/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 javax.swing.*;
-
-import jalview.datamodel.*;
+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.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
+public class IdPanel extends JPanel implements MouseListener,
+ MouseMotionListener, MouseWheelListener
{
- protected IdCanvas idCanvas;
- protected AlignViewport av;
+ private IdCanvas idCanvas;
+
+ protected AlignmentViewport av;
+
protected AlignmentPanel alignPanel;
+
ScrollThread scrollThread = null;
+
+ String linkImageURL;
+
int offy;
+
// int width;
int lastid = -1;
+
boolean mouseDragging = false;
+ private final SequenceAnnotationReport seqAnnotReport;
+
/**
* Creates a new IdPanel object.
- *
- * @param av DOCUMENT ME!
- * @param parent DOCUMENT ME!
+ *
+ * @param av
+ * @param parent
*/
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!
- *
- * @param e 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)
{
- int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
- String tmp;
- if (seq > -1 && seq < av.alignment.getHeight())
+ SeqPanel sp = alignPanel.getSeqPanel();
+ int seq = Math.max(0, sp.findSeq(e));
+ 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 (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();
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].begin == 0 && features[i].end == 0)
- {
- tmp = features[i].featureGroup
- + " " + features[i].getType() + " " +
- features[i].description;
- tip.append("<br>" + tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
- }
- }
-
- if(maxWidth > 60)
- {
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
- }
-
- tip.append("</html>");
-
- setToolTipText("<html>"+sequence.getDisplayId(true)+tip.toString());
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ StringBuffer tip = new StringBuffer(64);
+ seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(),
+ sp.seqCanvas.fr.getMinMax());
+ setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+ + tip.toString() + "</html>");
}
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Responds to a mouse drag by selecting the sequences under the dragged
+ * region.
+ *
+ * @param e
*/
+ @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)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ if (e.getWheelRotation() > 0)
+ {
+ if (e.isShiftDown())
+ {
+ alignPanel.scrollRight(true);
+ }
+ else
{
alignPanel.scrollUp(false);
}
+ }
+ else
+ {
+ if (e.isShiftDown())
+ {
+ alignPanel.scrollRight(false);
+ }
else
{
alignPanel.scrollUp(true);
}
+ }
}
/**
- * DOCUMENT ME!
- *
- * @param e 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
*/
+ @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;
}
- int seq = alignPanel.seqPanel.findSeq(e);
-
- //DEFAULT LINK IS FIRST IN THE LINK LIST
-
+ int seq = alignPanel.getSeqPanel().findSeq(e);
+ String url = null;
+ int i = 0;
String id = av.getAlignment().getSequenceAt(seq).getName();
- if (id.indexOf("|") > -1)
+ while (url == null && i < links.size())
{
- id = id.substring(id.lastIndexOf("|") + 1);
- }
-
- String url = links.elementAt(0).toString();
- url = url.substring(url.indexOf("|") + 1);
-
- int index = url.indexOf("$SEQUENCE_ID$");
- url = url.substring(0, index) + id + url.substring(index + 13);
+ // 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();
+ jalview.util.UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(url);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
+ foo);
+ url = null;
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ url = null;
+ continue;
+ }
+ String urls[] = urlLink.makeUrls(id, true);
+ if (urls == null || urls[0] == null || urls[0].length() < 4)
+ {
+ url = null;
+ continue;
+ }
+ // just take first URL made from regex
+ url = urls[1];
+ }
try
{
jalview.util.BrowserLauncher.openURL(url);
- }
- catch (Exception ex)
+ } 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);
+ 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!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
scrollThread = new ScrollThread(true);
}
- if (mouseDragging && (e.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
+ if (mouseDragging && (e.getY() >= getHeight())
+ && (av.getAlignment().getHeight() > av.getEndSeq()))
{
scrollThread = new ScrollThread(false);
}
}
/**
- * DOCUMENT ME!
- *
- * @param e 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
*/
+ @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 (SwingUtilities.isRightMouseButton(e))
{
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
- (Sequence) av.getAlignment().getSequenceAt(seq),
- Preferences.sequenceURLLinks);
+ 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.getSequenceFeatures();
+ for (int sl = 0; sf != null && sl < sf.length; sl++)
+ {
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ {
+ if (sf[sl].links != null && sf[sl].links.size() > 0)
+ {
+ for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(sf[sl].links.elementAt(l));
+ }
+ }
+ }
+ }
+
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
+ nlinks, new Vector(Preferences.getGroupURLLinks()));
pop.show(this, e.getX(), e.getY());
return;
}
- if ( (av.getSelectionGroup() == null) ||
- ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+ if ((av.getSelectionGroup() == null)
+ || ((!e.isControlDown() && !e.isShiftDown()) && av
+ .getSelectionGroup() != null))
{
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))
{
selectSeq(seq);
}
+ // TODO is this addition ok here?
+ av.isSelectionGroupChanged(true);
alignPanel.paintAlignment(true);
}
/**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ * Toggle whether the sequence is part of the current selection group.
+ *
+ * @param seq
*/
void selectSeq(int seq)
{
}
/**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
+ * Add contiguous rows of the alignment to the current selection group. Does
+ * nothing if there is no selection group.
+ *
+ * @param start
+ * @param end
*/
void selectSeqs(int start, int end)
{
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
- true);
+ av.getSelectionGroup().addSequence(
+ av.getAlignment().getSequenceAt(i), i == end);
}
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Respond to mouse released. Refreshes the display and triggers broadcast of
+ * the new selection group to any listeners.
+ *
+ * @param e
*/
+ @Override
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
}
/**
- * DOCUMENT ME!
- *
- * @param found DOCUMENT ME!
+ * Highlight sequence ids that match the given list, and if necessary scroll
+ * to the start sequence of the list.
+ *
+ * @param list
*/
- public void highlightSearchResults(java.util.Vector found)
+ public void highlightSearchResults(List<SequenceI> list)
{
- idCanvas.setHighlighted(found);
+ getIdCanvas().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))
+ if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
{
alignPanel.setScrollValues(av.getStartRes(), index);
}
}
+ 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
+ class ScrollThread extends Thread
{
boolean running = false;
+
boolean up = true;
public ScrollThread(boolean up)
running = false;
}
+ @Override
public void run()
{
running = true;
try
{
Thread.sleep(100);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
git://source.jalview.org / jalview.git / blobdiff