X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=4a4ea63f29c199444f6c5bc5ec35f5b5afdd33bc;hb=5aeb9ce3b99be8cbe7ca47c04a31dca3e3bbc282;hp=1889eb603a7a53fb915dc1d7ebe994bd66c20040;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 1889eb6..4a4ea63 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,231 +1,441 @@
+/*
+ * 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;
- ScrollThread scrollThread = null;
+/**
+ * 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)
+ {
+ this.av = av;
+ alignPanel = parent;
+ idCanvas = new IdCanvas(av);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent e)
+ {
+ int y = e.getY();
+
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
+
+ int seq = av.getIndex(y);
+ if(seq!=-1)
+ {
+ StringBuffer tip = new StringBuffer("");
+ tip.append(av.alignment.getSequenceAt(seq).getDisplayId(true, true));
+ if (av.alignment.getSequenceAt(seq).getDescription() != null)
+ {
+ tip.append("
");
+ tip.append(av.alignment.getSequenceAt(seq).getDescription());
+ tip.append(" |
");
+ }
+ tip.append("");
+ setToolTipText(tip.toString());
+ }
- int offy;
- int width;
- int lastid = -1;
- boolean mouseDragging = false;
+ }
- 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);
- }
+ int getWrappedY(int y)
+ {
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ hgap += av.charHeight;
- public void mouseMoved(MouseEvent e) {}
+ return y - hgap;
+ }
- public void mouseDragged(MouseEvent e) {
- mouseDragging = true;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent e)
+ {
+ mouseDragging = true;
- int y = e.getY();
- if(av.getWrapAlignment())
- y-=2*av.charHeight;
- int seq = av.getIndex(y);
+ int y = e.getY();
- if(seq<0)
- return;
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
- if (seq < lastid)
- selectSeqs(lastid - 1, seq);
- else if (seq > lastid)
- selectSeqs(lastid + 1, seq);
+ int seq = av.getIndex(y);
- lastid = seq;
- alignPanel.repaint();
- }
+ if (seq < 0)
+ {
+ return;
+ }
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() == 2)
- {
- 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();}
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid)
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ alignPanel.repaint();
}
- }
- public void mouseEntered(MouseEvent e)
- {
- if(scrollThread!=null)
- scrollThread.running = false;
- }
- public void mouseExited (MouseEvent e)
- {
- if(av.getWrapAlignment())
- return;
+ /**
+ * 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(mouseDragging && e.getY()<0 && av.getStartSeq()>0)
+ if (av.getWrapAlignment())
+ {
+ y = getWrappedY(y);
+ }
+
+ //DEFAULT LINK IS FIRST IN THE LINK LIST
+ int seq = av.getIndex(y);
+ String id = av.getAlignment().getSequenceAt(seq).getName();
+
+ 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();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e)
{
- scrollThread = new ScrollThread(true);
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
}
- if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq())
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e)
{
- scrollThread = new ScrollThread(false);
+ 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);
+ }
- public void mousePressed(MouseEvent e) {
- if (e.getClickCount() == 2)
- return;
+ 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));
+ pop.show(this, e.getX(), y);
+
+ return;
+ }
+
+ if (!e.isControlDown() && !e.isShiftDown() &&
+ (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
+ {
+ SequenceGroup selection = new SequenceGroup();
+ SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
+ seq));
+ selection.setStartRes(0);
+ selection.setEndRes(av.alignment.getWidth() - 1);
- int y = e.getY();
- if(av.getWrapAlignment())
- y-=2*av.charHeight;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ selection.addSequence(sg.getSequenceAt(i), true);
+ }
- int seq = av.getIndex(y);
- if (seq == -1)
- return;
+ av.setSelectionGroup(selection);
+
+ return;
+ }
+
+ if ((av.getSelectionGroup() == null) ||
+ (!e.isControlDown() && (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();
+ }
- if (javax.swing.SwingUtilities.isRightMouseButton(e))
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ void selectSeq(int seq)
{
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
- (Sequence)av.getAlignment().getSequenceAt(seq));
- pop.show(this, e.getX(), y);
- return;
+ lastid = seq;
+
+ SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
}
- if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ */
+ void selectSeqs(int start, int end)
{
+ if(av.getSelectionGroup()==null)
+ return;
- SequenceGroup selection = new SequenceGroup();
- SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
- selection.setStartRes(0);
- selection.setEndRes(av.alignment.getWidth());
- for (int i =0; i< sg.getSize(); i++)
- selection.addSequence(sg.getSequenceAt(i));
+ lastid = start;
+
+ if (end < start)
+ {
+ int tmp = start;
+ start = end;
+ end = tmp;
+ lastid = end;
+ }
- av.setSelectionGroup(selection);
- return;
+ for (int i = start; i <= end; i++)
+ {
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ true);
+ }
}
- if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))
- av.setSelectionGroup(new SequenceGroup());
-
- av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth());
-
- if(e.isShiftDown() && lastid!=-1)
- selectSeqs(lastid, seq);
- else
- selectSeq(seq);
-
- alignPanel.seqPanel.seqCanvas.paintFlag=true;
- alignPanel.repaint();
- repaint();
- }
-
- void selectSeq(int seq)
- {
- lastid = seq;
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq);
- }
-
- void selectSeqs(int start, int end) {
-
- 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));
-
- }
-
-
- public void mouseReleased(MouseEvent e)
- {
- if(scrollThread!=null)
- scrollThread.running = false;
-
- mouseDragging = false;
- PaintRefresher.Refresh(this);
- }
-
- // 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)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent e)
{
- this.up = up;
- start();
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+
+ mouseDragging = false;
+ PaintRefresher.Refresh(av.alignment);
}
- public void stopScrolling()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param found DOCUMENT ME!
+ */
+ public void highlightSearchResults(java.util.Vector found)
{
- running = false;
+ idCanvas.setHighlighted(found);
+
+ if (found == null)
+ {
+ return;
+ }
+
+ int index = av.alignment.findIndex((SequenceI) found.get(0));
+
+ // do we need to scroll the panel?
+ if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+ {
+ alignPanel.setScrollValues(av.getStartRes(), index);
+ }
}
- public void run()
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread extends Thread
{
- 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();
+ boolean running = false;
+ boolean up = true;
- if (seq < lastid)
- selectSeqs(lastid - 1, seq);
- else if (seq > lastid)
- selectSeqs(lastid + 1, seq);
+ public ScrollThread(boolean up)
+ {
+ this.up = up;
+ start();
+ }
- lastid = seq;
+ public void stopScrolling()
+ {
+ running = false;
}
- else
- running = false;
- alignPanel.repaint();
- try
+ public void run()
{
- Thread.sleep(100);
+ 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)
+ {
+ }
+ }
}
- catch (Exception ex)
- {}
- }
}
}
-
-}