* height
*/
public class AnnotationLabels extends JPanel
- implements MouseListener, MouseMotionListener, ActionListener
+ implements MouseListener, MouseMotionListener
{
/**
* width in pixels within which height adjuster arrows are shown and active
private final boolean debugRedraw = false;
- private AlignmentPanel ap;
+ AlignmentPanel ap;
AlignViewport av;
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * Set all annotations visible
*/
- @Override
- public void actionPerformed(ActionEvent evt)
+ void showAll()
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
-
- String action = evt.getActionCommand();
- if (ADDNEW.equals(action))
- {
- /*
- * non-returning dialog
- */
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
- null, new Annotation[ap.av.getAlignment().getWidth()]);
- editLabelDescription(newAnnotation, true);
- }
- else if (EDITNAME.equals(action))
- {
- /*
- * non-returning dialog
- */
- editLabelDescription(aa[selectedRow], false);
- }
- else if (HIDE.equals(action))
- {
- aa[selectedRow].visible = false;
- }
- else if (DELETE.equals(action))
- {
- ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
- ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
- }
- else if (SHOWALL.equals(action))
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible && aa[i].annotations != null)
- {
- aa[i].visible = true;
- }
- }
- }
- else if (OUTPUT_TEXT.equals(action))
- {
- new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
- }
- else if (COPYCONS_SEQ.equals(action))
+ for (int i = 0; i < aa.length; i++)
{
- SequenceI cons = null;
- if (aa[selectedRow].groupRef != null)
- {
- cons = aa[selectedRow].groupRef.getConsensusSeq();
- }
- else
+ if (!aa[i].visible && aa[i].annotations != null)
{
- cons = av.getConsensusSeq();
- }
- if (cons != null)
- {
- copy_annotseqtoclipboard(cons);
+ aa[i].visible = true;
}
}
- else if (TOGGLE_LABELSCALE.equals(action))
- {
- aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
- }
-
ap.refresh(true);
}
oldY = evt.getY();
if (evt.isPopupTrigger())
{
- showPopupMenu(evt);
+ showPopupMenu(evt, selectedRow);
}
}
* Build and show the Pop-up menu at the right-click mouse position
*
* @param evt
+ * @param row
*/
- void showPopupMenu(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt, final int row)
{
evt.consume();
final AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
-
JPopupMenu pop = new JPopupMenu(
MessageManager.getString("label.annotations"));
+
+ /*
+ * add new row
+ */
JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
+ editLabelDescription(newAnnotation, true);
+ ap.refresh(true);
+ }});
pop.add(item);
- if (selectedRow < 0)
+
+ /*
+ * if no rows shown, add option to show all
+ * (if rows are hidden), nothing else to add
+ */
+ if (row < 0)
{
if (hasHiddenRows)
- { // let the user make everything visible again
+ {
item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAll();
+ }
+ });
pop.add(item);
}
pop.show(this, evt.getX(), evt.getY());
return;
}
+
+ /*
+ * Edit Name/Description
+ */
item = new JMenuItem(EDITNAME);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ editLabelDescription(aa[row], false);
+ ap.refresh(false);
+ }
+ });
pop.add(item);
+
+ /*
+ * hide row
+ */
item = new JMenuItem(HIDE);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aa[row].visible = false;
+ ap.refresh(true);
+ }
+ });
pop.add(item);
- // JAL-1264 hide all sequence-specific annotations of this type
- if (selectedRow < aa.length)
+
+ /*
+ * JAL-1264 hide all sequence-specific annotations of this type
+ */
+ if (row < aa.length)
{
- if (aa[selectedRow].sequenceRef != null)
+ if (aa[row].sequenceRef != null)
{
- final String label = aa[selectedRow].label;
+ final String label = aa[row].label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " "
+ label;
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;
- // }
- // }
ap.refresh(true);
}
});
pop.add(hideType);
}
}
+
+ /*
+ * delete annotation
+ */
item = new JMenuItem(DELETE);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.getAlignment().deleteAnnotation(aa[row]);
+ ap.av.getCalcManager().removeWorkerForAnnotation(aa[row]);
+ ap.refresh(true);
+ }
+ });
pop.add(item);
+
+ /*
+ * show hidden rows
+ */
if (hasHiddenRows)
{
item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAll();
+ }
+ });
pop.add(item);
}
+
+ /*
+ * export annotation
+ */
item = new JMenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter(ap).exportAnnotation(aa[row]);
+ }
+ });
pop.add(item);
+
// TODO: annotation object should be typed for autocalculated/derived
// property methods
- if (selectedRow < aa.length)
+ if (row < aa.length)
{
- final String label = aa[selectedRow].label;
- if (!aa[selectedRow].autoCalculated)
+ final String label = aa[row].label;
+ if (!aa[row].autoCalculated)
{
- if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ if (aa[row].graph == AlignmentAnnotation.NO_GRAPH)
{
// display formatting settings for this row.
