/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
*/
package jalview.gui;
import java.util.*;
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.event.*;
import java.awt.image.*;
import javax.swing.*;
import jalview.datamodel.*;
import jalview.io.*;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
static String TOGGLE_LABELSCALE = "Scale Label to Column";
static String ADDNEW = "Add New Row";
static String EDITNAME = "Edit Label/Description";
static String HIDE = "Hide This Row";
static String DELETE = "Delete This Row";
static String SHOWALL = "Show All Hidden Rows";
static String OUTPUT_TEXT = "Export Annotation";
static String COPYCONS_SEQ = "Copy Consensus Sequence";
boolean resizePanel = false;
Image image;
AlignmentPanel ap;
AlignViewport av;
boolean resizing = false;
MouseEvent dragEvent;
int oldY;
int selectedRow;
int scrollOffset = 0;
Font font = new Font("Arial", Font.PLAIN, 11);
/**
* Creates a new AnnotationLabels object.
*
* @param ap
* DOCUMENT ME!
*/
public AnnotationLabels(AlignmentPanel ap)
{
this.ap = ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
java.net.URL url = getClass().getResource("/images/idwidth.gif");
Image temp = null;
if (url != null)
{
temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
}
try
{
MediaTracker mt = new MediaTracker(this);
mt.addImage(temp, 0);
mt.waitForID(0);
} catch (Exception ex)
{
}
BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
.getWidth(this), BufferedImage.TYPE_INT_RGB);
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
image = (Image) bi;
addMouseListener(this);
addMouseMotionListener(this);
}
public AnnotationLabels(AlignViewport av)
{
this.av = av;
}
/**
* DOCUMENT ME!
*
* @param y
* DOCUMENT ME!
*/
public void setScrollOffset(int y)
{
scrollOffset = y;
repaint();
}
void getSelectedRow(int y)
{
int height = 0;
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
if (!aa[i].visible)
{
continue;
}
height += aa[i].height;
if (y < height)
{
selectedRow = i;
break;
}
}
} else {
selectedRow = -1;
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
null, new Annotation[ap.av.alignment.getWidth()]);
if (!editLabelDescription(newAnnotation))
{
return;
}
ap.av.alignment.addAnnotation(newAnnotation);
ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
}
else if (evt.getActionCommand().equals(EDITNAME))
{
editLabelDescription(aa[selectedRow]);
repaint();
}
else if (evt.getActionCommand().equals(HIDE))
{
aa[selectedRow].visible = false;
if (aa[selectedRow].label.equals("Quality"))
{
ap.av.quality = null;
}
}
else if (evt.getActionCommand().equals(DELETE))
{
ap.av.alignment.deleteAnnotation(aa[selectedRow]);
}
else if (evt.getActionCommand().equals(SHOWALL))
{
for (int i = 0; i < aa.length; i++)
{
if (!aa[i].visible && aa[i].annotations != null)
{
aa[i].visible = true;
}
}
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
new AlignmentAnnotation[]
{ aa[selectedRow] }, null, null);
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
SequenceI cons = null;
if (aa[selectedRow].groupRef != null)
{
cons = aa[selectedRow].groupRef.getConsensusSeq();
}
else
{
cons = av.getConsensusSeq();
}
if (cons != null)
{
copy_annotseqtoclipboard(cons);
}
}
else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
ap.annotationPanel.adjustPanelHeight();
ap.annotationScroller.validate();
ap.paintAlignment(true);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
boolean editLabelDescription(AlignmentAnnotation annotation)
{
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Name ",
"Annotation Description ", "Edit Annotation Name/Description");
if (!dialog.accept)
{
return false;
}
annotation.label = dialog.getName();
String text = dialog.getDescription();
if (text != null && text.length() == 0)
{
text = null;
}
annotation.description = text;
return true;
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
getSelectedRow(evt.getY() - scrollOffset);
oldY = evt.getY();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
int start = selectedRow;
getSelectedRow(evt.getY() - scrollOffset);
int end = selectedRow;
if (start != end)
{
// Swap these annotations
AlignmentAnnotation startAA = ap.av.alignment
.getAlignmentAnnotation()[start];
AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
}
resizePanel = false;
dragEvent = null;
repaint();
ap.annotationPanel.repaint();
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
if (evt.getY() < 10)
{
resizePanel = true;
repaint();
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
if (dragEvent == null)
{
resizePanel = false;
repaint();
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
dragEvent = evt;
if (resizePanel)
{
Dimension d = ap.annotationScroller.getPreferredSize();
int dif = evt.getY() - oldY;
dif /= ap.av.charHeight;
dif *= ap.av.charHeight;
if ((d.height - dif) > 20)
{
ap.annotationScroller.setPreferredSize(new Dimension(d.width,
d.height - dif));
d = ap.annotationSpaceFillerHolder.getPreferredSize();
ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
d.width, d.height - dif));
ap.paintAlignment(true);
}
ap.addNotify();
}
else
{
repaint();
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
resizePanel = evt.getY() < 10;
getSelectedRow(evt.getY() - scrollOffset);
if (selectedRow > -1
&& ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
{
AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
StringBuffer desc = new StringBuffer("");
if (aa.description != null
&& !aa.description.equals("New description"))
{
desc.append(aa.getDescription(true));
if (aa.hasScore)
desc.append("
");
}
if (aa.hasScore())
{
desc.append("Score: " + aa.score);
}
if (desc.length() != 6)
{
desc.append("");
this.setToolTipText(desc.toString());
}
else
this.setToolTipText(null);
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
if (aa!=null && selectedRow < aa.length)
{
if (aa[selectedRow].groupRef != null)
{
if (evt.getClickCount() >= 2)
{
// todo: make the ap scroll to the selection
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
ap.av.setSelectionGroup(// new SequenceGroup(
aa[selectedRow].groupRef); // );
ap.paintAlignment(false);
}
else
{
ap.seqPanel.ap.idPanel
.highlightSearchResults(aa[selectedRow].groupRef
.getSequences(null));
}
return;
}
else if (aa[selectedRow].sequenceRef != null)
{
Vector sr = new Vector();
sr.addElement(aa[selectedRow].sequenceRef);
if (evt.getClickCount() == 1)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
SequenceGroup sg = new SequenceGroup();
sg.addSequence(aa[selectedRow].sequenceRef, false);
ap.av.setSelectionGroup(sg);
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
}
}
}
}
if (!SwingUtilities.isRightMouseButton(evt))
{
return;
}
JPopupMenu pop = new JPopupMenu("Annotations");
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
if ((aa == null) || (aa.length == 0))
{
item = new JMenuItem(SHOWALL);
item.addActionListener(this);
pop.add(item);
pop.show(this, evt.getX(), evt.getY());
return;
}
pop.add(item);
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(HIDE);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(SHOWALL);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(OUTPUT_TEXT);
item.addActionListener(this);
pop.add(item);
// TODO: annotation object should be typed for autocalculated/derived
// property methods
if (selectedRow < aa.length)
{
if (!aa[selectedRow].autoCalculated)
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
// display formatting settings for this row.
