X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d80c4b86144bc03388f143e62c974c1afaea856c;hb=a0205942210037198f48eb20480efe88d5eb951e;hp=cb13692444af52aca625250adeec02b2353caa56;hpb=4263dac5b885f760215fa599eb453e1221767d04;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index cb13692..d80c4b8 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,6 +1,6 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,13 +18,11 @@
*/
package jalview.gui;
-import jalview.datamodel.*;
-
import java.awt.*;
import java.awt.event.*;
-
import javax.swing.*;
+import jalview.datamodel.*;
/**
* DOCUMENT ME!
@@ -32,438 +30,407 @@ import javax.swing.*;
* @author $author$
* @version $Revision$
*/
-public class IdPanel extends JPanel implements MouseListener,
- MouseMotionListener
+public class IdPanel
+ extends JPanel implements MouseListener,
+ MouseMotionListener, MouseWheelListener
{
- 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)
+ 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);
+ addMouseWheelListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent e)
+ {
+ int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+ if (seq > -1 && seq < av.alignment.getHeight())
{
- int y = e.getY();
-
- if (av.getWrapAlignment())
+ SequenceI sequence = av.alignment.getSequenceAt(seq);
+ StringBuffer tip = new StringBuffer("");
+ tip.append(sequence.getDisplayId(true));
+ if (sequence.getDescription() != null)
{
- y = getWrappedY(y);
- }
+ tip.append("
");
+ tip.append(sequence.getDescription());
- final int seq = av.getIndex(y);
- if(seq!=-1)
- {
- StringBuffer tip = new StringBuffer("");
- tip.append(av.alignment.getSequenceAt(seq).getDisplayId(true));
- if (av.alignment.getSequenceAt(seq).getDescription() != null)
+ //ADD NON POSITIONAL SEQUENCE INFO
+ SequenceFeature[] features = sequence.getDatasetSequence().
+ getSequenceFeatures();
+ if (features != null)
{
- tip.append("");
- tip.append(av.alignment.getSequenceAt(seq).getDescription());
- tip.append(" | ");
- }
- tip.append("");
- setToolTipText(tip.toString());
- }
-
- if(av.hasHiddenRows)
- {
- if(av.adjustForHiddenSeqs(seq) -
- av.adjustForHiddenSeqs(seq-1)>1)
- {
- JPopupMenu pop = new JPopupMenu();
- JMenuItem item = new JMenuItem("Reveal");
- item.addActionListener(new ActionListener()
+ for (int i = 0; i < features.length; i++)
{
- public void actionPerformed(ActionEvent e)
+ if (features[i].begin == 0 && features[i].end == 0)
{
- av.showSequence(seq);
- alignPanel.repaint();
- if(alignPanel.overviewPanel!=null)
- alignPanel.overviewPanel.updateOverviewImage();
+ tip.append(" " + features[i].featureGroup
+ + " " + features[i].getType() + " " +
+ features[i].description);
}
- });
- pop.add(item);
- pop.show(this, e.getX(), e.getY());
+ }
}
+ tip.append(" |
");
}
- }
-
-
- int getWrappedY(int y)
- {
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- hgap += av.charHeight;
- return y - hgap;
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent e)
- {
- mouseDragging = true;
-
- int y = e.getY();
-
- if (av.getWrapAlignment())
+ DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
+ if (dbrefs != null)
+ {
+ tip.append("");
+ for (int i = 0; i < dbrefs.length; i++)
{
- y = getWrappedY(y);
+ tip.append("
");
+ tip.append(dbrefs[i].getSource() + " "
+ + dbrefs[i].getAccessionId());
}
+ tip.append("");
+ }
- int seq = av.getIndex(y);
+ tip.append("");
+ setToolTipText(tip.toString());
+ }
+ }
- if (seq < 0)
- {
- return;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent e)
+ {
+ mouseDragging = true;
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
+ int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
- lastid = seq;
- alignPanel.repaint();
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
}
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent e)
+ else if (seq > lastid)
{
- 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);
+ selectSeqs(lastid + 1, seq);
+ }
- int index = url.indexOf("$SEQUENCE_ID$");
- url = url.substring(0, index)+ id + url.substring(index+13);
+ lastid = seq;
+ alignPanel.paintAlignment(true);
+ }
- try
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ e.consume();
+ if (e.getWheelRotation() > 0)
{
- jalview.util.BrowserLauncher.openURL(url);
+ alignPanel.scrollUp(false);
}
- catch (Exception ex)
+ else
{
- 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();
+ alignPanel.scrollUp(true);
}
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent e)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() < 2)
{
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseExited(MouseEvent e)
+ java.util.Vector links = Preferences.sequenceURLLinks;
+ if (links == null || links.size() < 1)
{
- if (av.getWrapAlignment())
- {
- return;
- }
+ return;
+ }
- if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
- {
- scrollThread = new ScrollThread(true);
- }
+ int seq = alignPanel.seqPanel.findSeq(e);
- if (mouseDragging && (e.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
