X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=d3be0f2efa29af91e2d1a93be76243f38005ca31;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=051721bcb459ecc203c0ac49671d20a4bab0d03c;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 051721b..d3be0f2 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,35 +1,259 @@
-package jalview.gui;
-import java.awt.*;
-import java.util.*;
-
-public class PaintRefresher
-{
-  static Vector containers = new Vector();
-
-  public static void Register(Container c)
-  {
-    if(!containers.contains(c))
-      containers.add(c);
-    else
-      containers.remove(c);
-  }
-
-  public static void Refresh(Container c)
-  {
-    Container temp;
-    Enumeration e = containers.elements();
-    while( e.hasMoreElements() )
-    {
-      temp = (Container)e.nextElement();
-
-      if(!temp.isValid())
-        containers.removeElement( temp );
-      else if( temp == c )
-           continue;
-
-      temp.repaint();
-    }
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.gui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+/**
+ * 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 Map<String, List<Component>> components = new HashMap<String, List<Component>>();
+
+  /**
+   * Add the given component to those registered under the given sequence set
+   * id. Does nothing if already added.
+   * 
+   * @param comp
+   * @param al
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components.containsKey(seqSetId))
+    {
+      List<Component> comps = components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.add(comp);
+      }
+    }
+    else
+    {
+      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)
+  {
+    List<String> emptied = new ArrayList<String>();
+    for (Entry<String, List<Component>> registered : components.entrySet())
+    {
+      String id = registered.getKey();
+      List<Component> comps = components.get(id);
+      comps.remove(comp);
+      if (comps.isEmpty())
+      {
+        emptied.add(id);
+      }
+    }
+
+    /*
+     * Remove now empty ids after the above (to avoid
+     * ConcurrentModificationException).
+     */
+    for (String id : emptied)
+    {
+      components.remove(id);
+    }
+  }
+
+  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)
+  {
+    List<Component> comps = components.get(id);
+
+    if (comps == null)
+    {
+      return;
+    }
+
+    for (Component comp : comps)
+    {
+      if (comp == source)
+      {
+        continue;
+      }
+
+      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
+          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
+        {
+          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]);
+      }
+    }
+  }
+
+  static AlignmentPanel[] getAssociatedPanels(String id)
+  {
+    List<Component> comps = components.get(id);
+    if (comps == null)
+    {
+      return new AlignmentPanel[0];
+    }
+    List<AlignmentPanel> tmp = new ArrayList<AlignmentPanel>();
+    for (Component comp : comps)
+    {
+      if (comp instanceof AlignmentPanel)
+      {
+        tmp.add((AlignmentPanel) comp);
+      }
+    }
+    return tmp.toArray(new AlignmentPanel[tmp.size()]);
+  }
+
+}