*/
package jalview.datamodel;
-import jalview.util.ShiftList;
-
import java.util.*;
*/
public int getWidth();
- /**
- * Calculates the longest sequence Id of the alignment
- *
- * @return Number of characters in longest sequence Id.
- */
- public int getMaxIdLength();
/**
* Calculates if this set of sequences is all the same length
public void setSequenceAt(int i, SequenceI seq);
/**
- * Deletes a sequence from the alignment.
+ * Deletes a sequence from the alignment
*
* @param s Sequence to be deleted.
*/
*/
public void deleteSequence(int i);
- /**
- * Deletes all residues in every sequence of alignment within given columns.
- *
- * @param start Start index of columns to delete.
- * @param end End index to columns to delete.
- */
- public void deleteColumns(SequenceI seqs [], int start, int end);
-
/**
* Finds sequence in alignment using sequence name as query.
*/
public int findIndex(SequenceI s);
- /**
- * 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);
/**
* Finds group that given sequence is part of.