| Package | Description |
|---|---|
| info.bioinfweb.libralign.model |
Contains the
AlignmentModel interface which
is the bridge between LibrAlign and any source of alignment data that is displayed with it as well as
related classes and a set of implementations of this interface provided with LibrAlign. |
| info.bioinfweb.libralign.model.adapters |
Contains adapter classes that allow to access the data provided by
BasicAlignmentModelView in other ways
(e.g. |
| 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 | Interface and Description |
|---|---|
interface |
AlignmentModelView<T,U>
This interface should be implemented by all classes which return the contents of another implementation
of
AlignmentModel in a modified way. |
| Modifier and Type | Interface and Description |
|---|---|
interface |
SequenceDataAdapter<S,T>
Classes implementing this interface provide access to the data provided by an implementation of
AlignmentModel in a different way (e.g. |
interface |
SingleSequenceDataAdapter<T>
Adapter classes providing views of (sub-) sequences of single rows of an implementation of
AlignmentModel should implement this interface. |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractBasicAlignmentModelView<T>
All classes implementing
BasicAlignmentModelViews can inherit from this class,
which implements the access to the underlying data source. |
class |
AbstractSingleSequenceDataAdapter<T>
Implements basic functionality of
SingleSequenceDataAdapter. |
class |
BioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>
Adapter class that allows to access the contents of an implementation of
AlignmentModel
as a set of BioJava Sequence objects. |
class |
CharSequenceAdapter<T>
Adapter class that allows to access the contents of an implementation of
AlignmentModel
as a set of CharSequences or Strings. |
class |
SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>
Abstract base class for all implementations of
SingleSequenceDataAdapter that allow
to view one sequence of a AlignmentModel as a BioJava Sequence object. |
class |
SingleCharSequenceAdapter<T>
An adapter class allowing to view a single sequence provided by an implementation of
AlignmentModel as a CharSequence. |
class |
StringAdapter<T>
Returns the sequences contained in the underlying data source as strings.
|
| 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 |
DelegatedAlignmentModelView<T>
Implementation of
AlignmentModelView that delegates all methods to the underlying model
and uses the same token type as the underlying model. |
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. |