X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPaintRefresher.java;h=ddf590ec435573c758fd1c233dbcedb7f7a8e5c4;hb=789a8f2ab91523923a6fa307acb4323b2bd7e756;hp=50e5a62d84a4965d35e4bbf4c49b20207b8c8742;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 50e5a62..ddf590e 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,27 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
+ * 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.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -31,7 +38,7 @@ import jalview.datamodel.*;
*/
public class PaintRefresher
{
- static Hashtable components;
+ static Map> components;
/**
* DOCUMENT ME!
@@ -45,12 +52,12 @@ public class PaintRefresher
{
if (components == null)
{
- components = new Hashtable();
+ components = new Hashtable<>();
}
if (components.containsKey(seqSetId))
{
- Vector comps = (Vector) components.get(seqSetId);
+ Vector comps = components.get(seqSetId);
if (!comps.contains(comp))
{
comps.addElement(comp);
@@ -58,7 +65,7 @@ public class PaintRefresher
}
else
{
- Vector vcoms = new Vector();
+ Vector vcoms = new Vector<>();
vcoms.addElement(comp);
components.put(seqSetId, vcoms);
}
@@ -71,15 +78,14 @@ public class PaintRefresher
return;
}
- Enumeration en = components.keys();
- while (en.hasMoreElements())
+ Iterator it = components.keySet().iterator();
+ while (it.hasNext())
{
- String id = en.nextElement().toString();
- Vector comps = (Vector) components.get(id);
+ Vector comps = components.get(it.next());
comps.removeElement(comp);
- if (comps.size() == 0)
+ if (comps.isEmpty())
{
- components.remove(id);
+ it.remove();
}
}
}
@@ -98,17 +104,17 @@ public class PaintRefresher
}
Component comp;
- Vector comps = (Vector) components.get(id);
+ Vector comps = components.get(id);
if (comps == null)
{
return;
}
- Enumeration e = comps.elements();
- while (e.hasMoreElements())
+ Iterator it = comps.iterator();
+ while (it.hasNext())
{
- comp = (Component) e.nextElement();
+ comp = it.next();
if (comp == source)
{
@@ -117,13 +123,13 @@ public class PaintRefresher
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)
@@ -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 = comp.getSequences();
+ synchronized (alsq)
+ {
+ alsq.add(i, a1[i]);
+ }
}
else
{
@@ -228,18 +240,19 @@ public class PaintRefresher
public static AlignmentPanel[] getAssociatedPanels(String id)
{
- Vector comps = (Vector) components.get(id);
- Vector tmp = new Vector();
+ Vector comps = 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)));
+ tmp.addElement(comps.elementAt(i));
}
}
AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
- for (int ix=0;ix