X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=dabf8db01ba4863c6b2abda7ce6f7a0ca2f7e662;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=f974f0a0a5888c305c61dda0498d0988ea4894fa;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index f974f0a..dabf8db 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,30 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.util.*;
+import java.util.List;
import java.awt.*;
import jalview.datamodel.*;
/**
- * DOCUMENT ME!
+ * 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 $Revision$
@@ -118,8 +121,8 @@ public class PaintRefresher
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)
@@ -179,7 +182,20 @@ 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
+ 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 alsq;
+ synchronized (alsq = comp.getSequences())
+ {
+ alsq.add(i, a1[i]);
+ }
}
else
{
@@ -224,14 +240,24 @@ public class PaintRefresher
static AlignmentPanel[] getAssociatedPanels(String id)
{
+ if (components == null)
+ {
+ return new AlignmentPanel[0];
+ }
+ ;
Vector comps = (Vector) components.get(id);
+ if (comps == null)
+ {
+ return new AlignmentPanel[0];
+ }
+ ;
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)));
+ tmp.addElement(comps.elementAt(i));
}
}
AlignmentPanel[] result = new AlignmentPanel[tmp.size()];