| Package | Description |
|---|---|
| com.milaboratory.core.alignment | |
| com.milaboratory.core.alignment.batch | |
| com.milaboratory.core.alignment.benchmark | |
| com.milaboratory.core.alignment.blast | |
| com.milaboratory.core.alignment.kaligner1 | |
| com.milaboratory.core.alignment.kaligner2 | |
| com.milaboratory.core.io.binary |
Contains
PrimitivIO (see com.milaboratory.primitivio) serializers for MiLib classes that don't need
access to package only constructors and fields. |
| com.milaboratory.core.mutations | |
| com.milaboratory.core.tree |
| Class and Description |
|---|
| AbstractAlignmentScoring
AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.
|
| AffineGapAlignmentScoring
AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
|
| AlignerCustom.AffineMatrixCache |
| AlignerCustom.LinearMatrixCache |
| AlignerCustom.MatrixCache |
| Alignment |
| AlignmentHelper |
| AlignmentIterator
Iterates over all positions in alignment
|
| AlignmentIteratorForward
Iterates over all positions in alignment
|
| AlignmentIteratorReverse
Iterates over all positions in alignment
|
| AlignmentScoring
AlignmentScoring - interface which is to be implemented by any scoring system
|
| BandedAffineAligner.MatrixCache |
| BandedAlignerParameters |
| BandedSemiLocalResult
BandedSemiLocalResult - class which is result of BandedSemiLocal alignment.
|
| BLASTMatrix
BLASTMatrix - enum of available BLAST AminoAcid substitution matrices
|
| CachedIntArray
CachedIntArray - class which is used for storing alignment matrix.
|
| LinearGapAlignmentScoring
LinearGapAlignmentScoring - scoring system which uses penalty for gap
|
| MultiAlignmentHelper |
| MultiAlignmentHelper.Settings |
| Class and Description |
|---|
| Alignment |
| AlignmentScoring
AlignmentScoring - interface which is to be implemented by any scoring system
|
| Class and Description |
|---|
| AffineGapAlignmentScoring
AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
|
| Alignment |
| Class and Description |
|---|
| Alignment |
| Class and Description |
|---|
| Alignment |
| LinearGapAlignmentScoring
LinearGapAlignmentScoring - scoring system which uses penalty for gap
|
| Class and Description |
|---|
| AffineGapAlignmentScoring
AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
|
| Alignment |
| Class and Description |
|---|
| Alignment |
| Class and Description |
|---|
| Alignment |
| Class and Description |
|---|
| Alignment |
| LinearGapAlignmentScoring
LinearGapAlignmentScoring - scoring system which uses penalty for gap
|
Copyright © 2018. All rights reserved.