/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * 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.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.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* DOCUMENT ME!
*/
public class PaintRefresher
{
- static Hashtable components;
+ static Map<String, Vector<Component>> components;
/**
* DOCUMENT ME!
{
if (components == null)
{
- components = new Hashtable();
+ components = new Hashtable<String, Vector<Component>>();
}
if (components.containsKey(seqSetId))
{
- Vector comps = (Vector) components.get(seqSetId);
+ Vector<Component> comps = components.get(seqSetId);
if (!comps.contains(comp))
{
comps.addElement(comp);
}
else
{
- Vector vcoms = new Vector();
+ Vector<Component> vcoms = new Vector<>();
vcoms.addElement(comp);
components.put(seqSetId, vcoms);
}
return;
}
- Enumeration en = components.keys();
- while (en.hasMoreElements())
+ Iterator<String> it = components.keySet().iterator();
+ while (it.hasNext())
{
- String id = en.nextElement().toString();
- Vector comps = (Vector) components.get(id);
+ Vector<Component> comps = components.get(it.next());
comps.removeElement(comp);
- if (comps.size() == 0)
+ if (comps.isEmpty())
{
- components.remove(id);
+ it.remove();
}
}
}
}
Component comp;
- Vector comps = (Vector) components.get(id);
+ Vector<Component> comps = components.get(id);
if (comps == null)
{
return;
}
- Enumeration e = comps.elements();
- while (e.hasMoreElements())
+ Iterator<Component> it = comps.iterator();
+ while (it.hasNext())
{
- comp = (Component) e.nextElement();
+ comp = it.next();
if (comp == source)
{
if (!comp.isValid())
{
- comps.removeElement(comp);
+ it.remove();
}
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)
{
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<SequenceI> alsq;
+ synchronized (alsq = comp.getSequences())
+ {
+ alsq.add(i, a1[i]);
+ }
}
else
{
}
}
}
+
+ public static AlignmentPanel[] getAssociatedPanels(String id)
+ {
+ Vector<Component> comps = components.get(id);
+ Vector<Component> tmp = new Vector<>();
+ int i, iSize = comps.size();
+ for (i = 0; i < iSize; i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ tmp.addElement(comps.elementAt(i));
+ }
+ }
+ AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+ for (int ix = 0; ix < result.length; ix++)
+ {
+ result[ix] = (AlignmentPanel) tmp.elementAt(ix);
+ }
+
+ return result;
+ }
+
}