public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
- ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
- .asList(new SequenceI[]
- { aa[selectedRow].sequenceRef }));
+ 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();
}
else if (evt.getClickCount() >= 2)
{
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
SequenceGroup sg = ap.av.getSelectionGroup();
// see Enhancement JAL-1557
if (!(evt.isControlDown() || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
sg.addSequence(aa[selectedRow].sequenceRef, false);
// see Enhancement JAL-1557
if (!(evt.isControlDown() || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
sg.addSequence(aa[selectedRow].sequenceRef, false);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
.isIgnoreGapsConsensus());
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
.isIgnoreGapsConsensus());
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
hiddenColumns = new ArrayList<int[]>();
for (int[] region : av.getColumnSelection().getHiddenColumns())
{
hiddenColumns = new ArrayList<int[]>();
for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- Desktop.jalviewClipboard = new Object[]
- { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+ Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
+ // of a consensus
+ // sequence ? need to
+ // flag
- int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
- .getVisibleVRange() : null;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+ .getAnnotationPanel().getVisibleVRange() : null;