AlignmentModel
which are part of LibrAlign.See: Description
| Class | Description |
|---|---|
| AbstractAlignmentModel<T> |
This is the base class for all alignment models and alignment model decorators.
|
| AbstractListAlignmentModel<T> |
An abstract implementation of
AlignmentModel using a map of lists to store alignment data. |
| AbstractMapBasedAlignmentModel<S,T> |
Implements all methods dealing with the organization of the sequence set using some implementation
of
Map to identify the sequence object belonging to a sequence ID. |
| AbstractSequenceIDIterator<P extends AlignmentModel> |
Abstract implementation of an iterator returning the IDs of all sequences provided by an implementation
of
AlignmentModel. |
| AbstractUndecoratedAlignmentModel<T> |
Implements general functionality for alignment models that are not decorators of other models.
|
| AbstractUnmodifyableAlignmentModel<S,T> |
Implements basic functionality for a map based alignment model that uses unmodifiable sequence
objects as its underlying data source.
|
| ArrayListAlignmentModel<T> |
An implementation of
AlignmentModel using a map of array lists to store
alignment data. |
| BioJava3SequenceAlignmentModel<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> |
/**
An implementation of
AlignmentModel backed by a set of BioJava Sequence implementations. |
| CharSequenceAlignmentModel |
An implementation of
AlignmentModel backed by a set of CharSequence implementations
(e.g. |
| PackedAlignmentModel<T> |
An alignment model using a
PackedObjectArrayList as the underlying data source. |
| SequenceIDManager |
Manages mappings between sequence IDs and sequence names.
|
AlignmentModel
which are part of LibrAlign.