X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d1dc11de476c5f625a93841ea5d7a5aee3ee8b87;hb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;hp=3e8af1774586b0af7b2b76d3ca189b2339bb2820;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 3e8af17..d1dc11d 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,159 +1,466 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.gui;
+import jalview.datamodel.*;
+
import java.awt.*;
import java.awt.event.*;
-import jalview.datamodel.*;
-
import javax.swing.*;
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {
-
- protected IdCanvas idCanvas;
- protected AlignViewport av;
- protected AlignmentPanel alignPanel;
-
- protected int offy;
- public int width;
- public int lastid;
-
- SequenceGroup selectedSequenceGroup;
-
- public IdPanel(AlignViewport av, AlignmentPanel parent)
- {
- this.av = av;
- alignPanel = parent;
- idCanvas = new IdCanvas(av);
- setLayout(new BorderLayout());
- add(idCanvas, BorderLayout.CENTER);
- addMouseListener(this);
- addMouseMotionListener(this);
- }
-
- public void mouseMoved(MouseEvent e) {}
-
- public void selectSeqs(int start, int end) {
- if (end < start)
- {
- int tmp = start;
- start = end;
- end = tmp;
- }
-
- for (int i = start; i <= end; i++)
- {
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);
- if (av.getSelection().contains(pickedSeq))
- {
- av.getSelection().removeElement(pickedSeq);
- selectedSequenceGroup.deleteSequence(pickedSeq);
- }
- else
- {
- av.getSelection().addElement(pickedSeq);
- if(selectedSequenceGroup==null)
- {
- selectedSequenceGroup = new SequenceGroup();
- av.setRubberbandGroup( selectedSequenceGroup );
- // av.alignment.addGroup( selectedSequenceGroup );
- selectedSequenceGroup.setStartRes(0);
- selectedSequenceGroup.setEndRes( pickedSeq.getSequence().length());
- }
-
- selectedSequenceGroup.addSequence( pickedSeq );
- }
-
- }
-
- alignPanel.seqPanel.seqCanvas.paintFlag=true;
- alignPanel.repaint();
- repaint();
-
- }
-
- public void mouseDragged(MouseEvent e) {
- int y = e.getY();
- if(av.getWrapAlignment())
- y-=2*av.charHeight;
- int seq = av.getIndex(y);
-
- if (seq < lastid)
- selectSeqs(lastid - 1, seq);
- else if (seq > lastid)
- selectSeqs(lastid + 1, seq);
-
- lastid = seq;
-
- return;
- }
-
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() == 2)
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdPanel extends JPanel 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;
+
+ /**
+ * Creates a new IdPanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ */
+ public IdPanel(AlignViewport av, AlignmentPanel parent)
{
- int y = e.getY();
- if(av.getWrapAlignment())
- y-=2*av.charHeight;
-
- int seq = av.getIndex(y);
- String id = av.getAlignment().getSequenceAt(seq).getName();
-
- try{
- jalview.util.BrowserLauncher.openURL(
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
- "]+-vn+2");
- }catch(Exception ex){ex.printStackTrace();}
+ this.av = av;
+ alignPanel = parent;
+ idCanvas = new IdCanvas(av);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
}
- }
- public void mouseEntered(MouseEvent e) { }
- public void mouseExited (MouseEvent e) { }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent e)
+ {
+ int y = e.getY();
+
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
+
+ final int seq = av.getIndex(y);
+ if(seq!=-1)
+ {
+ SequenceI sequence = av.alignment.getSequenceAt(seq);
+ StringBuffer tip = new StringBuffer("");
+ tip.append(sequence.getDisplayId(true));
+ if (av.alignment.getSequenceAt(seq).getDescription() != null)
+ {
+ tip.append("
");
+ tip.append(av.alignment.getSequenceAt(seq).getDescription());
+
+ //ADD NON POSITIONAL SEQUENCE INFO
+ SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
+ if(features!=null)
+ {
+ for(int i=0; i"+features[i].featureGroup
+ +" "+ features[i].getType()+" "+features[i].description);
+ }
+ }
+ }
+
+ tip.append(" |
");
+ }
+ tip.append("");
+ setToolTipText(tip.toString());
+ }
+ }
- public void mousePressed(MouseEvent e) {
- if (e.getClickCount() == 2)
- return;
- int y = e.getY();
- if(av.getWrapAlignment())
- y-=2*av.charHeight;
+ int getWrappedY(int y)
+ {
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ hgap += av.charHeight;
+
+ return y - hgap;
+ }
- int seq = av.getIndex(y);
- if (javax.swing.SwingUtilities.isRightMouseButton(e))
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent e)
