JAL-3878 Annotation comments and questions

[jalview.git] / src / jalview / ws2 / operations / AnnotationOperation.java

diff --git a/src/jalview/ws2/operations/AnnotationOperation.java b/src/jalview/ws2/operations/AnnotationOperation.java
index eeb51ef..31ac0a8 100644 (file)
--- a/src/jalview/ws2/operations/AnnotationOperation.java
+++ b/src/jalview/ws2/operations/AnnotationOperation.java
@@ -1,37 +1,28 @@
 package jalview.ws2.operations;
 
-import java.io.IOException;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
-import java.util.concurrent.CancellationException;
 import java.util.concurrent.CompletionStage;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 
-import jalview.bin.Cache;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
 import jalview.gui.WsJobParameters;
-import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
-import jalview.util.MathUtils;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws2.MenuEntryProviderI;
 import jalview.ws2.ResultSupplier;
-import jalview.ws2.WSJob;
-import jalview.ws2.WSJobStatus;
-import jalview.ws2.WebServiceExecutor;
+import jalview.ws2.PollingTaskExecutor;
 import jalview.ws2.WebServiceI;
-import jalview.ws2.WebServiceWorkerI;
-import jalview.ws2.utils.WSJobList;
-
-import static java.lang.String.format;
 
 /**
- * 
+ *
  * @author mmwarowny
  *
  */
@@ -41,12 +32,20 @@ public class AnnotationOperation implements Operation
 
   final String typeName;
 
-  final ResultSupplier<AnnotationFile> annotationSupplier;
+  final ResultSupplier<List<AlignmentAnnotation>> annotationSupplier;
 
   final ResultSupplier<FeaturesFile> featuresSupplier;
 
+  boolean alignmentAnalysis = false;
+
+  boolean interactive = false;
+
+  /*
+   * Is it fine to get rid of AlignAnalysisUIText?
+   */
+
   public AnnotationOperation(WebServiceI service,
-      ResultSupplier<AnnotationFile> annotSupplier,
+      ResultSupplier<List<AlignmentAnnotation>> annotSupplier,
       ResultSupplier<FeaturesFile> featSupplier, String operationName)
   {
     this.service = service;
@@ -106,6 +105,34 @@ public class AnnotationOperation implements Operation
   @Override
   public boolean isInteractive()
   {
+    return interactive;
+  }
+
+  public void setInteractive(boolean value)
+  {
+    this.interactive = value;
+  }
+
+  @Override
+  public boolean isAlignmentAnalysis()
+  {
+    return alignmentAnalysis;
+  }
+
+  public void setAlignmentAnalysis(boolean value)
+  {
+    this.alignmentAnalysis = value;
+  }
+
+  @Override
+  public boolean getFilterNonStandardSymbols()
+  {
+    return false;
+  }
+
+  @Override
+  public boolean getNeedsAlignedSequences()
+  {
     return false;
   }
 
@@ -118,13 +145,22 @@ public class AnnotationOperation implements Operation
   protected void buildMenu(JMenu parent, AlignFrame frame)
   {
     final var calcName = service.getName();
-    WebServiceExecutor wsExecutor = frame.getViewport().getWSExecutor();
+    PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
+    final var calcManager = frame.getViewport().getCalcManager();
     {
       var item = new JMenuItem(MessageManager.formatMessage(
           "label.calcname_with_default_settings", calcName));
       item.addActionListener((event) -> {
-        WebServiceWorkerI worker = new AnnotationWorker();
-        wsExecutor.submit(worker);
+        /* What is the purpose of AlignViewport and AlignmentViewPanel? */
+        AlignViewport viewport = frame.getCurrentView();
+        AlignmentViewPanel alignPanel = frame.alignPanel;
+        var worker = new AnnotationServiceWorker(this, service,
+            Collections.emptyList(), viewport, alignPanel, frame, frame,
+            calcManager);
+        if (isInteractive())
+          calcManager.registerWorker(worker);
+        else
+          calcManager.startWorker(worker);
       });
       parent.add(item);
     }
@@ -139,10 +175,19 @@ public class AnnotationOperation implements Operation
             .thenAcceptAsync((arguments) -> {
               if (arguments != null)
               {
-                
+                AlignViewport viewport = frame.getCurrentView();
+                AlignmentViewPanel alignPanel = frame.alignPanel;
+                var worker = new AnnotationServiceWorker(
+                    AnnotationOperation.this, service, arguments, viewport,
+                    alignPanel, frame, frame, calcManager);
+                if (isInteractive())
+                  calcManager.registerWorker(worker);
+                else
+                  calcManager.startWorker(worker);
               }
             });
       });
+      parent.add(item);
     }
   }
 
@@ -177,85 +222,4 @@ public class AnnotationOperation implements Operation
     });
   }
 
-  private class AnnotationWorker implements WebServiceWorkerI
-  {
-    private long uid = MathUtils.getUID();
-
-    private WSJobList jobs = new WSJobList();
-
-    private HashMap<Long, Integer> exceptionCount = new HashMap<>();
-
-    private static final int MAX_RETRY = 5;
-
-    @Override
-    public long getUID()
-    {
-      return uid;
-    }
-
-    @Override
-    public WebServiceI getWebService()
-    {
-      return service;
-    }
-
-    @Override
-    public List<WSJob> getJobs()
-    {
-      return Collections.unmodifiableList(jobs);
-    }
-
-    @Override
-    public void startJobs() throws IOException
-    {
-      
-    }
-
-    @Override
-    public boolean pollJobs() throws IOException
-    {
-      boolean done = true;
-      for (WSJob job : getJobs())
-      {
-        if (!job.getStatus().isDone() && !job.getStatus().isFailed())
-        {
-          Cache.log.debug(format("Polling job %s", job));
-          try
-          {
-            service.updateProgress(job);
-            exceptionCount.remove(job.getUid());
-          } catch (IOException e)
-          {
-            Cache.log.error(format("Polling job %s failed.", job), e);
-            int count = exceptionCount.getOrDefault(job.getUid(),
-                MAX_RETRY);
-            if (--count <= 0)
-            {
-              job.setStatus(WSJobStatus.SERVER_ERROR);
-              Cache.log.warn(format(
-                  "Attempts limit exceeded. Droping job %s.", job));
-            }
-            exceptionCount.put(job.getUid(), count);
-          } catch (OutOfMemoryError e)
-          {
-            job.setStatus(WSJobStatus.BROKEN);
-            Cache.log.error(
-                format("Out of memory when retrieving job %s", job), e);
-          }
-          Cache.log.debug(
-              format("Job %s status is %s", job, job.getStatus()));
-        }
-        done &= job.getStatus().isDone() || job.getStatus().isFailed();
-      }
-      return done;
-    }
-
-    @Override
-    public void done()
-    {
-      // TODO Auto-generated method stub
-
-    }
-
-  }
 }