import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
void clearSequenceColours();
/**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
- /**
* return a compact representation of the current alignment selection to pass
* to an analysis function
*
*
* @return
*/
+ @Override
boolean isProteinFontAsCdna();
/**
*
* @return
*/
+ @Override
void setProteinFontAsCdna(boolean b);
public abstract TreeModel getCurrentTree();