import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
String colourSchemeName = ((ComplexAlignFile) source)
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
String colourSchemeName = ((ComplexAlignFile) source)