/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.gui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Vector;
+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 javax.swing.*;
+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 jalview.datamodel.*;
-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 $Revision$
boolean mouseDragging = false;
+ private final SequenceAnnotationReport seqAnnotReport;
+
/**
* Creates a new IdPanel object.
*
* @param av
- * DOCUMENT ME!
* @param parent
- * DOCUMENT ME!
*/
public IdPanel(AlignViewport av, AlignmentPanel parent)
{
alignPanel = parent;
idCanvas = new IdCanvas(av);
linkImageURL = getClass().getResource("/images/link.gif").toString();
+ seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
addMouseListener(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;
int seq = Math.max(0, sp.findSeq(e));
- String tmp;
- if (seq > -1 && seq < av.alignment.getHeight())
+ if (seq > -1 && seq < av.getAlignment().getHeight())
{
- SequenceI sequence = av.alignment.getSequenceAt(seq);
- StringBuffer tip = new StringBuffer();
- tip.append("<i>");
-
- int maxWidth = 0;
- if (sequence.getDescription() != null)
- {
- tmp = sequence.getDescription();
- tip.append("<br>" + tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
-
- DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
- if (av.isShowDbRefs() && dbrefs != null)
- {
- for (int i = 0; i < dbrefs.length; i++)
- {
- tip.append("<br>");
- tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
- tip.append(tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
- }
-
- // ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = sequence.getDatasetSequence()
- .getSequenceFeatures();
- SequenceFeature[] tfeat = new SequenceFeature[1];
- if (av.isShowNpFeats() && features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].begin == 0 && features[i].end == 0)
- {
- int sz = -tip.length();
- tfeat[0] = features[i];
- sp.appendFeatures(tip, linkImageURL, 0, tfeat,
- sp.seqCanvas.fr.minmax);
- sz += tip.length();
- maxWidth = Math.max(maxWidth, sz);
- }
- }
- }
-
- if (maxWidth > 60)
- {
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
- }
-
- tip.append("</html>");
-
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ StringBuffer tip = new StringBuffer(64);
+ seqAnnotReport
+ .createSequenceAnnotationReport(tip, sequence,
+ av.isShowDbRefs(), av.isShowNpFeats(),
+ sp.seqCanvas.fr.minmax);
setToolTipText("<html>" + sequence.getDisplayId(true) + " "
- + tip.toString());
+ + tip.toString() + "</html>");
}
}
/**
- * 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;
alignPanel.paintAlignment(true);
}
+ /**
+ * Response to the mouse wheel by scrolling the alignment panel.
+ */
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
if (e.getWheelRotation() > 0)
{
- alignPanel.scrollUp(false);
+ if (e.isShiftDown())
+ {
+ alignPanel.scrollRight(true);
+ }
+ else
+ {
+ alignPanel.scrollUp(false);
+ }
}
else
{
- alignPanel.scrollUp(true);
+ if (e.isShiftDown())
+ {
+ alignPanel.scrollRight(false);
+ }
+ else
+ {
+ alignPanel.scrollUp(true);
+ }
}
}
/**
- * 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))
{
return;
}
- java.util.Vector links = Preferences.sequenceURLLinks;
+ Vector links = Preferences.sequenceURLLinks;
if (links == null || links.size() < 1)
{
return;
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);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
-
}
/**
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
}
if (mouseDragging && (e.getY() >= getHeight())
- && (av.alignment.getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getEndSeq()))
{
scrollThread = new ScrollThread(false);
}
}
/**
- * 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);
- if (javax.swing.SwingUtilities.isRightMouseButton(e))
+ if (SwingUtilities.isRightMouseButton(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);
- SequenceFeature sf[] = sq.getDatasetSequence().getSequenceFeatures();
+ SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
+ .getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
if (e.isShiftDown() && (lastid != -1))
}
/**
- * 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)
{
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), true);
+ av.getAlignment().getSequenceAt(i), i == 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)
{
if (scrollThread != null)
}
/**
- * DOCUMENT ME!
+ * Highlight sequence ids that match the given list, and if necessary scroll
+ * to the start sequence of the list.
*
- * @param found
- * DOCUMENT ME!
+ * @param list
*/
- public void highlightSearchResults(java.util.Vector found)
+ public void highlightSearchResults(List<SequenceI> list)
{
- idCanvas.setHighlighted(found);
+ idCanvas.setHighlighted(list);
- if (found == null)
+ if (list == null)
{
return;
}
- int index = av.alignment.findIndex((SequenceI) found.get(0));
+ int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
running = false;
}
+ @Override
public void run()
{
running = true;
git://source.jalview.org / jalview.git / blobdiff