/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
}
} catch (InvalidSessionDocumentException e)
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
MessageManager
.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
Thread udthread = new Thread(new Runnable()
{
+ @Override
public void run()
{
Cache.log.info("Jalview updating to the Vamsas Session.");
final VamsasApplication client = this;
vclient.addDocumentUpdateHandler(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
Cache.log.debug("Dealing with document update event.");
uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (client.promptUser)
{
Cache.log
.debug("Asking user if the vamsas session should be stored.");
- int reply = JOptionPane
+ int reply = JvOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
"The current VAMSAS session has unsaved data - do you want to save it ?",
"VAMSAS Session Shutdown",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
Cache.log.debug("Prompting for vamsas store filename.");
Desktop.instance.vamsasSave_actionPerformed(null);
{
String last = null;
+ @Override
public void handleMessage(Message message)
{
if (vobj2jv == null)
selecter = new SelectionListener()
{
+ @Override
public void selection(SequenceGroup seqsel,
ColumnSelection colsel, SelectionSource source)
{
{
// gather selected columns outwith the sequence positions
// too
- for (Object obj : colsel.getSelected())
+ for (Integer ival : colsel.getSelected())
{
- int ival = ((Integer) obj).intValue();
Pos p = new Pos();
- p.setI(ival + 1);
+ p.setI(ival.intValue() + 1);
range.addPos(p);
}
}