aps[a].av.setSelectionGroup(selected);
}
- selected.setEndRes(aps[a].av.alignment.getWidth() - 1);
+ selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
}
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
- aps[a].av.alignment.deleteAllGroups();
+ aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.sequenceColours = null;
}
colourGroups();
}
else
{
- cs = ColourSchemeProperty.getColour(sequences, av.alignment
+ cs = ColourSchemeProperty.getColour(sequences, av.getAlignment()
.getWidth(), ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
}
SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.alignment.getWidth() - 1);
+ false, 0, av.getAlignment().getWidth() - 1);
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
sg.cs.setConservation(c);
}
- aps[a].av.alignment.addGroup(sg);
+ aps[a].av.getAlignment().addGroup(sg);
}
}
// notify the panel to redo any group specific stuff.