/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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
+ * 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.
+ *
+ * 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.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+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.util.UrlLink;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.Timer;
+import javax.swing.ToolTipManager;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
/**
- * 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;
+ private IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
ScrollThread scrollThread = null;
- String linkImageURL;
-
int offy;
// int width;
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)
{
this.av = av;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
- linkImageURL = getClass().getResource("/images/link.gif").toString();
+ setIdCanvas(new IdCanvas(av));
+ seqAnnotReport = new SequenceAnnotationReport(true);
setLayout(new BorderLayout());
- add(idCanvas, BorderLayout.CENTER);
+ add(getIdCanvas(), BorderLayout.CENTER);
addMouseListener(this);
addMouseMotionListener(this);
addMouseWheelListener(this);
}
/**
- * DOCUMENT ME!
- *
+ * Responds to mouse movement by setting tooltip text for the sequence id
+ * under the mouse (or possibly annotation label, when in wrapped mode)
+ *
* @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.getAlignment().getHeight())
+ SeqPanel sp = alignPanel.getSeqPanel();
+ MousePos pos = sp.findMousePosition(e);
+ if (pos.isOverAnnotation())
{
- SequenceI sequence = av.getAlignment().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)
+ /*
+ * mouse is over an annotation label in wrapped mode
+ */
+ AlignmentAnnotation[] anns = av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation annotation = anns[pos.annotationIndex];
+ setToolTipText(AnnotationLabels.getTooltip(annotation));
+ alignPanel.alignFrame.setStatus(
+ AnnotationLabels.getStatusMessage(annotation, anns));
+ }
+ else
+ {
+ int seq = Math.max(0, pos.seqIndex);
+ if (seq < av.getAlignment().getHeight())
{
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ StringBuilder tip = new StringBuilder(64);
+ tip.append(sequence.getDisplayId(true)).append(" ");
+ seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
+ setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString()));
+
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(String.valueOf(seq + 1))
+ .append(" ID: ")
+ .append(sequence.getName());
+ alignPanel.alignFrame.setStatus(text.toString());
}
-
- tip.append("</html>");
-
- setToolTipText("<html>" + 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));
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ if (pos.isOverAnnotation())
+ {
+ // mouse is over annotation label in wrapped mode
+ return;
+ }
+
+ int seq = Math.max(0, pos.seqIndex);
if (seq < lastid)
{
}
lastid = seq;
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
+ /**
+ * Response to the mouse wheel by scrolling the alignment panel.
+ */
@Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
- alignPanel.scrollUp(false);
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(true);
+ }
+ else
+ {
+ av.getRanges().scrollUp(false);
+ }
}
- else
+ else if (wheelRotation < 0)
{
- alignPanel.scrollUp(true);
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(false);
+ }
+ else
+ {
+ av.getRanges().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))
{
+ // 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;
- if (links == null || links.size() < 1)
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ int seq = pos.seqIndex;
+ if (pos.isOverAnnotation() || seq < 0)
{
return;
}
- int seq = alignPanel.seqPanel.findSeq(e);
- String url = null;
- int i = 0;
String id = av.getAlignment().getSequenceAt(seq).getName();
- while (url == null && i < links.size())
- {
- // 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 url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
- 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)
{
- 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);
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
-
}
/**
- * DOCUMENT ME!
- *
+ * On (re-)entering the panel, stop any scrolling
+ *
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
{
+ stopScrolling();
+ }
+
+ /**
+ * Interrupts the scroll thread if one is running
+ */
+ void stopScrolling()
+ {
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
+ scrollThread = null;
}
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
return;
}
- if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+ if (mouseDragging)
{
- scrollThread = new ScrollThread(true);
+ /*
+ * on mouse drag above or below the panel, start
+ * scrolling if there are more sequences to show
+ */
+ ViewportRanges ranges = av.getRanges();
+ if (e.getY() < 0 && ranges.getStartSeq() > 0)
+ {
+ startScrolling(true);
+ }
+ else if (e.getY() >= getHeight()
+ && ranges.getEndSeq() <= av.getAlignment().getHeight())
+ {
+ startScrolling(false);
+ }
}
+ }
- if (mouseDragging && (e.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ /**
+ * Starts scrolling either up or down
+ *
+ * @param up
+ */
+ void startScrolling(boolean up)
+ {
+ scrollThread = new ScrollThread(up);
+ if (Platform.isJS())
{
- scrollThread = new ScrollThread(false);
+ /*
+ * for JalviewJS using Swing Timer
+ */
+ Timer t = new Timer(20, new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (scrollThread != null)
+ {
+ // if (!scrollOnce() {t.stop();}) gives compiler error :-(
+ scrollThread.scrollOnce();
+ }
+ }
+ });
+ t.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (scrollThread == null)
+ {
+ // IdPanel.stopScrolling called
+ t.stop();
+ }
+ }
+ });
+ t.start();
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ scrollThread.start();
}
}
/**
- * 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))
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
+ if (e.isPopupTrigger()) // Mac reports this in mousePressed
{
- 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++)
- {
- 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());
+ showPopupMenu(e, pos);
+ return;
+ }
+ /*
+ * defer right-mouse click handling to mouseReleased on Windows
+ * (where isPopupTrigger() will answer true)
+ * NB isRightMouseButton is also true for Cmd-click on Mac
+ */
+ if (Platform.isWinRightButton(e))
+ {
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);
if (e.isShiftDown() && (lastid != -1))
{
- selectSeqs(lastid, seq);
+ selectSeqs(lastid, pos.seqIndex);
}
else
{
- selectSeq(seq);
+ selectSeq(pos.seqIndex);
}
- alignPanel.paintAlignment(true);
+
+ av.isSelectionGroupChanged(true);
+
+ alignPanel.paintAlignment(false, false);
}
/**
- * DOCUMENT ME!
