X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcWorker.java;h=0ad8726e34bdac33c7f5216f4c761ad4e0c17748;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=f1b30194df3c1ec5050c1172309bfe4b35dde2ad;hpb=42ec35a792d480c73027da6e7fc617146850ce44;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index f1b3019..0ad8726 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -1,21 +1,40 @@
-/**
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.workers;
 
-import java.util.List;
-
 import jalview.api.AlignCalcManagerI;
 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 
+ * Base class for alignment calculation workers
+ * 
  * @author jimp
- *
+ * 
  */
 public abstract class AlignCalcWorker implements AlignCalcWorkerI
 {
@@ -23,49 +42,98 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
    * manager and data source for calculations
    */
   protected AlignViewportI alignViewport;
+
   protected AlignCalcManagerI calcMan;
+
   protected AlignmentViewPanel ap;
-  protected List<AlignmentAnnotation> ourAnnots=null;
-  
+
+  protected List<AlignmentAnnotation> ourAnnots;
+
   public AlignCalcWorker(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     this.alignViewport = alignViewport;
-    calcMan=alignViewport.getCalcManager();
-    ap = alignPanel;    
+    calcMan = alignViewport.getCalcManager();
+    ap = alignPanel;
   }
+
   protected void abortAndDestroy()
   {
-    if (calcMan!=null) {
+    if (calcMan != null)
+    {
       calcMan.workerComplete(this);
     }
-    alignViewport=null;
-    calcMan=null;
-    ap=null;
-    
+    alignViewport = null;
+    calcMan = null;
+    ap = null;
+
   }
+
+  @Override
   public boolean involves(AlignmentAnnotation i)
   {
-    return ourAnnots!=null && ourAnnots.contains(i);
+    return ourAnnots != null && ourAnnots.contains(i);
   }
 
   /**
-   * permanently remove from the alignment all annotation rows managed by this worker
+   * Permanently removes from the alignment all annotation rows managed by this
+   * worker
    */
   @Override
-  public void removeOurAnnotation()
+  public void removeAnnotation()
   {
-    if (ourAnnots!=null && alignViewport!=null)
+    if (ourAnnots != null && alignViewport != null)
     {
-      AlignmentI alignment=alignViewport.getAlignment();
-      synchronized (ourAnnots) {
-        for (AlignmentAnnotation aa:ourAnnots)
+      AlignmentI alignment = alignViewport.getAlignment();
+      synchronized (ourAnnots)
+      {
+        for (AlignmentAnnotation aa : ourAnnots)
         {
           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;
     }
   }
-  // TODO: allow GUI to query workers associated with annotation to add items to annotation label panel popup menu
 
 }