setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
- autoCalculateConsensus = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
+ autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
*/
if (align != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMappings(align.getCodonFrames());
}
List<AlignedCodonFrame> mappings = al.getCodonFrames();
if (mappings != null)
{
- StructureSelectionManager ssm = Desktop.getInstance()
+ StructureSelectionManager ssm = Desktop
.getStructureSelectionManager();
for (AlignedCodonFrame acf : mappings)
{
@Override
public void sendSelection()
{
- Desktop.getInstance().getStructureSelectionManager().sendSelection(
+ Desktop.getStructureSelectionManager().sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()), this);
@Override
public StructureSelectionManager getStructureSelectionManager()
{
- return Desktop.getInstance().getStructureSelectionManager();
+ return Desktop.getStructureSelectionManager();
}
@Override