JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 8f1fc83..77210ee 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -24,6 +24,8 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcManagerI2;
+import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -57,6 +59,7 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
+import jalview.workers.AlignCalcManager2;
 import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.InformationThread;
@@ -848,7 +851,7 @@ public abstract class AlignmentViewport
     return strucConsensus;
   }
 
-  protected AlignCalcManagerI calculator = new AlignCalcManager();
+  protected AlignCalcManagerI2 calculator = new AlignCalcManager2();
 
   /**
    * trigger update of conservation annotation
@@ -862,8 +865,8 @@ public abstract class AlignmentViewport
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(
-            jalview.workers.ConservationThread.class) == null)
+    if (calculator.getWorkersOfClass(
+            jalview.workers.ConservationThread.class).isEmpty())
     {
       calculator.registerWorker(
               new jalview.workers.ConservationThread(this, ap));
@@ -880,8 +883,7 @@ public abstract class AlignmentViewport
     {
       return;
     }
-    if (calculator
-            .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+    if (calculator.getWorkersOfClass(ConsensusThread.class).isEmpty())
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -912,11 +914,9 @@ public abstract class AlignmentViewport
       }
       if (doConsensus)
       {
-        if (calculator.getRegisteredWorkersOfClass(
-                ComplementConsensusThread.class) == null)
+        if (calculator.getWorkersOfClass(ComplementConsensusThread.class).isEmpty())
         {
-          calculator
-                  .registerWorker(new ComplementConsensusThread(this, ap));
+          calculator.registerWorker(new ComplementConsensusThread(this, ap));
         }
       }
     }
@@ -925,8 +925,7 @@ public abstract class AlignmentViewport
   @Override
   public void initInformationWorker(final AlignmentViewPanel ap)
   {
-    if (calculator
-            .getRegisteredWorkersOfClass(InformationThread.class) == null)
+    if (calculator.getWorkersOfClass(InformationThread.class).isEmpty())
     {
       calculator.registerWorker(new InformationThread(this, ap));
     }
@@ -947,8 +946,7 @@ public abstract class AlignmentViewport
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(
-            StrucConsensusThread.class) == null)
+    if (calculator.getWorkersOfClass(StrucConsensusThread.class).isEmpty())
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -967,7 +965,7 @@ public abstract class AlignmentViewport
     {
       return false;
     }
-    if (calculator.workingInvolvedWith(alignmentAnnotation))
+    if (calculator.isWorkingWithAnnotation(alignmentAnnotation))
     {
       // System.err.println("grey out ("+alignmentAnnotation.label+")");
       return true;
@@ -1020,7 +1018,7 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignCalcManagerI getCalcManager()
+  public AlignCalcManagerI2 getCalcManager()
   {
     return calculator;
   }
@@ -1094,9 +1092,15 @@ public abstract class AlignmentViewport
       // TODO: decouple settings setting from calculation when refactoring
       // annotation update method from alignframe to viewport
       this.showSequenceLogo = showSequenceLogo;
-      calculator.updateAnnotationFor(ConsensusThread.class);
-      calculator.updateAnnotationFor(ComplementConsensusThread.class);
-      calculator.updateAnnotationFor(StrucConsensusThread.class);
+      for (AlignCalcWorkerI worker : calculator.getWorkers())
+      {
+        if (worker.getClass().equals(ConsensusThread.class) ||
+                worker.getClass().equals(ComplementConsensusThread.class) ||
+                worker.getClass().equals(StrucConsensusThread.class))
+        {
+          worker.updateAnnotation();
+        }
+      }
     }
     this.showSequenceLogo = showSequenceLogo;
   }