pop.addSeparator();
- // av and sequencegroup need to implement same interface for
+
+ /*
+ * scale label to column
+ */
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()
- {
- @Override
- 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);
- }
- ap.alignmentChanged();
- }
- });
- 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()
- {
- @Override
- 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()
+ aa[row].scaleColLabel);
+ item.addActionListener(new ActionListener()
{
@Override
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());
+ aa[row].scaleColLabel = !aa[row].scaleColLabel;
+ ap.refresh(false);
}
});
- pop.add(cprofl);
- final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
- aa[selectedRow].groupRef.isNormaliseSequenceLogo());
- cproflnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
+ pop.add(item);
+ }
+ }
+ else if (label.indexOf("Consensus") > -1)
+ {
+ addConsensusMenuItems(pop, aa[row]);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
- // 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);
+ /**
+ * Helper method to add Consensus-specific menu items, for alignment or group
+ * consensus annotation
+ *
+ * @param menu
+ * @param aa
+ */
+ private void addConsensusMenuItems(JPopupMenu menu,
+ final AlignmentAnnotation aa)
+ {
+ menu.addSeparator();
+
+ /*
+ * ignore gaps in consensus
+ */
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa.groupRef != null)
+ ? aa.groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aa.groupRef != null)
+ {
+ aa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ // AnnotationLabels.this.repaint();
+ // ap.getAnnotationPanel()
+ // .paint(ap.getAnnotationPanel().getGraphics());
}
else
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"),
- av.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- 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()
- {
- @Override
- 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()
- {
- @Override
- 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);
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
+ ap.alignmentChanged();
}
+ });
+ menu.add(cbmi);
+
+ if (aa.groupRef != null)
+ {
+ /*
+ * show group histogram
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ aa.groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ menu.add(chist);
+
+ /*
+ * show group logo
+ */
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ aa.groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ menu.add(cprofl);
+
+ /*
+ * normalise group logo
+ */
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa.groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ menu.add(cproflnorm);
}
- pop.show(this, evt.getX(), evt.getY());
+ else
+ {
+ /*
+ * show histogram
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ menu.add(chist);
+
+ /*
+ * show logo
+ */
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ menu.add(cprof);
+
+ /*
+ * normalise logo
+ */
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ menu.add(cprofnorm);
+ }
+
+ /*
+ * copy consensus sequence
+ */
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_annotseqtoclipboard(aa);
+ }
+ });
+ menu.add(consclipbrd);
}
/**
{
if (evt.isPopupTrigger())
{
- showPopupMenu(evt);
+ showPopupMenu(evt, selectedRow);
return;
}
/**
* do a single sequence copy to jalview and the system clipboard
*
- * @param sq
- * sequence to be copied to clipboard
+ * @param cons
+ * Consensus annotation
*/
- protected void copy_annotseqtoclipboard(SequenceI sq)
+ protected void copy_annotseqtoclipboard(AlignmentAnnotation cons)
{
+ SequenceI sq = null;
+ if (cons.groupRef != null)
+ {
+ sq = cons.groupRef.getConsensusSeq();
+ }
+ else
+ {
+ sq = av.getConsensusSeq();
+ }
+ if (sq == null)
+ {
+ return;
+ }
+
SequenceI[] seqs = new SequenceI[] { sq };
String[] omitHidden = null;
SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
git://source.jalview.org / jalview.git / commitdiff