X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=c6d3b588755f5a457a51045aebead9e1ba3ae3d2;hb=9efc6af45120e24f7a11cc8ce6409139844e5001;hp=6755a88b42aa42bd150c4f0eb7c2ea355a53ae8b;hpb=7b3241c464d774516c4295a5023f4aef7939298e;p=jalview.git

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 6755a88..c6d3b58 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,12 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -33,190 +32,212 @@ import java.util.*;
  */
 public class PaintRefresher
 {
-    static Hashtable components;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param comp DOCUMENT ME!
-     * @param al DOCUMENT ME!
-     */
-    public static void Register(Component comp, String seqSetId)
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param comp DOCUMENT ME!
+   * @param al DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
     {
-      if (components == null)
-        components = new Hashtable();
+      components = new Hashtable();
+    }
 
-        if (components.containsKey(seqSetId))
-        {
-            Vector comps = (Vector) components.get(seqSetId);
-            if(!comps.contains(comp))
-            {
-              comps.addElement(comp);
-            }
-        }
-        else
-        {
-            Vector vcoms = new Vector();
-            vcoms.addElement(comp);
-            components.put(seqSetId, vcoms);
-        }
+    if (components.containsKey(seqSetId))
+    {
+      Vector comps = (Vector) components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.addElement(comp);
+      }
+    }
+    else
+    {
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(seqSetId, vcoms);
     }
+  }
 
-    public static void RemoveComponent(Component comp)
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
     {
-      if (components == null)
-        return;
+      return;
+    }
 
-      Enumeration en = components.keys();
-      while(en.hasMoreElements())
+    Enumeration en = components.keys();
+    while (en.hasMoreElements())
+    {
+      String id = en.nextElement().toString();
+      Vector comps = (Vector) components.get(id);
+      comps.remove(comp);
+      if (comps.size() == 0)
       {
-        String id = en.nextElement().toString();
-        Vector comps = (Vector) components.get(id);
-        comps.remove(comp);
-        if(comps.size()==0)
-        {
-          components.remove(id);
-        }
+        components.remove(id);
       }
     }
-
-    public static void Refresh(Component source, String 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)
+  {
+    if (components == null)
     {
-      Refresh( source, id, false, false);
+      return;
     }
 
-    public static void Refresh(Component source,
-                               String id,
-                               boolean alignmentChanged,
-                               boolean validateSequences)
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
     {
-      if (components == null)
-        return;
+      return;
+    }
 
-      Component comp;
-      Vector comps = (Vector) components.get(id);
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
 
-      if(comps==null)
+      if (comp == source)
       {
-        return;
+        continue;
       }
 
-      Enumeration e = comps.elements();
-      while (e.hasMoreElements())
+      if (validateSequences
+          && comp instanceof AlignmentPanel
+          && source instanceof AlignmentPanel)
       {
-        comp = (Component) e.nextElement();
-
-        if(comp==source)
-        {
-          continue;
-        }
+        validateSequences( ( (AlignmentPanel) source).av.alignment,
+                          ( (AlignmentPanel) comp).av.alignment);
+      }
 
-        if (!comp.isValid())
-        {
-          comps.removeElement(comp);
-        }
-        else if(validateSequences
-                && comp instanceof AlignmentPanel
-                && source instanceof AlignmentPanel )
-        {
-          validateSequences( ((AlignmentPanel)source).av.alignment,
-                             ((AlignmentPanel)comp).av.alignment);
-        }
+      if (comp instanceof AlignmentPanel && alignmentChanged)
+      {
+        ( (AlignmentPanel) comp).alignmentChanged();
+      }
 
-        if(comp instanceof AlignmentPanel && alignmentChanged)
-        {
-          ((AlignmentPanel)comp).alignmentChanged();
-        }
+      comp.repaint();
+    }
+  }
 
-        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();
     }
 
-    static void validateSequences(AlignmentI source, AlignmentI comp)
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
     {
-      SequenceI[] a1;
-      if(source.getHiddenSequences().getSize()>0)
-        a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-      else
-        a1 = source.getSequencesArray();
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.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;
 
-      int i, iSize=a1.length, j, jSize=a2.length;
+    if (iSize == jSize)
+    {
+      return;
+    }
 
-      if(iSize == jSize)
-        return;
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
 
-      boolean exists = false;
-      for(i=0; i<iSize; i++)
+      for (j = 0; j < jSize; j++)
       {
-        exists = false;
-
-        for(j=0; j<jSize; j++)
-          if (a2[j]==a1[i] )
-          {
-            exists = true;
-            break;
-          }
-
-        if(!exists)
+        if (a2[j] == a1[i])
         {
-          if (i < jSize)
-            comp.getSequences().insertElementAt(a1[i], i);
-          else
-            comp.addSequence(a1[i]);
-
-          jSize++;
-
-          if (comp.getHiddenSequences().getSize() > 0)
-            a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-          else
-            a2 = comp.getSequencesArray();
+          exists = true;
+          break;
         }
       }
 
-      iSize=a1.length;
-      jSize=a2.length;
-
-      for(j=0; j<jSize; j++)
+      if (!exists)
       {
-        exists = false;
-        for(i=0; i<iSize; i++)
+        if (i < comp.getHeight())
+        {
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
         {
-          if (a2[j]==a1[i])
-          {
-            exists = true;
-            break;
-          }
+          comp.addSequence(a1[i]);
         }
 
-        if(!exists)
+        if (comp.getHiddenSequences().getSize() > 0)
         {
-          comp.deleteSequence(a2[j]);
+          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
         }
+        else
+        {
+          a2 = comp.getSequencesArray();
+        }
+
+        jSize = a2.length;
       }
     }
 
-    static AlignmentPanel [] getAssociatedPanels(String id)
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
     {
-      Vector comps = (Vector)components.get(id);
-      Vector tmp = new Vector();
-      int i, iSize = comps.size();
+      exists = false;
       for (i = 0; i < iSize; i++)
       {
-        if (comps.elementAt(i) instanceof AlignmentPanel)
+        if (a2[j] == a1[i])
         {
-          tmp.addElement(((AlignmentPanel)comps.elementAt(i)));
+          exists = true;
+          break;
         }
       }
-      AlignmentPanel [] result = new AlignmentPanel[tmp.size()];
-      tmp.toArray(result);
 
-      return result;
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
+      }
+    }
+  }
+
+  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++)
+    {
+      if (comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        tmp.addElement( ( (AlignmentPanel) comps.elementAt(i)));
+      }
     }
+    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+    tmp.toArray(result);
+
+    return result;
+  }
 
 }