import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactMatrixI;
}
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
- showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ showSSConsensusHistogram = Cache.getDefault("SHOW_SSCONSENSUS_HISTOGRAM",
+ true);
+ showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", true);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
if (residueShading != null)
{
residueShading.setConsensus(hconsensus);
+ residueShading.setSsConsensus(hSSConsensus);
}
setColourAppliesToAllGroups(true);
}
*/
protected boolean noReferencesTo(AlignedCodonFrame acf)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
if (frames == null)
{
return true;