JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / api / AlignCalcManagerI.java

diff --git a/src/jalview/api/AlignCalcManagerI.java b/src/jalview/api/AlignCalcManagerI.java
index 2641c96..18605b8 100644 (file)
--- a/src/jalview/api/AlignCalcManagerI.java
+++ b/src/jalview/api/AlignCalcManagerI.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.api;
@@ -33,17 +35,12 @@ public interface AlignCalcManagerI
   void notifyStart(AlignCalcWorkerI worker);
 
   /**
-   * check if a calculation of this type is already active
-   * 
-   * @param worker
-   * @return
-   */
-  boolean alreadyDoing(AlignCalcWorkerI worker);
-
-  /**
-   * tell manager that worker is now processing data
+   * tell manager that a thread running worker's run() loop is ready to start
+   * processing data
    * 
    * @param worker
+   * @return true if worker should start processing, false if another thread is
+   *         in progress
    */
   boolean notifyWorking(AlignCalcWorkerI worker);
 
@@ -61,7 +58,7 @@ public interface AlignCalcManagerI
    * 
    * @param worker
    */
-  void workerCannotRun(AlignCalcWorkerI worker);
+  void disableWorker(AlignCalcWorkerI worker);
 
   /**
    * indicate that a worker like this may be run on the platform.
@@ -69,7 +66,15 @@ public interface AlignCalcManagerI
    * @param worker
    *          of class to be removed from the execution blacklist
    */
-  void workerMayRun(AlignCalcWorkerI worker);
+  void enableWorker(AlignCalcWorkerI worker);
+
+  /**
+   * Answers true if the worker is disabled from running
+   * 
+   * @param worker
+   * @return
+   */
+  boolean isDisabled(AlignCalcWorkerI worker);
 
   /**
    * launch a new worker
@@ -81,7 +86,7 @@ public interface AlignCalcManagerI
   /**
    * 
    * @param worker
-   * @return
+   * @return true if the worker is currently running
    */
   boolean isWorking(AlignCalcWorkerI worker);
 
@@ -118,7 +123,7 @@ public interface AlignCalcManagerI
    * 
    * @param workerClass
    */
-  void updateAnnotationFor(Class workerClass);
+  void updateAnnotationFor(Class<? extends AlignCalcWorkerI> workerClass);
 
   /**
    * return any registered workers of the given class
@@ -126,17 +131,8 @@ public interface AlignCalcManagerI
    * @param workerClass
    * @return null or one or more workers of the given class
    */
-  List<AlignCalcWorkerI> getRegisteredWorkersOfClass(Class workerClass);
-
-  /**
-   * start any workers of the given class
-   * 
-   * @param workerClass
-   * @return false if no workers of given class were registered (note -
-   *         blacklisted classes cannot be restarted, so this method will return
-   *         true for blacklisted workers)
-   */
-  boolean startRegisteredWorkersOfClass(Class workerClass);
+  List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> workerClass);
 
   /**
    * work out if there is an instance of a worker that is *waiting* to start
@@ -154,6 +150,15 @@ public interface AlignCalcManagerI
    * 
    * @param typeToRemove
    */
-  void removeRegisteredWorkersOfClass(Class typeToRemove);
+  void removeRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> typeToRemove);
 
+  /**
+   * Removes the worker that produces the given annotation, provided it is
+   * marked as 'deletable'. Some workers may need to continue to run as the
+   * results of their calculations are needed, e.g. for colour schemes.
+   * 
+   * @param ann
+   */
+  void removeWorkerForAnnotation(AlignmentAnnotation ann);
 }