndexOf("/") == (getHostURL().length() - 1)
-                    ? ""
-                    : "/")
-            + getName();
-  }
-
   private boolean hasParams = false, lookedForParams = false;
 
   @Override
@@ -230,18 +218,6 @@ public class Jws2Instance extends ServiceWithParameters
     }
   }
 
-  public String getNameURI()
-  {
-    return "java:" + getName();
-  }
-
-  jalview.ws.uimodel.AlignAnalysisUIText aaui;
-
-  public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
-  {
-    return aaui;
-  }
-
   /**
    * initialise a parameter store for this service
    * 
@@ -300,40 +276,4 @@ public class Jws2Instance extends ServiceWithParameters
       return null;
     }
   }
-
-  public boolean isInteractiveUpdate()
-  {
-    return aaui != null && aaui.isAA();
-  }
-  // config flags for SeqAnnotationServiceCalcWorker
-
-  public boolean isProteinService()
-  {
-    return aaui == null ? true : aaui.isPr();
-  }
-
-  public boolean isNucleotideService()
-  {
-    return aaui == null ? false : aaui.isNa();
-  }
-
-  public boolean isNeedsAlignedSequences()
-  {
-    return aaui == null ? false : aaui.isNeedsAlignedSeqs();
-  }
-
-  public boolean isAlignmentAnalysis()
-  {
-    return aaui == null ? false : aaui.isAA();
-  }
-
-  public boolean isFilterSymbols()
-  {
-    return aaui != null ? aaui.isFilterSymbols() : true;
-  }
-
-  public int getMinimumInputSequences()
-  {
-    return aaui != null ? aaui.getMinimumSequences() : 1;
-  }
 }

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
index 00127b1..c328670 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
@@ -85,7 +85,7 @@ public class Jws2InstanceFactory
     init();
     Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
             category_rewrite(name), description, service);
-    svc.aaui = aaConGUI.get(serviceType.toString());
+    svc.setAlignAnalysisUI(aaConGUI.get(serviceType.toString()));
     return svc;
   }