| Interface | Description |
|---|---|
| AlignerCustom.MatrixCache | |
| AlignmentIterator<S extends Sequence<S>> |
Iterates over all positions in alignment
|
| AlignmentScoring<S extends Sequence<S>> |
AlignmentScoring - interface which is to be implemented by any scoring system
|
| Class | Description |
|---|---|
| AbstractAlignmentScoring<S extends Sequence<S>> |
AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.
|
| AffineGapAlignmentScoring<S extends Sequence<S>> |
AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
|
| AffineGapAlignmentScoring.SerializationObject | |
| Aligner | |
| AlignerCustom |
Collection of custom aligners
|
| AlignerCustom.AffineMatrixCache | |
| AlignerCustom.LinearMatrixCache | |
| AlignerCustom.Matrix | |
| Alignment<S extends Sequence<S>> | |
| AlignmentCache |
AlignmentCache - class which is providing cached array for
BandedLinearAligner. |
| AlignmentHelper | |
| AlignmentIteratorForward<S extends Sequence<S>> |
Iterates over all positions in alignment
|
| AlignmentIteratorReverse<S extends Sequence<S>> |
Iterates over all positions in alignment
|
| AlignmentTrimmer | |
| AlignmentUtils | |
| BandedAffineAligner | |
| BandedAffineAligner.MatrixCache | |
| BandedAligner | |
| BandedAlignerParameters<S extends Sequence<S>> | |
| BandedLinearAligner | |
| BandedMatrix |
BandedMatrix - class which used to store alignment matrix for
BandedLinearAligner. |
| BandedSemiLocalResult |
BandedSemiLocalResult - class which is result of BandedSemiLocal alignment.
|
| CachedIntArray |
CachedIntArray - class which is used for storing alignment matrix.
|
| LinearGapAlignmentScoring<S extends Sequence<S>> |
LinearGapAlignmentScoring - scoring system which uses penalty for gap
|
| LinearGapAlignmentScoring.SerializationObject | |
| MultiAlignmentHelper | |
| MultiAlignmentHelper.Settings | |
| ScoringUtils |
ScoringUtils - class which contains some useful helpers used in scoring systems
|
| Enum | Description |
|---|---|
| BLASTMatrix |
BLASTMatrix - enum of available BLAST AminoAcid substitution matrices
|
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