From 753bf06169312d77bfde25bad81f87511abe072a Mon Sep 17 00:00:00 2001
From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Thu, 21 Oct 2021 16:52:48 +0200
Subject: [PATCH] JAL-3878 Add methods to get and remove workers by their calc
 name.

---
 src/jalview/api/AlignCalcManagerI2.java    |   55 +++++++++++++++++-----------
 src/jalview/workers/AlignCalcManager2.java |   29 +++++++++++++++
 2 files changed, 62 insertions(+), 22 deletions(-)

diff --git a/src/jalview/api/AlignCalcManagerI2.java b/src/jalview/api/AlignCalcManagerI2.java
index 0bd6c3c..1e54e3e 100644
--- a/src/jalview/api/AlignCalcManagerI2.java
+++ b/src/jalview/api/AlignCalcManagerI2.java
@@ -8,7 +8,7 @@ import jalview.datamodel.AlignmentAnnotation;
  * An abstract manager which controls the execution of interactive jobs.
  * There is always one instance of AlignCancManager per AlignmenViewport
  * which runs the jobs, notifies observers and ensures no race conditions.
- * 
+ *
  * @author mmwarowny
  *
  */
@@ -19,76 +19,87 @@ public interface AlignCalcManagerI2
    * for execution.
    */
   void registerWorker(AlignCalcWorkerI worker);
-  
+
   /**
-   * Returns the list of all registered workers or an empty list if 
+   * Returns the list of all registered workers or an empty list if
    * there are none
    */
   List<AlignCalcWorkerI> getWorkers();
-  
+
   /**
    * Returns the list of all workers of a given class or an empty list
-   * if there are none. The classes are compared using 
+   * if there are none. The classes are compared using
    * {@ink Class#equals(Object)} rather than {@code instanceof}.
    */
   List<AlignCalcWorkerI> getWorkersOfClass(Class<? extends AlignCalcWorkerI> cls);
-  
+
+  /**
+   * Returns the list of all workers for the given name or an empty list
+   * if there are none.
+   */
+  List<AlignCalcWorkerI> getWorkersForName(String name);
+
   /**
    * Removes the worker from the scheduler. It does not cancel workers
    * already scheduled for execution.
    */
   void removeWorker(AlignCalcWorkerI worker);
-  
+
   /**
    * Removes all workers which are involved with the given annotation.
    */
   void removeWorkerForAnnotation(AlignmentAnnotation annot);
-  
+
   /**
    * Alias of removeWorkerForAnnotation
    */
   default void removeWorkersForAnnotation(AlignmentAnnotation annot) {
     removeWorkerForAnnotation(annot);
   }
-  
+
+  /**
+   * Removes all workers with matching name.
+   */
+  void removeWorkersForName(String name);
+
   /**
    * Removes all workers of a given class. The classes are compared using
-   * {@link Class#equals(Object)}. 
+   * {@link Class#equals(Object)}.
    */
   void removeWorkersOfClass(Class<? extends AlignCalcWorkerI> cls);
-  
+
   /**
    * Disables a worker so it won't be run during the following restarts.
    */
   void disableWorker(AlignCalcWorkerI worker);
-  
+
   /**
    * Restores the previously disabled worker back to operation.
    */
   void enableWorker(AlignCalcWorkerI worker);
-  
+
   /**
    * Checks whether the worker is disabled either due to failure or
    * disabling it manually.
    */
   boolean isDisabled(AlignCalcWorkerI worker);
-  
+
   /**
    * Checks whether the given worker is currently running.
    */
   boolean isWorking(AlignCalcWorkerI worker);
-  
+
   /**
    * Checks whether the currently running worker (if any) is processing
    * the given annotation.
    */
   boolean isWorkingWithAnnotation(AlignmentAnnotation annot);
-  
+
   /**
    * Checks whether this manager is running a worker.
    */
   boolean isWorking();
-  
+
   /**
    * Scheduler the worker for one-time execution. The worker does not need
    * to be registered with this manager and will be scheduler regardless
@@ -96,29 +107,29 @@ public interface AlignCalcManagerI2
    * previous one will be cancelled.
    */
   void startWorker(AlignCalcWorkerI worker);
-  
+
   /**
    * Schedules all registered and not-disabled workers for next execution.
    */
   void restartWorkers();
-  
+
   /**
    * Cancels the execution of the worker. Note, if the worker is already
    * running, this method may, but doesn't have to, interrupt it in
    * the middle of the work.
    */
   void cancelWorker(AlignCalcWorkerI worker);
-  
+
   /**
    * Connect the listener of the worker state changes.
    */
   void addAlignCalcListener(AlignCalcListener listener);
-  
+
   /**
    * Remove previously registered worker listener.
    */
   void removeAlignCalcListener(AlignCalcListener listener);
-  
+
   /**
    * Stops the manager from running new jobs and cleans-up all
    * resources such as threads and thread pools.
diff --git a/src/jalview/workers/AlignCalcManager2.java b/src/jalview/workers/AlignCalcManager2.java
index 8d4796d..5c25668 100644
--- a/src/jalview/workers/AlignCalcManager2.java
+++ b/src/jalview/workers/AlignCalcManager2.java
@@ -312,6 +312,20 @@ public class AlignCalcManager2 implements AlignCalcManagerI2
   }
 
   @Override
+  public List<AlignCalcWorkerI> getWorkersForName(String name)
+  {
+    List<AlignCalcWorkerI> collected = new ArrayList<>();
+    for (var worker : getWorkers())
+    {
+      if (worker.getCalcName().equals(name))
+      {
+        collected.add(worker);
+      }
+    }
+    return collected;
+  }
+
+  @Override
   public void removeWorker(AlignCalcWorkerI worker)
   {
     if (worker.isDeletable())
@@ -351,6 +365,21 @@ public class AlignCalcManager2 implements AlignCalcManagerI2
   }
 
   @Override
+  public void removeWorkersForName(String name)
+  {
+    synchronized (registered)
+    {
+      for (var worker : getWorkers())
+      {
+        if (worker.getCalcName().equals(name))
+        {
+          removeWorker(worker);
+        }
+      }
+    }
+  }
+
+  @Override
   public void disableWorker(AlignCalcWorkerI worker)
   {
     // Null pointer check might be needed
-- 
1.7.10.2