- {
- scrollThread = new ScrollThread(false);
- }
- }
+ //DEFAULT LINK IS FIRST IN THE LINK LIST
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mousePressed(MouseEvent e)
+ String id = av.getAlignment().getSequenceAt(seq).getName();
+ if (id.indexOf("|") > -1)
{
- if (e.getClickCount() == 2)
- {
- return;
- }
+ id = id.substring(id.lastIndexOf("|") + 1);
+ }
- int y = e.getY();
+ String url = links.elementAt(0).toString();
+ url = url.substring(url.indexOf("|") + 1);
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
+ int index = url.indexOf("$SEQUENCE_ID$");
+ url = url.substring(0, index) + id + url.substring(index + 13);
- int seq = av.getIndex(y);
+ 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)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
- if (seq == -1)
- {
- return;
- }
+ if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+ {
+ scrollThread = new ScrollThread(true);
+ }
- 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);
+ 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;
+ }
- return;
- }
+ int seq = alignPanel.seqPanel.findSeq(e);
- 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);
+ 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(), e.getY());
- for (int i = 0; i < sg.getSize(); i++)
- {
- selection.addSequence(sg.getSequenceAt(i), true);
- }
+ return;
+ }
- av.setSelectionGroup(selection);
+ 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);
+ }
- return;
- }
+ if (e.isShiftDown() && (lastid != -1))
+ {
+ selectSeqs(lastid, seq);
+ }
+ else
+ {
+ selectSeq(seq);
+ }
- if ((av.getSelectionGroup() == null) ||
- (!e.isControlDown() && (av.getSelectionGroup() != null)))
- {
- av.setSelectionGroup(new SequenceGroup());
- }
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ void selectSeq(int seq)
+ {
+ lastid = seq;
+
+ 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)
+ {
+ if (av.getSelectionGroup() == null)
+ {
+ return;
+ }
- av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ if (end >= av.getAlignment().getHeight())
+ {
+ end = av.getAlignment().getHeight() - 1;
+ }
- if (e.isShiftDown() && (lastid != -1))
- {
- selectSeqs(lastid, seq);
- }
- else
- {
- selectSeq(seq);
- }
+ lastid = start;
- alignPanel.repaint();
+ if (end < start)
+ {
+ int tmp = start;
+ start = end;
+ end = tmp;
+ lastid = end;
}
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- void selectSeq(int seq)
+ for (int i = start; i <= end; i++)
{
- lastid = seq;
-
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ true);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- */
- void selectSeqs(int start, int end)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent e)
+ {
+ if (scrollThread != null)
{
- if(av.getSelectionGroup()==null)
- return;
+ scrollThread.running = false;
+ }
- lastid = start;
+ mouseDragging = false;
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ }
- if (end < start)
- {
- int tmp = start;
- start = end;
- end = tmp;
- lastid = end;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param found DOCUMENT ME!
+ */
+ public void highlightSearchResults(java.util.Vector found)
+ {
+ idCanvas.setHighlighted(found);
- for (int i = start; i <= end; i++)
- {
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
- true);
- }
+ if (found == null)
+ {
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent e)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
+ int index = av.alignment.findIndex( (SequenceI) found.get(0));
- mouseDragging = false;
- PaintRefresher.Refresh(av.alignment);
+ // 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;
- /**
- * DOCUMENT ME!
- *
- * @param found DOCUMENT ME!
- */
- public void highlightSearchResults(java.util.Vector found)
+ public ScrollThread(boolean up)
{
- idCanvas.setHighlighted(found);
+ this.up = up;
+ start();
+ }
- if (found == null)
- {
- return;
- }
+ public void stopScrolling()
+ {
+ running = false;
+ }
- int index = av.alignment.findIndex((SequenceI) found.get(0));
+ public void run()
+ {
+ running = true;
- // do we need to scroll the panel?
- if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+ while (running)
+ {
+ if (alignPanel.scrollUp(up))
{
- alignPanel.setScrollValues(av.getStartRes(), index);
- }
- }
+ // scroll was ok, so add new sequence to selection
+ int seq = av.getStartSeq();
- // this class allows scrolling off the bottom of the visible alignment
- class ScrollThread extends Thread
- {
- boolean running = false;
- boolean up = true;
+ if (!up)
+ {
+ seq = av.getEndSeq();
+ }
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid)
+ {
+ selectSeqs(lastid + 1, seq);
+ }
- public ScrollThread(boolean up)
+ lastid = seq;
+ }
+ else
{
- this.up = up;
- start();
+ running = false;
}
- public void stopScrolling()
+ alignPanel.paintAlignment(true);
+
+ try
{
- running = false;
+ Thread.sleep(100);
}
-
- public void run()
+ catch (Exception ex)
{
- 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)
- {
- }
- }
}
+ }
}
+ }
}