X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=01dfa3b703d9cffe0e255ddc773bb64d7425d67f;hb=2799bb913bbda0455b0f5f43737da678794e1961;hp=19fe4c9405b874fb86a00fb4715340c29932a0fd;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 19fe4c9..01dfa3b 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,31 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 $Revision$
@@ -38,9 +42,9 @@ public class PaintRefresher
* DOCUMENT ME!
*
* @param comp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param al
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static void Register(Component comp, String seqSetId)
{
@@ -119,8 +123,8 @@ 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)
@@ -180,7 +184,20 @@ 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
{
@@ -225,14 +242,24 @@ 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()];