X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=ced554482e83da5104a0f2fea34c10e12c5cd176;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=f505453939ac40827051df952f34797ebbfde6ed;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index f505453..ced5544 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,70 +1,77 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 
 /**
- * DOCUMENT ME!
+ * Route datamodel/view update events for a sequence set to any display
+ * components involved TODO: JV3 refactor to abstract gui/view package
  * 
  * @author $author$
  * @version $Revision$
  */
 public class PaintRefresher
 {
-  static Hashtable components;
+  static Map<String, List<Component>> components = new HashMap<String, List<Component>>();
 
   /**
-   * DOCUMENT ME!
+   * Add the given component to those registered under the given sequence set
+   * id. Does nothing if already added.
    * 
    * @param comp
-   *                DOCUMENT ME!
    * @param al
-   *                DOCUMENT ME!
    */
   public static void Register(Component comp, String seqSetId)
   {
-    if (components == null)
-    {
-      components = new Hashtable();
-    }
-
     if (components.containsKey(seqSetId))
     {
-      Vector comps = (Vector) components.get(seqSetId);
+      List<Component> comps = components.get(seqSetId);
       if (!comps.contains(comp))
       {
-        comps.addElement(comp);
+        comps.add(comp);
       }
     }
     else
     {
-      Vector vcoms = new Vector();
-      vcoms.addElement(comp);
+      List<Component> vcoms = new ArrayList<Component>();
+      vcoms.add(comp);
       components.put(seqSetId, vcoms);
     }
   }
 
+  /**
+   * Remove this component from all registrations. Also removes a registered
+   * sequence set id if there are no remaining components registered against it.
+   * 
+   * @param comp
+   */
   public static void RemoveComponent(Component comp)
   {
     if (components == null)
@@ -72,15 +79,14 @@ public class PaintRefresher
       return;
     }
 
-    Enumeration en = components.keys();
-    while (en.hasMoreElements())
+    Iterator<String> it = components.keySet().iterator();
+    while (it.hasNext())
     {
-      String id = en.nextElement().toString();
-      Vector comps = (Vector) components.get(id);
+      List<Component> comps = components.get(it.next());
       comps.remove(comp);
-      if (comps.size() == 0)
+      if (comps.isEmpty())
       {
-        components.remove(id);
+        it.remove();
       }
     }
   }
@@ -93,24 +99,15 @@ public class PaintRefresher
   public static void Refresh(Component source, String id,
           boolean alignmentChanged, boolean validateSequences)
   {
-    if (components == null)
-    {
-      return;
-    }
-
-    Component comp;
-    Vector comps = (Vector) components.get(id);
+    List<Component> comps = components.get(id);
 
     if (comps == null)
     {
       return;
     }
 
-    Enumeration e = comps.elements();
-    while (e.hasMoreElements())
+    for (Component comp : comps)
     {
-      comp = (Component) e.nextElement();
-
       if (comp == source)
       {
         continue;
@@ -119,8 +116,8 @@ public class PaintRefresher
       if (validateSequences && comp instanceof AlignmentPanel
               && source instanceof AlignmentPanel)
       {
-        validateSequences(((AlignmentPanel) source).av.alignment,
-                ((AlignmentPanel) comp).av.alignment);
+        validateSequences(((AlignmentPanel) source).av.getAlignment(),
+                ((AlignmentPanel) comp).av.getAlignment());
       }
 
       if (comp instanceof AlignmentPanel && alignmentChanged)
@@ -180,7 +177,20 @@ public class PaintRefresher
       {
         if (i < comp.getHeight())
         {
-          comp.getSequences().insertElementAt(a1[i], i);
+          // TODO: the following does not trigger any recalculation of
+          // height/etc, or maintain the dataset
+          if (comp.getDataset() != source.getDataset())
+          {
+            // raise an implementation warning here - not sure if this situation
+            // will ever occur
+            System.err.println(
+                    "IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
+          }
+          List<SequenceI> alsq;
+          synchronized (alsq = comp.getSequences())
+          {
+            alsq.add(i, a1[i]);
+          }
         }
         else
         {
@@ -225,20 +235,20 @@ public class PaintRefresher
 
   static AlignmentPanel[] getAssociatedPanels(String id)
   {
-    Vector comps = (Vector) components.get(id);
-    Vector tmp = new Vector();
-    int i, iSize = comps.size();
-    for (i = 0; i < iSize; i++)
+    List<Component> comps = components.get(id);
+    if (comps == null)
     {
-      if (comps.elementAt(i) instanceof AlignmentPanel)
+      return new AlignmentPanel[0];
+    }
+    List<AlignmentPanel> tmp = new ArrayList<AlignmentPanel>();
+    for (Component comp : comps)
+    {
+      if (comp instanceof AlignmentPanel)
       {
-        tmp.addElement(((AlignmentPanel) comps.elementAt(i)));
+        tmp.add((AlignmentPanel) comp);
       }
     }
-    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
-    tmp.toArray(result);
-
-    return result;
+    return tmp.toArray(new AlignmentPanel[tmp.size()]);
   }
 
 }