From 42ec35a792d480c73027da6e7fc617146850ce44 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 19 Jun 2012 17:22:52 +0100
Subject: [PATCH] JAL-961 JAL-975 extend api to support removal of workers
 no-longer required by the user

---
 src/jalview/api/AlignCalcManagerI.java    |    7 ++++
 src/jalview/api/AlignCalcWorkerI.java     |    2 ++
 src/jalview/workers/AlignCalcManager.java |   54 +++++++++++++++++++++++++++++
 src/jalview/workers/AlignCalcWorker.java  |   20 ++++++++++-
 4 files changed, 82 insertions(+), 1 deletion(-)

diff --git a/src/jalview/api/AlignCalcManagerI.java b/src/jalview/api/AlignCalcManagerI.java
index 1eedc74..35374c5 100644
--- a/src/jalview/api/AlignCalcManagerI.java
+++ b/src/jalview/api/AlignCalcManagerI.java
@@ -3,6 +3,7 @@ package jalview.api;
 import java.util.List;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.ws.jws2.AAConsClient;
 
 public interface AlignCalcManagerI
 {
@@ -115,4 +116,10 @@ public interface AlignCalcManagerI
    */
   boolean isPending(AlignCalcWorkerI workingClass);
 
+  /**
+   * deregister and otherwise remove any registered and working instances of the given worker type
+   * @param typeToRemove
+   */
+  void removeRegisteredWorkersOfClass(Class typeToRemove);
+
 }
diff --git a/src/jalview/api/AlignCalcWorkerI.java b/src/jalview/api/AlignCalcWorkerI.java
index 00f967a..7c14786 100644
--- a/src/jalview/api/AlignCalcWorkerI.java
+++ b/src/jalview/api/AlignCalcWorkerI.java
@@ -8,4 +8,6 @@ public interface AlignCalcWorkerI extends Runnable
   public boolean involves(AlignmentAnnotation annot);
 
   public void updateAnnotation();
+
+  void removeOurAnnotation();
 }
diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index bc5e8e3..544c2c8 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -6,6 +6,7 @@ import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignCalcWorkerI;
@@ -315,4 +316,57 @@ public class AlignCalcManager implements AlignCalcManagerI
       }
     }
   }
+
+  @Override
+  public void removeRegisteredWorkersOfClass(Class typeToRemove)
+  {
+    List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(typeToRemove);
+    List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
+    Set<AlignCalcWorkerI> toremovannot=new HashSet<AlignCalcWorkerI>();
+    synchronized (restartable)
+    {
+      for (AlignCalcWorkerI worker:restartable) {
+        if (typeToRemove.equals(worker.getClass())) {
+          removable.add(worker);
+          toremovannot.add(worker);
+        }
+      }
+      restartable.removeAll(removable);
+    }
+    synchronized (canUpdate)
+    {
+      for (AlignCalcWorkerI worker:canUpdate) {
+        if (typeToRemove.equals(worker.getClass())) {
+          removable.add(worker);
+          toremovannot.add(worker);
+        }
+      }
+      canUpdate.removeAll(removable);
+    }
+    // TODO: finish testing this extension
+
+/*    synchronized (inProgress)
+    {
+      // need to kill or mark as dead any running threads...
+      (inProgress.get(typeToRemove));
+    }
+    
+    if (workers == null)
+    {
+      return;
+    }
+    for (AlignCalcWorkerI worker : workers)
+    {
+      
+      if (isPending(worker))
+      {
+        worker.abortAndDestroy();
+        startWorker(worker);
+      }
+      else
+      {
+        System.err.println("Pending exists for " + workerClass);
+      }
+    }*/
+  }
 }
diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 19a92fb..f1b3019 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -10,6 +10,7 @@ import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 
 /**
  * Base class for alignment calculation workers 
@@ -47,7 +48,24 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
   {
     return ourAnnots!=null && ourAnnots.contains(i);
   }
-  
+
+  /**
+   * permanently remove from the alignment all annotation rows managed by this worker
+   */
+  @Override
+  public void removeOurAnnotation()
+  {
+    if (ourAnnots!=null && alignViewport!=null)
+    {
+      AlignmentI alignment=alignViewport.getAlignment();
+      synchronized (ourAnnots) {
+        for (AlignmentAnnotation aa:ourAnnots)
+        {
+          alignment.deleteAnnotation(aa, true);
+        }
+      }
+    }
+  }
   // TODO: allow GUI to query workers associated with annotation to add items to annotation label panel popup menu
 
 }
-- 
1.7.10.2