| Package | Description |
|---|---|
| info.bioinfweb.libralign.model.implementations |
Contains common implementations of
AlignmentModel
which are part of LibrAlign. |
| info.bioinfweb.libralign.model.implementations.decorate | |
| info.bioinfweb.libralign.model.implementations.swingundo |
Contains classes that allow to edit the underlying data source of an implementation of
AlignmentModel using swing edit objects
(implementations of UndoableEdit). |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractListAlignmentModel<T>
An abstract implementation of
AlignmentModel using a map of lists to store alignment data. |
class |
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. |
class |
AbstractUndecoratedAlignmentModel<T>
Implements general functionality for alignment models that are not decorators of other models.
|
class |
AbstractUnmodifyableAlignmentModel<S,T>
Implements basic functionality for a map based alignment model that uses unmodifiable sequence
objects as its underlying data source.
|
class |
ArrayListAlignmentModel<T>
An implementation of
AlignmentModel using a map of array lists to store
alignment data. |
class |
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. |
class |
CharSequenceAlignmentModel
An implementation of
AlignmentModel backed by a set of CharSequence implementations
(e.g. |
class |
PackedAlignmentModel<T>
An alignment model using a
PackedObjectArrayList as the underlying data source. |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractAlignmentModelDecorator<T,U>
Basic implementation of
AlignmentModelView which delegates sequence specific methods
(which are independent of the token type) to the underlying model. |
class |
AbstractTokenReplacementAlignmentModelDecorator<T,U>
Abstract base class for implementations of
AlignmentModelView that simply replace a set
of tokens by other tokens of the same type. |
class |
DNAAlignmentModelDecorator<T,U>
Shows the underlying nucleotide data source as a DNA sequence, i.e.
|
class |
RNAAlignmentModelDecorator<T,U>
Shows the underlying nucleotide data source as a RNA sequence, i.e.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SwingUndoAlignmentModel<T>
An implementation of
AlignmentModel that creates an UndoableEdit object for every
modification that is made to the underlying data source using any of the methods specified by
AlignmentModel. |