import jalview.util.MapList;
import jalview.ws.params.InvalidArgumentException;
+import java.awt.Color;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
* get a range on the sequence as a string
*
* @param start
- * position relative to start of sequence including gaps (from 0)
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
* @param end
- * position relative to start of sequence including gaps (from 0)
+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
*
* @return String containing all gap and symbols in specified range
*/
* - last column, base 1
* @return
*/
- public Range findPositions(int fromColum, int toColumn);
+ public ContiguousI findPositions(int fromColum, int toColumn);
/**
* Returns an int array where indices correspond to each residue in the
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+ public Color getColor(int i);
+
+ public Color setColor(int i, Color c);
+
+ public void resetColors();
}