import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureSelectionManager;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureSelectionManager;
- cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(groups[i].getPidThreshold(), true);
+ cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
- }
+ // if (cs != null)
+ // {
+ // cs.setThreshold(view.getPidThreshold(), true);
+ // cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ // }
- af.viewport.setGlobalColourScheme(cs);
+ af.viewport.getViewportColourScheme().setThreshold(
+ view.getPidThreshold(), true);
+ af.viewport.getViewportColourScheme().setConsensus(
+ af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{