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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. |
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.
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