Package org.sStu

Sequence studio main package provides classes and interfaces, needed to perform various kinds of sequence alignment.

See:
          Description

Interface Summary
Aligner Implements abstract aligner.
Alignment Represents the alignment.
AlignmentRangeAligner Defines a most comprehensive (but slowest) alingner able to return the range of suboptimal alignments when required.
ScoreOnlyAligner Defines an aligner that returns the score of the best alignment only.
SingleAlingmentAligner Defines an aligner that returns one (best) alignment and its score.
 

Class Summary
AlignerFactory AlignerFactory creates and returns various aligners with the given parameters
CharComparator Class for comparing two characters in the sequence.
 

Package org.sStu Description

Sequence studio main package provides classes and interfaces, needed to perform various kinds of sequence alignment. Spreading of existing libraries is often slowed down by necessity to study large amounts of documentation before any possibility to try the package. With only two classes and five interfaces in the top level, this package is limiting simple to understand and start using. The implementation engine (that obviously contain much more components) requires no attention and can be accessed only when the details are really needed. Sequence studio contains something like a simple expert system (AlignerFactory) that chooses the correct aligner class depending from the user-specified parameters (global or local, simple or gapped, are sub optimal alignments required, etc). Sequences studio comes with the applet that not just demonstrates the work of different aligners, but also generates a complete working samples of java code.


Sequences studio, collection of sequence alignment algorithms is Copyright (C) 2003 Audrius Meškauskas. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License (GPL.txt) for more details You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.