pop.addSeparator();
// av and sequencegroup need to implement same interface for
item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
aa[selectedRow].scaleColLabel);
item.addActionListener(this);
pop.add(item);
}
}
else if (aa[selectedRow].label.indexOf("Consensus") > -1)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
"Ignore Gaps In Consensus",
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus()
: ap.av.getIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (aaa.groupRef != null)
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
else
{
ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
}
});
pop.add(cbmi);
// av and sequencegroup need to implement same interface for
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
"Show Group Histogram", aa[selectedRow].groupRef
.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
aaa.groupRef.setShowConsensusHistogram(chist.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
"Show Group Logo", aa[selectedRow].groupRef
.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprof);
}
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
"Show Histogram", av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
"Show Logo", av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
av.setShowSequenceLogo(cprof.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprof);
}
final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
}
pop.show(this, evt.getX(), evt.getY());
}
/**
* do a single sequence copy to jalview and the system clipboard
*
* @param sq
* sequence to be copied to clipboard
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
SequenceI[] seqs = new SequenceI[]
{ sq };
String[] omitHidden = null;
SequenceI[] dseqs = new SequenceI[]
{ sq.getDatasetSequence() };
if (dseqs[0] == null)
{
dseqs[0] = new Sequence(sq);
dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
sq.setDatasetSequence(dseqs[0]);
}
Alignment ds = new Alignment(dseqs);
if (av.hasHiddenColumns)
{
omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
sq.getLength(), seqs);
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
omitHidden);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
new StringSelection(output), Desktop.instance);
Vector hiddenColumns = null;
if (av.hasHiddenColumns)
{
hiddenColumns = new Vector();
for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
{
int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
.elementAt(i);
hiddenColumns.addElement(new int[]
{ region[0], region[1] });
}
}
Desktop.jalviewClipboard = new Object[]
{ seqs, ds, // what is the dataset of a consensus sequence ? need to flag
// sequence as special.
hiddenColumns };
}
/**
* DOCUMENT ME!
*
* @param g1
* DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
int width = getWidth();
if (width == 0)
{
width = ap.calculateIdWidth().width + 4;
}
Graphics2D g2 = (Graphics2D) g;
if (av.antiAlias)
{
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
}
drawComponent(g2, width);
}
/**
* DOCUMENT ME!
*
* @param g
* DOCUMENT ME!
*/
public void drawComponent(Graphics g, int width)
{
if (av.getFont().getSize() < 10)
{
g.setFont(font);
}
else
{
g.setFont(av.getFont());
}
FontMetrics fm = g.getFontMetrics(g.getFont());
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
g.translate(0, scrollOffset);
g.setColor(Color.black);
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
int y = 0;
int x = 0;
int graphExtras = 0;
int offset = 0;
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
g.setColor(Color.black);
if (!aa[i].visible)
{
continue;
}
y += aa[i].height;
offset = -aa[i].height / 2;
if (aa[i].hasText)
{
offset += fm.getHeight() / 2;
offset -= fm.getDescent();
}
else
offset += fm.getDescent();
x = width - fm.stringWidth(aa[i].label) - 3;
if (aa[i].graphGroup > -1)
{
int groupSize = 0;
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
{
groupSize++;
}
}
if (groupSize * (fontHeight + 8) < aa[i].height)
{
graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
}
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
{
x = width - fm.stringWidth(aa[gg].label) - 3;
g.drawString(aa[gg].label, x, y - graphExtras);
if (aa[gg].annotations[0] != null)
{
g.setColor(aa[gg].annotations[0].colour);
}
g.drawLine(x, y - graphExtras - 3, x
+ fm.stringWidth(aa[gg].label), y - graphExtras - 3);
g.setColor(Color.black);
graphExtras += fontHeight + 8;
}
}
}
else
{
g.drawString(aa[i].label, x, y + offset);
}
}
}
if (resizePanel)
{
g.drawImage(image, 2, 0 - scrollOffset, this);
}
else if (dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
.getY()
- scrollOffset);
}
if ((aa == null) || (aa.length < 1))
{
g.drawString("Right click", 2, 8);
g.drawString("to add annotation", 2, 18);
}
}
}