- *
+ * Build and show the popup-menu at the right-click mouse position
+ *
+ * @param e
+ */
+ void showPopupMenu(MouseEvent e, MousePos pos)
+ {
+ if (pos.isOverAnnotation())
+ {
+ showAnnotationMenu(e, pos);
+ return;
+ }
+
+ Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
+ if (sq != null)
+ {
+ PopupMenu pop = new PopupMenu(alignPanel, sq,
+ Preferences.getGroupURLLinks());
+ pop.show(this, e.getX(), e.getY());
+ }
+ }
+
+ /**
+ * On right mouse click on a Consensus annotation label, shows a limited popup
+ * menu, with options to configure the consensus calculation and rendering.
+ *
+ * @param e
+ * @param pos
+ * @see AnnotationLabels#showPopupMenu(MouseEvent)
+ */
+ void showAnnotationMenu(MouseEvent e, MousePos pos)
+ {
+ if (pos.annotationIndex == -1)
+ {
+ return;
+ }
+ AlignmentAnnotation[] anns = this.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (anns == null || pos.annotationIndex >= anns.length)
+ {
+ return;
+ }
+ AlignmentAnnotation ann = anns[pos.annotationIndex];
+ if (!ann.label.contains("Consensus"))
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop);
+ pop.show(this, e.getX(), e.getY());
+ }
+
+ /**
+ * Toggle whether the sequence is part of the current selection group.
+ *
* @param seq
- * DOCUMENT ME!
*/
void selectSeq(int seq)
{
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);
}
/**
- * 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.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ false);
}
}
/**
- * 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)
{
- scrollThread.running = false;
+ stopScrolling();
}
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
// always send selection message when mouse is released
av.sendSelection();
+
+ if (e.isPopupTrigger()) // Windows reports this in mouseReleased
+ {
+ showPopupMenu(e, pos);
+ }
}
/**
- * 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)
+ if (list == null || list.isEmpty())
{
return;
}
int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
- if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+ if ((av.getRanges().getStartSeq() > index)
+ || (av.getRanges().getEndSeq() < index))
{
- alignPanel.setScrollValues(av.getStartRes(), index);
+ av.getRanges().setStartSeq(index);
}
}
- // this class allows scrolling off the bottom of the visible alignment
+ public IdCanvas getIdCanvas()
+ {
+ return idCanvas;
+ }
+
+ public void setIdCanvas(IdCanvas idCanvas)
+ {
+ this.idCanvas = idCanvas;
+ }
+
+ /**
+ * Performs scrolling of the visible alignment up or down, adding newly
+ * visible sequences to the current selection
+ */
class ScrollThread extends Thread
{
- boolean running = false;
+ private boolean running = false;
- boolean up = true;
+ private boolean up;
+ /**
+ * Constructor for a thread that scrolls either up or down
+ *
+ * @param up
+ */
public ScrollThread(boolean up)
{
this.up = up;
- start();
+ setName("IdPanel$ScrollThread$" + String.valueOf(up));
}
+ /**
+ * Sets a flag to stop the scrolling
+ */
public void stopScrolling()
{
running = false;
}
+ /**
+ * Scrolls the alignment either up or down, one row at a time, adding newly
+ * visible sequences to the current selection. Speed is limited to a maximum
+ * of ten rows per second. The thread exits when the end of the alignment is
+ * reached or a flag is set to stop it by a call to stopScrolling.
+ */
@Override
public void run()
{
while (running)
{
- if (alignPanel.scrollUp(up))
- {
- // scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
-
- if (!up)
- {
- seq = av.getEndSeq();
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
- }
- else
- {
- running = false;
- }
-
- alignPanel.paintAlignment(false);
-
+ running = scrollOnce();
try
{
Thread.sleep(100);
{
}
}
+ IdPanel.this.scrollThread = null;
+ }
+
+ /**
+ * Scrolls one row up or down. Answers true if a scroll could be done, false
+ * if not (top or bottom of alignment reached).
+ */
+ boolean scrollOnce()
+ {
+ ViewportRanges ranges = IdPanel.this.av.getRanges();
+ if (ranges.scrollUp(up))
+ {
+ int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+ int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+ IdPanel.this.selectSeqs(fromSeq, toSeq);
+ lastid = toSeq;
+ alignPanel.paintAlignment(false, false);
+ return true;
+ }
+
+ return false;
}
}
}