/*
- * 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
- * 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.
- *
- * 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
+ * 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
+ *
+ * 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
+ * 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/>.
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
+import java.util.Vector;
+
import javax.swing.*;
import jalview.datamodel.*;
/**
* DOCUMENT ME!
- *
+ *
* @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;
+
protected AlignmentPanel alignPanel;
+
ScrollThread scrollThread = null;
+
+ String linkImageURL;
+
int offy;
+
// int width;
int lastid = -1;
+
boolean mouseDragging = false;
/**
* Creates a new IdPanel object.
- *
- * @param av DOCUMENT ME!
- * @param parent DOCUMENT ME!
+ *
+ * @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();
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
addMouseListener(this);
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent e)
{
- int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+ SeqPanel sp = alignPanel.seqPanel;
+ int seq = Math.max(0, sp.findSeq(e));
String tmp;
if (seq > -1 && seq < av.alignment.getHeight())
{
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- tip.append("<br>"+tmp);
+ tip.append("<br>" + tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
- if (dbrefs != null)
+ if (av.isShowDbRefs() && dbrefs != null)
{
for (int i = 0; i < dbrefs.length; i++)
{
}
}
-
- //ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = sequence.getDatasetSequence().
- getSequenceFeatures();
- if (features != null)
+ // 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)
{
- tmp = features[i].featureGroup
- + " " + features[i].getType() + " " +
- features[i].description;
- tip.append("<br>" + tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
+ 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)
+ if (maxWidth > 60)
{
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
+ 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());
+ setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+ + tip.toString());
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent e)
{
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.scrollUp(true);
- }
+ if (e.getWheelRotation() > 0)
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.scrollUp(true);
+ }
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent e)
{
}
String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0]==null || urls[0].length()<4)
+ if (urls == null || urls[0] == null || urls[0].length() < 4)
{
url = null;
continue;
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);
+ 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);
ex.printStackTrace();
}
-
+
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent e)
{
scrollThread = new ScrollThread(true);
}
- if (mouseDragging && (e.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
+ if (mouseDragging && (e.getY() >= getHeight())
+ && (av.alignment.getHeight() > av.getEndSeq()))
{
scrollThread = new ScrollThread(false);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent e)
{
if (javax.swing.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.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());
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);
{
selectSeq(seq);
}
-
alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
void selectSeq(int seq)
{
/**
* DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
+ *
+ * @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), true);
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent e)
{
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
}
/**
* DOCUMENT ME!
- *
- * @param found DOCUMENT ME!
+ *
+ * @param found
+ * DOCUMENT ME!
*/
public void highlightSearchResults(java.util.Vector found)
{
return;
}
- int index = av.alignment.findIndex( (SequenceI) found.get(0));
+ int index = av.alignment.findIndex((SequenceI) found.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);
}
}
// 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)
try
{
Thread.sleep(100);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
git://source.jalview.org / jalview.git / blobdiff