JAL-2069 update spike branch with latest

[jalview.git] / src / jalview / appletgui / PaintRefresher.java

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 25e529b..fe99187 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,27 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Component;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -31,7 +38,7 @@ import jalview.datamodel.*;
  */
 public class PaintRefresher
 {
-  static Hashtable components;
+  static Map<String, Vector<Component>> components;
 
   /**
    * DOCUMENT ME!
@@ -45,12 +52,12 @@ public class PaintRefresher
   {
     if (components == null)
     {
-      components = new Hashtable();
+      components = new Hashtable<String, Vector<Component>>();
     }
 
     if (components.containsKey(seqSetId))
     {
-      Vector comps = (Vector) components.get(seqSetId);
+      Vector<Component> comps = components.get(seqSetId);
       if (!comps.contains(comp))
       {
         comps.addElement(comp);
@@ -58,7 +65,7 @@ public class PaintRefresher
     }
     else
     {
-      Vector vcoms = new Vector();
+      Vector<Component> vcoms = new Vector<>();
       vcoms.addElement(comp);
       components.put(seqSetId, vcoms);
     }
@@ -71,15 +78,14 @@ 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);
+      Vector<Component> comps = components.get(it.next());
       comps.removeElement(comp);
-      if (comps.size() == 0)
+      if (comps.isEmpty())
       {
-        components.remove(id);
+        it.remove();
       }
     }
   }
@@ -98,17 +104,17 @@ public class PaintRefresher
     }
 
     Component comp;
-    Vector comps = (Vector) components.get(id);
+    Vector<Component> comps = components.get(id);
 
     if (comps == null)
     {
       return;
     }
 
-    Enumeration e = comps.elements();
-    while (e.hasMoreElements())
+    Iterator<Component> it = comps.iterator();
+    while (it.hasNext())
     {
-      comp = (Component) e.nextElement();
+      comp = it.next();
 
       if (comp == source)
       {
@@ -117,7 +123,7 @@ public class PaintRefresher
 
       if (!comp.isValid())
       {
-        comps.removeElement(comp);
+        it.remove();
       }
       else if (validateSequences && comp instanceof AlignmentPanel
               && source instanceof AlignmentPanel)
@@ -183,7 +189,13 @@ 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
+          List<SequenceI> alsq;
+          synchronized (alsq = comp.getSequences())
+          {
+            alsq.add(i, a1[i]);
+          }
         }
         else
         {
@@ -228,18 +240,19 @@ public class PaintRefresher
 
   public static AlignmentPanel[] getAssociatedPanels(String id)
   {
-    Vector comps = (Vector) components.get(id);
-    Vector tmp = new Vector();
+    Vector<Component> comps = components.get(id);
+    Vector<Component> tmp = new Vector<>();
     int i, iSize = comps.size();
     for (i = 0; i < iSize; i++)
     {
       if (comps.elementAt(i) instanceof AlignmentPanel)
       {
-        tmp.addElement(((AlignmentPanel) comps.elementAt(i)));
+        tmp.addElement(comps.elementAt(i));
       }
     }
     AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
-    for (int ix=0;ix<result.length;ix++) {
+    for (int ix = 0; ix < result.length; ix++)
+    {
       result[ix] = (AlignmentPanel) tmp.elementAt(ix);
     }