X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPaintRefresher.java;h=ddf590ec435573c758fd1c233dbcedb7f7a8e5c4;hb=58735c979dbb573eb12d57e33ef7d6e3f3a82c8e;hp=f696640964629df38146903c88859f792928805f;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index f696640..ddf590e 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,35 +1,262 @@
-package jalview.appletgui;
-import java.awt.*;
-import java.util.*;
-
-public class PaintRefresher
-{
-  static Vector components = new Vector();
-
-  public static void Register(Component c)
-  {
-    if(!components.contains(c))
-      components.addElement(c);
-    else
-      components.removeElement(c);
-  }
-
-  public static void Refresh(Component c)
-  {
-    Component temp;
-    Enumeration e = components.elements();
-    while( e.hasMoreElements() )
-    {
-      temp = (Component)e.nextElement();
-
-      if(!temp.isValid())
-        components.removeElement( temp );
-      else if( temp == c )
-           continue;
-
-      temp.repaint();
-    }
-
-  }
-
-}
+/*
+ * 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.appletgui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+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!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class PaintRefresher
+{
+  static Map<String, Vector<Component>> components;
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @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<Component> comps = components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.addElement(comp);
+      }
+    }
+    else
+    {
+      Vector<Component> vcoms = new Vector<>();
+      vcoms.addElement(comp);
+      components.put(seqSetId, vcoms);
+    }
+  }
+
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Iterator<String> it = components.keySet().iterator();
+    while (it.hasNext())
+    {
+      Vector<Component> comps = components.get(it.next());
+      comps.removeElement(comp);
+      if (comps.isEmpty())
+      {
+        it.remove();
+      }
+    }
+  }
+
+  public static void Refresh(Component source, String id)
+  {
+    Refresh(source, id, false, false);
+  }
+
+  public static void Refresh(Component source, String id,
+          boolean alignmentChanged, boolean validateSequences)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Component comp;
+    Vector<Component> comps = components.get(id);
+
+    if (comps == null)
+    {
+      return;
+    }
+
+    Iterator<Component> it = comps.iterator();
+    while (it.hasNext())
+    {
+      comp = it.next();
+
+      if (comp == source)
+      {
+        continue;
+      }
+
+      if (!comp.isValid())
+      {
+        it.remove();
+      }
+      else if (validateSequences && comp instanceof AlignmentPanel
+              && source instanceof AlignmentPanel)
+      {
+        validateSequences(((AlignmentPanel) source).av.getAlignment(),
+                ((AlignmentPanel) comp).av.getAlignment());
+      }
+
+      if (comp instanceof AlignmentPanel && alignmentChanged)
+      {
+        ((AlignmentPanel) comp).alignmentChanged();
+      }
+
+      comp.repaint();
+    }
+  }
+
+  static void validateSequences(AlignmentI source, AlignmentI comp)
+  {
+    SequenceI[] a1;
+    if (source.getHiddenSequences().getSize() > 0)
+    {
+      a1 = source.getHiddenSequences().getFullAlignment()
+              .getSequencesArray();
+    }
+    else
+    {
+      a1 = source.getSequencesArray();
+    }
+
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
+    {
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.getSequencesArray();
+    }
+
+    int i, iSize = a1.length, j, jSize = a2.length;
+
+    if (iSize == jSize)
+    {
+      return;
+    }
+
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
+
+      for (j = 0; j < jSize; j++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        if (i < comp.getHeight())
+        {
+          // TODO: the following does not trigger any recalculation of
+          // height/etc, or maintain the dataset
+          List<SequenceI> alsq = comp.getSequences();
+          synchronized (alsq)
+          {
+            alsq.add(i, a1[i]);
+          }
+        }
+        else
+        {
+          comp.addSequence(a1[i]);
+        }
+
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment()
+                  .getSequencesArray();
+        }
+        else
+        {
+          a2 = comp.getSequencesArray();
+        }
+
+        jSize = a2.length;
+      }
+    }
+
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
+    {
+      exists = false;
+      for (i = 0; i < iSize; i++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
+      }
+    }
+  }
+
+  public static AlignmentPanel[] getAssociatedPanels(String id)
+  {
+    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(comps.elementAt(i));
+      }
+    }
+    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+    for (int ix = 0; ix < result.length; ix++)
+    {
+      result[ix] = (AlignmentPanel) tmp.elementAt(ix);
+    }
+
+    return result;
+  }
+
+}