| Package | Description |
|---|---|
| de.jstacs.data.sequences |
Provides classes for representing sequences.
The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may
contain continuous values as well.As sub-package provides the facilities to annotate Sequences. |
| de.jstacs.sequenceScores.statisticalModels.differentiable |
Provides all
DifferentiableStatisticalModels, which can compute the gradient with
respect to their parameters for a given input Sequence. |
| Modifier and Type | Field and Description |
|---|---|
protected DiscreteAlphabetMapping[] |
MappedDiscreteSequence.transformation
The
DiscreteAlphabetMappings used for mapping the original Sequence. |
| Modifier and Type | Method and Description |
|---|---|
static AlphabetContainer |
MappedDiscreteSequence.getNewAlphabetContainer(AlphabetContainer original,
DiscreteAlphabetMapping... transformation)
This method allows to create a new
AlphabetContainer given an old AlphabetContainer and some DiscreteAlphabetMappings. |
| Constructor and Description |
|---|
MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer,
SequenceAnnotation[] seqAn,
DiscreteAlphabetMapping... transformation)
This method allows to create an empty
MappedDiscreteSequence. |
MappedDiscreteSequence(SimpleDiscreteSequence original,
DiscreteAlphabetMapping... transformation)
This method allows to create a
MappedDiscreteSequence from a given Sequence and some given DiscreteAlphabetMappings. |
| Constructor and Description |
|---|
MappingDiffSM(AlphabetContainer originalAlphabetContainer,
DifferentiableStatisticalModel nsf,
DiscreteAlphabetMapping... mapping)
The main constructor creating a
MappingDiffSM. |