JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

[jalview.git] / src / jalview / workers / AlignCalcWorker.java

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 9fbd500..c94032f 100644 (file)
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -1,31 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.workers;
 
-import java.util.List;
-
 import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcManagerI2;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+
+import java.util.List;
 
 /**
  * Base class for alignment calculation workers
@@ -40,11 +44,11 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
    */
   protected AlignViewportI alignViewport;
 
-  protected AlignCalcManagerI calcMan;
+  protected AlignCalcManagerI2 calcMan;
 
   protected AlignmentViewPanel ap;
 
-  protected List<AlignmentAnnotation> ourAnnots = null;
+  protected List<AlignmentAnnotation> ourAnnots;
 
   public AlignCalcWorker(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
@@ -58,7 +62,8 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
   {
     if (calcMan != null)
     {
-      calcMan.workerComplete(this);
+      calcMan.cancelWorker(this);
+      calcMan.removeWorker(this);
     }
     alignViewport = null;
     calcMan = null;
@@ -66,17 +71,18 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
 
   }
 
+  @Override
   public boolean involves(AlignmentAnnotation i)
   {
     return ourAnnots != null && ourAnnots.contains(i);
   }
 
   /**
-   * permanently remove from the alignment all annotation rows managed by this
+   * Permanently removes from the alignment all annotation rows managed by this
    * worker
    */
   @Override
-  public void removeOurAnnotation()
+  public void removeAnnotation()
   {
     if (ourAnnots != null && alignViewport != null)
     {
@@ -88,9 +94,52 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
           alignment.deleteAnnotation(aa, true);
         }
       }
+      ourAnnots.clear();
     }
   }
+
   // TODO: allow GUI to query workers associated with annotation to add items to
   // annotation label panel popup menu
 
+  @Override
+  public boolean isDeletable()
+  {
+    return false;
+  }
+
+  /**
+   * Calculate min and max values of annotations and set as graphMin, graphMax
+   * on the AlignmentAnnotation. This is needed because otherwise, well, bad
+   * things happen.
+   * 
+   * @param ann
+   * @param anns
+   */
+  protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
+  {
+    // TODO feels like this belongs inside AlignmentAnnotation!
+    float max = Float.MIN_VALUE;
+    float min = Float.MAX_VALUE;
+    boolean set = false;
+    for (Annotation a : anns)
+    {
+      if (a != null)
+      {
+        set = true;
+        float val = a.value;
+        max = Math.max(max, val);
+        min = Math.min(min, val);
+      }
+    }
+    if (set)
+    {
+      ann.graphMin = min;
+      ann.graphMax = max;
+    }
+  }
+
+  public AlignViewportI getAlignViewport()
+  {
+    return alignViewport;
+  }
 }