/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
import jalview.io.SequenceAnnotationReport;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
{
private IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
StringBuffer tip = new StringBuffer(64);
- seqAnnotReport
- .createSequenceAnnotationReport(tip, sequence,
- av.isShowDbRefs(), av.isShowNpFeats(),
- sp.seqCanvas.fr.getMinMax());
+ seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(),
+ sp.seqCanvas.fr.getMinMax());
setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+ tip.toString() + "</html>");
}
return;
}
- Vector links = Preferences.sequenceURLLinks;
+ List<String> links = Preferences.getSequenceURLLinks();
if (links == null || links.size() < 1)
{
return;
{
// DEFAULT LINK IS FIRST IN THE LINK LIST
// BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
- url = links.elementAt(i++).toString();
+ url = links.get(i++).toString();
jalview.util.UrlLink urlLink = null;
try
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
@Override
public void mouseEntered(MouseEvent e)
{
}
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
@Override
public void mouseExited(MouseEvent e)
{
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
// build a new links menu based on the current links + any non-positional
// features
- Vector nlinks = new Vector(Preferences.sequenceURLLinks);
+ List<String> nlinks = new ArrayList<String>(
+ Preferences.getSequenceURLLinks());
SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
{
for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
{
- nlinks.addElement(sf[sl].links.elementAt(l));
+ nlinks.add(sf[sl].links.elementAt(l));
}
}
}
}
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
- nlinks, new Vector(Preferences.getGroupURLLinks()));
+ PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+ Preferences.getGroupURLLinks());
pop.show(this, e.getX(), e.getY());
return;
{
selectSeq(seq);
}
+ // TODO is this addition ok here?
+ av.isSelectionGroupChanged(true);
+
alignPanel.paintAlignment(true);
}