JAL-3878 Make interactive service arguments persistent between starts.

[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 1eb5da0..55ed03b 100644 (file)
--- a/src/jalview/ws2/operations/AnnotationOperation.java
+++ b/src/jalview/ws2/operations/AnnotationOperation.java
@@ -1,41 +1,34 @@
 package jalview.ws2.operations;
 
-import java.io.IOException;
+import java.util.ArrayList;
 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.JCheckBoxMenuItem;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
 
+import jalview.api.AlignCalcManagerI2;
 import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
 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.Format;
 import jalview.util.MessageManager;
-import jalview.workers.AlignCalcManager2;
 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.PollingTaskExecutor;
 import jalview.ws2.WebServiceI;
-import jalview.ws2.WebServiceWorkerI;
-import jalview.ws2.utils.WSJobList;
-
-import static java.lang.String.format;
 
 /**
- * 
+ *
  * @author mmwarowny
  *
  */
@@ -49,6 +42,14 @@ public class AnnotationOperation implements Operation
 
   final ResultSupplier<FeaturesFile> featuresSupplier;
 
+  boolean alignmentAnalysis = false;
+
+  boolean interactive = false;
+
+  /*
+   * Is it fine to get rid of AlignAnalysisUIText?
+   */
+
   public AnnotationOperation(WebServiceI service,
       ResultSupplier<List<AlignmentAnnotation>> annotSupplier,
       ResultSupplier<FeaturesFile> featSupplier, String operationName)
@@ -110,13 +111,23 @@ public class AnnotationOperation implements Operation
   @Override
   public boolean isInteractive()
   {
-    return false;
+    return interactive;
+  }
+
+  public void setInteractive(boolean value)
+  {
+    this.interactive = value;
   }
 
   @Override
   public boolean isAlignmentAnalysis()
   {
-    return false;
+    return alignmentAnalysis;
+  }
+
+  public void setAlignmentAnalysis(boolean value)
+  {
+    this.alignmentAnalysis = value;
   }
 
   @Override
@@ -134,10 +145,13 @@ public class AnnotationOperation implements Operation
   @Override
   public MenuEntryProviderI getMenuBuilder()
   {
-    return this::buildMenu;
+    if (isInteractive())
+      return this::buildInteractiveMenu;
+    else
+      return this::buildClassicMenu;
   }
 
-  protected void buildMenu(JMenu parent, AlignFrame frame)
+  protected void buildClassicMenu(JMenu parent, AlignFrame frame)
   {
     final var calcName = service.getName();
     PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
@@ -146,13 +160,8 @@ public class AnnotationOperation implements Operation
       var item = new JMenuItem(MessageManager.formatMessage(
           "label.calcname_with_default_settings", calcName));
       item.addActionListener((event) -> {
-        AlignViewport viewport = frame.getCurrentView();
-        AlignmentViewPanel alignPanel = frame.alignPanel;
-        var worker = new AnnotationServiceWorker(this, service,
-            Collections.emptyList(), viewport, alignPanel, frame, frame,
-            calcManager);
+        var worker = createWorker(Collections.emptyList(), frame, calcManager);
         calcManager.startWorker(worker);
-        // TODO create and submit AnnotataionServiceWorker
       });
       parent.add(item);
     }
@@ -167,16 +176,87 @@ 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);
+                var worker = createWorker(arguments, frame, calcManager);
                 calcManager.startWorker(worker);
               }
             });
       });
+      parent.add(item);
+    }
+  }
+
+  protected void buildInteractiveMenu(JMenu parent, AlignFrame frame)
+  {
+    final var calcName = service.getName();
+    final var calcManager = frame.getViewport().getCalcManager();
+    final var arguments = new ArrayList<ArgumentI>();
+    final JCheckBoxMenuItem runItem;
+    {
+      // TODO use MessageManager and set tool tip text
+      runItem = new JCheckBoxMenuItem(
+          String.format("%s calculations", calcName));
+      runItem.addActionListener((event) -> {
+        calcManager.removeWorkersForName(calcName);
+        var worker = createWorker(arguments, frame, calcManager);
+        calcManager.registerWorker(worker);
+      });
+      parent.add(runItem);
+    }
+    JMenuItem _editItem = null;
+    if (service.hasParameters())
+    {
+      // TODO use MessageManager and set tool tip text
+      _editItem = new JMenuItem(
+          String.format("Edit %s settings", calcName));
+      _editItem.addActionListener((event) -> {
+        openEditParamsDialog(service, null, null)
+            .thenAcceptAsync((args) -> {
+              if (arguments != null)
+              {
+                arguments.clear();
+                arguments.addAll(args);
+                calcManager.removeWorkersForName(calcName);
+                var worker = createWorker(arguments, frame, calcManager);
+                calcManager.registerWorker(worker);
+              }
+            });
+      });
+      parent.add(_editItem);
     }
+    final var editItem = _editItem;
+
+    parent.addMenuListener(new MenuListener()
+      {
+        @Override
+        public void menuSelected(MenuEvent e)
+        {
+          var isNuc = frame.getViewport().getAlignment().isNucleotide();
+          var menuEnabled = (isNuc && isNucleotideOperation()) ||
+              (!isNuc && isProteinOperation());
+          runItem.setEnabled(menuEnabled);
+          if (editItem != null)
+            editItem.setEnabled(menuEnabled);
+          boolean currentlyRunning = calcManager.getWorkersForName(calcName).size() > 0;
+          runItem.setSelected(currentlyRunning);
+        }
+
+        @Override
+        public void menuDeselected(MenuEvent e) {}
+
+        @Override
+        public void menuCanceled(MenuEvent e) {}
+      });
+  }
+
+  private AnnotationServiceWorker createWorker(
+      List<ArgumentI> arguments, AlignFrame frame, AlignCalcManagerI2 calcManager)
+  {
+    /* What is the purpose of AlignViewport and AlignmentViewPanel? */
+    AlignViewport viewport = frame.getCurrentView();
+    AlignmentViewPanel alignPanel = frame.alignPanel;
+    return new AnnotationServiceWorker(this, service,
+        arguments, viewport, alignPanel, frame, frame,
+        calcManager);
   }
 
   private CompletionStage<List<ArgumentI>> openEditParamsDialog(