/*
- * 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.
*
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+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.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
import java.util.List;
import java.util.Vector;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.SequenceAnnotationReport;
-import jalview.util.UrlLink;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
+ * This panel hosts alignment sequence ids and responds to mouse clicks on them,
+ * as well as highlighting ids matched by a search from the Find menu.
*
* @author $author$
* @version $Revision$
public class IdPanel extends JPanel implements MouseListener,
MouseMotionListener, MouseWheelListener
{
- protected IdCanvas idCanvas;
+ private IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
* Creates a new IdPanel object.
*
* @param av
- * DOCUMENT ME!
* @param parent
- * DOCUMENT ME!
*/
public IdPanel(AlignViewport av, AlignmentPanel parent)
{
this.av = av;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ setIdCanvas(new IdCanvas(av));
linkImageURL = getClass().getResource("/images/link.gif").toString();
seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
setLayout(new BorderLayout());
- add(idCanvas, BorderLayout.CENTER);
+ add(getIdCanvas(), BorderLayout.CENTER);
addMouseListener(this);
addMouseMotionListener(this);
addMouseWheelListener(this);
}
/**
- * DOCUMENT ME!
+ * Respond to mouse movement by constructing tooltip text for the sequence id
+ * under the mouse.
*
* @param e
* DOCUMENT ME!
@Override
public void mouseMoved(MouseEvent e)
{
- SeqPanel sp = alignPanel.seqPanel;
+ SeqPanel sp = alignPanel.getSeqPanel();
int seq = Math.max(0, sp.findSeq(e));
if (seq > -1 && seq < av.getAlignment().getHeight())
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- StringBuffer tip = new StringBuffer();
- seqAnnotReport
- .createSequenceAnnotationReport(tip, sequence,
- av.isShowDbRefs(), av.isShowNpFeats(),
- sp.seqCanvas.fr.minmax);
- setToolTipText("<html>" + sequence.getDisplayId(true) + " "
- + tip.toString() + "</html>");
+ StringBuffer tip = new StringBuffer(64);
+ seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(),
+ sp.seqCanvas.fr.getMinMax());
+ setToolTipText(JvSwingUtils.wrapTooltip(true,
+ sequence.getDisplayId(true) + " " + tip.toString()));
}
}
/**
- * DOCUMENT ME!
+ * Responds to a mouse drag by selecting the sequences under the dragged
+ * region.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
- int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+ int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
if (seq < lastid)
{
alignPanel.paintAlignment(true);
}
+ /**
+ * Response to the mouse wheel by scrolling the alignment panel.
+ */
@Override
public void mouseWheelMoved(MouseWheelEvent e)
{
if (e.isShiftDown())
{
alignPanel.scrollRight(true);
-
}
else
{
}
/**
- * DOCUMENT ME!
+ * Handle a mouse click event. Currently only responds to a double-click. The
+ * action is to try to open a browser window at a URL that searches for the
+ * selected sequence id. The search URL is configured in Preferences |
+ * Connections | URL link from Sequence ID. For example:
+ *
+ * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseClicked(MouseEvent e)
{
- if (e.getClickCount() < 2)
+ /*
+ * Ignore single click. Ignore 'left' click followed by 'right' click (user
+ * selects a row then its pop-up menu).
+ */
+ if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
{
+ // reinstate isRightMouseButton check to ignore mouse-related popup events
+ // note - this does nothing on default MacBookPro force-trackpad config!
return;
}
- java.util.Vector links = Preferences.sequenceURLLinks;
+ Vector links = Preferences.sequenceURLLinks;
if (links == null || links.size() < 1)
{
return;
}
- int seq = alignPanel.seqPanel.findSeq(e);
+ int seq = alignPanel.getSeqPanel().findSeq(e);
String url = null;
int i = 0;
String id = av.getAlignment().getSequenceAt(seq).getName();
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "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!
+ * Respond to a mouse press. Does nothing for (left) double-click as this is
+ * handled by mouseClicked().
+ *
+ * Right mouse down - construct and show context menu.
+ *
+ * Ctrl-down or Shift-down - add to or expand current selection group if there
+ * is one.
+ *
+ * Mouse down - select this sequence.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent e)
{
- if (e.getClickCount() == 2)
+ if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
{
return;
}
- int seq = alignPanel.seqPanel.findSeq(e);
+ int seq = alignPanel.getSeqPanel().findSeq(e);
- if (javax.swing.SwingUtilities.isRightMouseButton(e))
+ if (e.isPopupTrigger())
{
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);
- SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
- .getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ Vector<String> nlinks = new Vector<String>(
+ Preferences.sequenceURLLinks);
+ SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
+ if (sfs != null)
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ for (SequenceFeature sf : sfs)
{
- if (sf[sl].links != null && sf[sl].links.size() > 0)
+ if (sf.begin == sf.end && sf.begin == 0)
{
- for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+ if (sf.links != null && sf.links.size() > 0)
{
- nlinks.addElement(sf[sl].links.elementAt(l));
+ for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(sf.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;
}
-
if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
- .getSelectionGroup() != null))
+ || (!jalview.util.Platform.isControlDown(e)
+ && !e.isShiftDown() && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
{
selectSeq(seq);
}
+ // TODO is this addition ok here?
+ av.isSelectionGroupChanged(true);
+
alignPanel.paintAlignment(true);
}
/**
- * DOCUMENT ME!
+ * Toggle whether the sequence is part of the current selection group.
*
* @param seq
- * DOCUMENT ME!
*/
void selectSeq(int seq)
{
}
/**
- * DOCUMENT ME!
+ * Add contiguous rows of the alignment to the current selection group. Does
+ * nothing if there is no selection group.
*
* @param start
- * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
*/
void selectSeqs(int start, int end)
{
}
/**
- * DOCUMENT ME!
+ * Respond to mouse released. Refreshes the display and triggers broadcast of
+ * the new selection group to any listeners.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent e)
}
/**
- * DOCUMENT ME!
+ * Highlight sequence ids that match the given list, and if necessary scroll
+ * to the start sequence of the list.
*
* @param list
- * DOCUMENT ME!
*/
public void highlightSearchResults(List<SequenceI> list)
{
- idCanvas.setHighlighted(list);
+ getIdCanvas().setHighlighted(list);
if (list == null)
{
}
}
+ public IdCanvas getIdCanvas()
+ {
+ return idCanvas;
+ }
+
+ public void setIdCanvas(IdCanvas idCanvas)
+ {
+ this.idCanvas = idCanvas;
+ }
+
// this class allows scrolling off the bottom of the visible alignment
class ScrollThread extends Thread
{