JAL-3070 rename AbstractJabaCalcWorker to SeqAnnotationServiceCalcWorker

diff --git a/src/jalview/ws/api/SequenceAnnotationServiceI.java b/src/jalview/ws/api/SequenceAnnotationServiceI.java
index d0965e5..a224bac 100644 (file)
--- a/src/jalview/ws/api/SequenceAnnotationServiceI.java
+++ b/src/jalview/ws/api/SequenceAnnotationServiceI.java
@@ -3,7 +3,7 @@ package jalview.ws.api;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.ws.gui.AnnotationWsJob;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
@@ -34,7 +34,7 @@ public interface SequenceAnnotationServiceI extends JalviewWebServiceI
    * @return
    */
   List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
-          AbstractJabaCalcWorker abstractJabaCalcWorker) throws Throwable;
+          SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable;
 
 
 }

diff --git a/src/jalview/ws/jws2/Jws2ClientFactory.java b/src/jalview/ws/jws2/Jws2ClientFactory.java
index 2a3b4a5..99edbec 100644 (file)
--- a/src/jalview/ws/jws2/Jws2ClientFactory.java
+++ b/src/jalview/ws/jws2/Jws2ClientFactory.java
@@ -55,7 +55,7 @@ public class Jws2ClientFactory
               .getRegisteredWorkersOfClass(aaui.getClient());
       if (aaconClient != null && aaconClient.size() > 0)
       {
-        AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
+        SeqAnnotationServiceCalcWorker worker = (SeqAnnotationServiceCalcWorker) aaconClient
                 .get(0);
         if (!worker.service.getHostURL().equals(service.getHostURL()))
         {
@@ -138,14 +138,14 @@ public class Jws2ClientFactory
           }
           List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
                   .getCalcManager().getRegisteredWorkersOfClass(
-                          AbstractJabaCalcWorker.class);
+                          SeqAnnotationServiceCalcWorker.class);
 
           boolean serviceEnabled = false;
           if (aaconClient != null)
           {
             for (AlignCalcWorkerI _worker : aaconClient)
             {
-              AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) _worker;
+              SeqAnnotationServiceCalcWorker worker = (SeqAnnotationServiceCalcWorker) _worker;
               // this could be cleaner ?
               if (worker.hasService()
                       && aaui.getClient()

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
similarity index 98%
rename from src/jalview/ws/jws2/AbstractJabaCalcWorker.java
rename to src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index fae8089..6793f1e 100644 (file)
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@ -52,7 +52,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-public class AbstractJabaCalcWorker extends AlignCalcWorker
+public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
         implements WSAnnotationCalcManagerI
 {
 
@@ -151,13 +151,13 @@ public class AbstractJabaCalcWorker extends AlignCalcWorker
     return gapMap;
   }
 
-  public AbstractJabaCalcWorker(AlignViewportI alignViewport,
+  public SeqAnnotationServiceCalcWorker(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     super(alignViewport, alignPanel);
   }
 
-  public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+  public SeqAnnotationServiceCalcWorker(Jws2Instance service, AlignFrame alignFrame,
           WsParamSetI preset, List<ArgumentI> paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index 58478d6..bf5dc23 100644 (file)
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -84,14 +84,14 @@ public class SequenceAnnotationWSClient extends Jws2Client
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
               .getCalcManager()
-              .getRegisteredWorkersOfClass(AbstractJabaCalcWorker.class);
+              .getRegisteredWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
 
-      AbstractJabaCalcWorker worker = null;
+      SeqAnnotationServiceCalcWorker worker = null;
       if (clnts != null)
       {
         for (AlignCalcWorkerI _worker : clnts)
         {
-          worker = (AbstractJabaCalcWorker) _worker;
+          worker = (SeqAnnotationServiceCalcWorker) _worker;
           if (worker.hasService()
                   && worker.getService().getClass().equals(clientClass))
           {
@@ -108,7 +108,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
         try
         {
-          worker = new AbstractJabaCalcWorker(sh, alignFrame, this.preset,
+          worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
                   paramset);
         } catch (Exception x)
         {
@@ -149,7 +149,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
       }
 
       alignFrame.getViewport().getCalcManager().startWorker(
-              new AbstractJabaCalcWorker(sh, alignFrame, preset, paramset));
+              new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
     }
   }
 

diff --git a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
index 3c269c4..8acf64f 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
+++ b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
@@ -8,7 +8,7 @@ import jalview.util.MessageManager;
 import jalview.ws.api.JobId;
 import jalview.ws.api.SequenceAnnotationServiceI;
 import jalview.ws.gui.AnnotationWsJob;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.JabaPreset;
 import jalview.ws.params.ArgumentI;
@@ -108,7 +108,7 @@ public abstract class JabawsAnnotationInstance
   @Override
   public List<AlignmentAnnotation> getAlignmentAnnotation(
           AnnotationWsJob running,
-          AbstractJabaCalcWorker abstractJabaCalcWorker) throws Throwable
+          SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable
   {
     if (scoremanager == null)
     {

diff --git a/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java b/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
index aff7ad6..edcc05c 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
@@ -21,14 +21,14 @@
 package jalview.ws.jws2.jabaws2;
 
 import jalview.gui.AlignFrame;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.List;
 
 public abstract class JabawsMsaInterfaceAlignCalcWorker
-        extends AbstractJabaCalcWorker
+        extends SeqAnnotationServiceCalcWorker
 {
 
   public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index 3e3a06d..de72020 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -32,7 +32,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 
@@ -65,7 +65,7 @@ public class DisorderAnnotExportImport
 
   public static List<Jws2Instance> iupreds;
 
-  jalview.ws.jws2.AbstractJabaCalcWorker disorderClient;
+  jalview.ws.jws2.SeqAnnotationServiceCalcWorker disorderClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -114,7 +114,7 @@ public class DisorderAnnotExportImport
   @Test(groups = { "External", "Network" })
   public void testDisorderAnnotExport()
   {
-    disorderClient = new AbstractJabaCalcWorker(iupreds.get(0), af, null,
+    disorderClient = new SeqAnnotationServiceCalcWorker(iupreds.get(0), af, null,
             null);
     af.getViewport().getCalcManager().startWorker(disorderClient);
     do

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 4af8086..25d015a 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -33,7 +33,7 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.project.Jalview2XML;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
@@ -79,7 +79,7 @@ public class RNAStructExportImport
 
   public static Jws2Instance rnaalifoldws;
 
-  AbstractJabaCalcWorker alifoldClient;
+  SeqAnnotationServiceCalcWorker alifoldClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -155,7 +155,7 @@ public class RNAStructExportImport
   public void testRNAAliFoldValidStructure()
   {
 
-    alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
             null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
@@ -189,7 +189,7 @@ public class RNAStructExportImport
   public void testRNAStructExport()
   {
 
-    alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
             null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
@@ -283,7 +283,7 @@ public class RNAStructExportImport
         opts.add(rg);
       }
     }
-    alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
             JabaParamStore.getJwsArgsfromJaba(opts));
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);