/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
*/
-
package jalview.appletgui;
import java.awt.*;
import java.awt.event.*;
+import java.util.Vector;
import jalview.datamodel.*;
import jalview.util.UrlLink;
-public class IdPanel
- extends Panel implements MouseListener, MouseMotionListener
+public class IdPanel extends Panel implements MouseListener,
+ MouseMotionListener
{
protected IdCanvas idCanvas;
+
protected AlignViewport av;
+
protected AlignmentPanel alignPanel;
+
ScrollThread scrollThread = null;
int offy;
+
int width;
+
int lastid = -1;
+
boolean mouseDragging = false;
+
java.util.Vector links = new java.util.Vector();
public IdPanel(AlignViewport av, AlignmentPanel parent)
if (links.size() < 1)
{
links = new java.util.Vector();
- links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ links
+ .addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
}
}
Tooltip tooltip;
+
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ // look for non-pos features
+ StringBuffer tooltiptext = new StringBuffer();
+
- if (sequence.getDescription() == null)
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ SequenceFeature sf[] = sequence.getSequenceFeatures();
+ for (int sl=0;sf!=null && sl<sf.length;sl++)
+ {
+ if (sf[sl].begin==sf[sl].end && sf[sl].begin==0)
+ {
+ boolean nl=false;
+ if (sf[sl].getFeatureGroup()!=null) { tooltiptext.append(sf[sl].getFeatureGroup()); nl=true;};
+ if (sf[sl].getType()!=null) { tooltiptext.append(" "); tooltiptext.append(sf[sl].getType()); nl=true;};
+ if (sf[sl].getDescription()!=null) { tooltiptext.append(" "); tooltiptext.append(sf[sl].getDescription()); nl=true;};
+ if (sf[sl].getScore()!=Float.NaN && sf[sl].getScore()!=0f) { tooltiptext.append(" Score = "); tooltiptext.append(sf[sl].getScore()); nl=true;};
+ if (sf[sl].getStatus()!=null && sf[sl].getStatus().length()>0) { tooltiptext.append(" ("); tooltiptext.append(sf[sl].getStatus()); tooltiptext.append(")");nl=true;};
+ if (nl) {tooltiptext.append("\n"); }
+ }
+ }
+
+ if (tooltiptext.length()==0)
{
+ // nothing to display - so clear tooltip if one is visible
if (tooltip != null)
{
tooltip.setVisible(false);
}
tooltip = null;
+ tooltiptext = null;
return;
}
-
if (tooltip == null)
{
- tooltip = new Tooltip(
- sequence.getDisplayId(true)
- + "\n" + sequence.getDescription(), idCanvas);
+ tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString(), idCanvas);
}
else
{
- tooltip.setTip(sequence.getDisplayId(true)
- + "\n" + sequence.getDescription());
+ tooltip.setTip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString());
}
+ tooltiptext=null;
}
public void mouseDragged(MouseEvent e)
return;
}
- //DEFAULT LINK IS FIRST IN THE LINK LIST
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
int seq = alignPanel.seqPanel.findSeq(e);
String id = av.getAlignment().getSequenceAt(seq).getName();
-
+
String target = null;
String url = null;
- int i=0;
+ int i = 0;
while (url == null && i < links.size())
{
// DEFAULT LINK IS FIRST IN THE LINK LIST
}
String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0]==null || urls[0].length()<1)
+ if (urls == null || urls[0] == null || urls[0].length() < 1)
{
url = null;
continue;
{
alignPanel.alignFrame.showURL(url, target);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
scrollThread = new ScrollThread(true);
}
- if (mouseDragging && e.getY() >= getSize().height &&
- av.alignment.getHeight() > av.getEndSeq())
+ if (mouseDragging && e.getY() >= getSize().height
+ && av.alignment.getHeight() > av.getEndSeq())
{
scrollThread = new ScrollThread(false);
}
int seq = alignPanel.seqPanel.findSeq(e);
- if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
- InputEvent.BUTTON3_MASK)
+ if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- APopupMenu popup = new APopupMenu(alignPanel,
- (Sequence) av.getAlignment().
- getSequenceAt(seq), links);
+ 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();
+ for (int l=0,lSize=links.size();l<lSize; l++)
+ {
+ nlinks.addElement(links.elementAt(l));
+ }
+ SequenceFeature sf[] = 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));
+ }
+ }
+ }
+ }
+
+ APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
this.add(popup);
popup.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);
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
+ av.getSelectionGroup().addSequence(
+ av.getAlignment().getSequenceAt(i), false);
}
}
return;
}
- int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
+ int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
// do we need to scroll the panel?
if (av.getStartSeq() > index || av.getEndSeq() < 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)
{
this.up = up;
try
{
Thread.sleep(100);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
}
}
git://source.jalview.org / jalview.git / blobdiff