org.sStu
Interface Aligner

All Known Subinterfaces:

AlignmentRangeAligner, ScoreOnlyAligner, SingleAlingmentAligner

public interface Aligner

Implements abstract aligner. It has no methods for retrieving the results, these are provided by subinterfaces.

Author:

Audrius Meskauskas

See Also:

http://www.gnu.org/licenses/gpl.txt

Method Summary

void	align() Compute the alignment now.
void	setSequence(java.lang.CharSequence seq, int number) Set the sequence with the given number to the given value.

Method Detail

align

public void align()

Compute the alignment now. This method is placed separately to perform the most time intensive step at the desired time (can be important during parallel computing). It is NOT required to call this method. If not previously called, it must be called automatically when the properties of the alignment are requested.

setSequence

public void setSequence(java.lang.CharSequence seq,
                        int number)

Set the sequence with the given number to the given value. For the double alignment, the valid values are 0 and 1. If multiple sequences are compared against one, this one (main) sequence should have the number 0. This ensures optimal preprocessing. For multiple alingments, a larger values may be allowed. Some implementations may call preprocessing routines after the main sequence is set.

Parameters:

seq - Sequence to set. By default, any character is allowed in the sequences. The alignments are case sensitive by default

number - The number of the sequence in alignment. For two sequence alignments, this parameter can only take values 0 and 1. Optimizations and pre-processing are implemented supposing that the sequence 0 is longer and more frequently used.