{
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
- (Sequence)av.getAlignment().getSequenceAt(seq));
- pop.show(this, e.getX(), y);
- return;
+ mouseDragging = true;
+
+ int y = e.getY();
+
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
+
+ int seq = av.getIndex(y);
+
+ if (seq < 0)
+ {
+ return;
+ }
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid)
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ alignPanel.repaint();
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() < 2)
+ return;
+
+ java.util.Vector links = Preferences.sequenceURLLinks;
+ if (links == null || links.size() < 1)
+ return;
+
+ int y = e.getY();
+
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
+
+ //DEFAULT LINK IS FIRST IN THE LINK LIST
+ int seq = av.getIndex(y);
+ if(seq==-1)
+ return;
+
+ String id = av.getAlignment().getSequenceAt(seq).getName();
+ if (id.indexOf("|") > -1)
+ 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);
+
+ 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 );
+ ex.printStackTrace();
+ }
+ }
- if(av.getRubberbandGroup()!=null && (av.getRubberbandGroup().getSize() == av.getSelection().size()))
- selectedSequenceGroup = av.getRubberbandGroup();
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+ {
+ scrollThread = new ScrollThread(true);
+ }
+
+ if (mouseDragging && (e.getY() >= getHeight()) &&
+ (av.alignment.getHeight() > av.getEndSeq()))
+ {
+ scrollThread = new ScrollThread(false);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ return;
+ }
+
+ int y = e.getY();
+
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
+
+ int seq = av.getIndex(y);
+
+ if (seq == -1)
+ {
+ return;
+ }
+
+ if (javax.swing.SwingUtilities.isRightMouseButton(e))
+ {
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
+ (Sequence) av.getAlignment().getSequenceAt(seq),
+ Preferences.sequenceURLLinks);
+ pop.show(this, e.getX(), y);
+
+ return;
+ }
+
+ /* if (!e.isControlDown() && !e.isShiftDown() &&
+ (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
+ {
+ System.out.println("no modifiers");
+ SequenceGroup selection = new SequenceGroup();
+ SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
+ seq));
+ selection.setStartRes(0);
+ selection.setEndRes(av.alignment.getWidth() - 1);
+
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ selection.addSequence(sg.getSequenceAt(i), true);
+ }
+
+ av.setSelectionGroup(selection);
+
+ return;
+ }*/
+
+ 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);
+ }
+
+
+
+ if (e.isShiftDown() && (lastid != -1))
+ {
+ selectSeqs(lastid, seq);
+ }
+ else
+ {
+ selectSeq(seq);
+ }
+
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ void selectSeq(int seq)
+ {
+ lastid = seq;
- if (selectedSequenceGroup == null)
+ SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ */
+ void selectSeqs(int start, int end)
{
- selectedSequenceGroup = new SequenceGroup();
- av.setRubberbandGroup(selectedSequenceGroup);
+ if(av.getSelectionGroup()==null)
+ return;
+
+ lastid = start;
+
+ if (end < start)
+ {
+ int tmp = start;
+ start = end;
+ end = tmp;
+ lastid = end;
+ }
+
+ for (int i = start; i <= end; i++)
+ {
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ true);
+ }
}
- selectedSequenceGroup.setStartRes(0);
- selectedSequenceGroup.setEndRes(av.getAlignment().getWidth() - 1);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
- if (seq != -1)
- selectSeqs(seq, seq);
+ mouseDragging = false;
+ PaintRefresher.Refresh(av.alignment);
+ }
- lastid = seq;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param found DOCUMENT ME!
+ */
+ public void highlightSearchResults(java.util.Vector found)
+ {
+ idCanvas.setHighlighted(found);
+ if (found == null)
+ {
+ return;
+ }
- return;
- }
+ int index = av.alignment.findIndex((SequenceI) found.get(0));
- public void mouseReleased(MouseEvent e)
- {
- lastid = -1;
- PaintRefresher.Refresh(this);
- selectedSequenceGroup = null;
- }
+ // do we need to scroll the panel?
+ 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
+ {
+ boolean running = false;
+ boolean up = true;
+
+ public ScrollThread(boolean up)
+ {
+ this.up = up;
+ start();
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ public void run()
+ {
+ running = true;
+
+ 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.repaint();
+
+ try
+ {
+ Thread.sleep(100);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
}