X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FPaintRefresher.java;h=772488025cdebebabab929e1a9ddb549ab9bd818;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=722dd322e7206f287594b96f6f06b4599510782a;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 722dd32..7724880 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,27 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -122,8 +128,8 @@ public class PaintRefresher
else 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)
@@ -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 alsq;
+ synchronized (alsq = comp.getSequences())
+ {
+ alsq.add(i, a1[i]);
+ }
}
else
{
@@ -235,11 +247,12 @@ public class PaintRefresher
{
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