");
// }
}
else
{
// begin the tooltip's html fragment
desc.append("");
if (aa.hasScore())
{
// TODO: limit precision of score to avoid noise from imprecise
// doubles
// (64.7 becomes 64.7+/some tiny value).
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)
{
final AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
if (selectedRow > -1 && selectedRow < aa.length)
{
if (aa[selectedRow].groupRef != null)
{
if (evt.getClickCount() >= 2)
{
// todo: make the ap scroll to the selection - not necessary, first
// click highlights/scrolls, second selects
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
ap.av.setSelectionGroup(// new SequenceGroup(
aa[selectedRow].groupRef); // );
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
else
{
ap.getSeqPanel().ap.getIdPanel()
.highlightSearchResults(aa[selectedRow].groupRef
.getSequences(null));
}
return;
}
else if (aa[selectedRow].sequenceRef != null)
{
if (evt.getClickCount() == 1)
{
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
.asList(new SequenceI[]
{ aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg!=null)
{
// we make a copy rather than edit the current selection if no modifiers pressed
// see Enhancement JAL-1557
if (!(evt.isControlDown() || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
sg.addSequence(aa[selectedRow].sequenceRef, false);
} else {
if (evt.isControlDown())
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
} else {
// notionally, we should also add intermediate sequences from last added sequence ?
sg.addSequence(aa[selectedRow].sequenceRef, true);
}
}
} else {
sg = new SequenceGroup();
sg.setStartRes(0);
sg.setEndRes(ap.av.getAlignment().getWidth()-1);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
ap.av.sendSelection();
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
}
}
}
}
if (!SwingUtilities.isRightMouseButton(evt))
{
return;
}
JPopupMenu pop = new JPopupMenu(
MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
if (selectedRow < 0)
{
if (hasHiddenRows)
{ // let the user make everything visible again
item = new JMenuItem(SHOWALL);
item.addActionListener(this);
pop.add(item);
}
pop.show(this, evt.getX(), evt.getY());
return;
}
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(HIDE);
item.addActionListener(this);
pop.add(item);
// JAL-1264 hide all sequence-specific annotations of this type
if (selectedRow < aa.length)
{
if (aa[selectedRow].sequenceRef != null)
{
final String label = aa[selectedRow].label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " " + label;
hideType.setText(text);
hideType.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
AlignmentUtils.showOrHideSequenceAnnotations(
ap.av.getAlignment(), Collections.singleton(label),
null, false, false);
// for (AlignmentAnnotation ann : ap.av.getAlignment()
// .getAlignmentAnnotation())
// {
// if (ann.sequenceRef != null && ann.label != null
// && ann.label.equals(label))
// {
// ann.visible = false;
// }
// }
refresh();
}
});
pop.add(hideType);
}
}
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
if (hasHiddenRows)
{
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)
{
final String label = aa[selectedRow].label;
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 (label.indexOf("Consensus") > -1)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
.isIgnoreGapsConsensus());
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.getAnnotationPanel().paint(ap.getAnnotationPanel().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(
MessageManager.getString("label.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 cprofl = new JCheckBoxMenuItem(
MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
aaa.groupRef.setshowSequenceLogo(cprofl.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprofl);
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
// automatically enable logo display if we're clicked
aaa.groupRef.setshowSequenceLogo(true);
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cproflnorm);
}
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
MessageManager.getString("label.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.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
MessageManager.getString("label.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.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
// to ap
// so the
// view
// can be
// updated.
av.setShowSequenceLogo(true);
av.setNormaliseSequenceLogo(cprofnorm.getState());
ap.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprofnorm);
}
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);
}
int[] alignmentStartEnd = new int[]
{ 0, ds.getWidth() - 1 };
List hiddenCols = av.getColumnSelection().getHiddenColumns();
if (hiddenCols != null)
{
alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd,
hiddenCols);
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
omitHidden, alignmentStartEnd);
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
ArrayList hiddenColumns = null;
if (av.hasHiddenColumns())
{
hiddenColumns = new ArrayList();
for (int[] region : av.getColumnSelection().getHiddenColumns())
{
hiddenColumns.add(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, true, width);
}
/**
* Draw the full set of annotation Labels for the alignment at the given
* cursor
*
* @param g
* Graphics2D instance (needed for font scaling)
* @param width
* Width for scaling labels
*
*/
public void drawComponent(Graphics g, int width)
{
drawComponent(g, false, width);
}
private final boolean debugRedraw = false;
/**
* Draw the full set of annotation Labels for the alignment at the given
* cursor
*
* @param g
* Graphics2D instance (needed for font scaling)
* @param clip
* - true indicates that only current visible area needs to be
* rendered
* @param width
* Width for scaling labels
*/
public void drawComponent(Graphics g, boolean clip, 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, getScrollOffset());
g.setColor(Color.black);
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
int y = 0;
int x = 0;
int graphExtras = 0;
int offset = 0;
Font baseFont = g.getFont();
FontMetrics baseMetrics = fm;
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
.getVisibleVRange() : null;
if (clip && visr != null)
{
sOffset = visr[0];
visHeight = visr[1];
}
boolean visible = true, before = false, after = false;
if (aa != null)
{
hasHiddenRows = false;
int olY = 0;
for (int i = 0; i < aa.length; i++)
{
visible = true;
if (!aa[i].visible)
{
hasHiddenRows = true;
continue;
}
olY = y;
y += aa[i].height;
if (clip)
{
if (y < sOffset)
{
if (!before)
{
if (debugRedraw)
{
System.out.println("before vis: " + i);
}
before = true;
}
// don't draw what isn't visible
continue;
}
if (olY > visHeight)
{
if (!after)
{
if (debugRedraw)
{
System.out.println("Scroll offset: " + sOffset
+ " after vis: " + i);
}
after = true;
}
// don't draw what isn't visible
continue;
}
}
g.setColor(Color.black);
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;
// TODO: JAL-1291 revise rendering model so the graphGroup map is
// computed efficiently for all visible labels
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;
}
else
{
// scale font to fit
float h = aa[i].height / (float) groupSize, s;
if (h < 9)
{
visible = false;
}
else
{
fontHeight = -8 + (int) h;
s = ((float) fontHeight) / (float) ofontH;
Font f = baseFont.deriveFont(AffineTransform
.getScaleInstance(s, s));
g.setFont(f);
fm = g.getFontMetrics();
graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
}
}
if (visible)
{
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]._linecolour != null)
{
g.setColor(aa[gg]._linecolour);
g.drawLine(x, y - graphExtras + 3,
x + fm.stringWidth(aa[gg].label), y - graphExtras
+ 3);
}
g.setColor(Color.black);
graphExtras += fontHeight + 8;
}
}
}
g.setFont(baseFont);
fm = baseMetrics;
fontHeight = ofontH;
}
else
{
g.drawString(aa[i].label, x, y + offset);
}
}
}
if (resizePanel)
{
g.drawImage(image, 2, 0 - getScrollOffset(), this);
}
else if (dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
dragEvent.getY() - getScrollOffset());
}
if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
18);
}
}
public int getScrollOffset()
{
return scrollOffset;
}
}