- /**
- * All sequences will be cut from beginning to given index.
- *
- * @param i Remove all residues in sequences up to this column.
- */
- public void trimLeft(int i);
-
- /**
- * All sequences will be cut from given index.
- *
- * @param i Remove all residues in sequences beyond this column.
- */
- public void trimRight(int i);
-
- /**
- * Removes all columns containing entirely gap characters.
- */
- public void removeGaps();
- /**
- * remove gaps in alignment - recording any frame shifts in shiftrecord
- * @param shiftrecord
- */
- public void removeGaps(ShiftList shiftrecord);