| Package | Description |
|---|---|
| info.bioinfweb.libralign.actions | |
| info.bioinfweb.libralign.alignmentarea |
Contains basic implementations for displaying an alignment area.
|
| info.bioinfweb.libralign.alignmentarea.content |
Contains classes related to
AlignmentContentArea which display
the contents of an alignment. |
| info.bioinfweb.libralign.alignmentarea.label |
Contains general classes implementing the labeling of sequences and data areas.
|
| info.bioinfweb.libralign.alignmentarea.order | |
| info.bioinfweb.libralign.alignmentarea.paintsettings |
Contains classes managing the painting of the contents of
AlignmentAreas. |
| info.bioinfweb.libralign.alignmentarea.rowsarea | |
| info.bioinfweb.libralign.alignmentarea.selection |
Contains classes necessary to perform the selection of rows and/or columns in an
AlignmentArea. |
| info.bioinfweb.libralign.alignmentarea.tokenpainter |
Contains implementations of
TokenPainter |
| info.bioinfweb.libralign.dataarea |
Contains
DataArea from which all data areas used in LibrAlign
must be inherited as well as related classes and a set of general data area implementations provided with
LibrAlign which are located in the subpackage implementations. |
| info.bioinfweb.libralign.dataarea.implementations |
Contains classes that implement a concrete data area.
|
| info.bioinfweb.libralign.dataarea.implementations.charset |
Contains data area related classes to display character sets of an alignment.
|
| info.bioinfweb.libralign.dataarea.implementations.charset.events |
Contains event classes used to report changes in a
CharSetDataModel. |
| info.bioinfweb.libralign.dataarea.implementations.pherogram |
Contains
PherogramArea and other classes used in its
implementation. |
| info.bioinfweb.libralign.dataarea.implementations.sequenceindex | |
| info.bioinfweb.libralign.editsettings |
Contains classes implementing the edit settings of an
AlignmentContentArea or an
MultipleAlignmentsContainer. |
| 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.concatenated |
Contains the interface
ConcatenatedAlignmentModel and
related implementations. |
| info.bioinfweb.libralign.model.data | |
| info.bioinfweb.libralign.model.events |
Contains the event objects used by implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.exception |
Contains exceptions thrown by implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.factory |
Contains factory classes to create instances of implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.factory.biojava |
Contains alignment models working with BioJava
Compounds. |
| info.bioinfweb.libralign.model.factory.continuous |
Contains factories for alignment models that work with continuous values (e.g.
|
| 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). |
| info.bioinfweb.libralign.model.implementations.swingundo.edits |
Contains the edit objects used by
SwingUndoAlignmentModel. |
| info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence |
Contains the edit objects to manipulate sequences in an implementations of
AlignmentModel used by
SwingUndoAlignmentModel. |
| info.bioinfweb.libralign.model.implementations.swingundo.edits.token |
Contains the edit objects to manipulate sets of tokens in sequences in an implementations of
AlignmentModel used by
SwingUndoAlignmentModel. |
| info.bioinfweb.libralign.model.io | |
| info.bioinfweb.libralign.model.tokenset | |
| info.bioinfweb.libralign.model.tokenset.continuous |
Contains classes implementing token sets for continuous character states (e.g.
|
| info.bioinfweb.libralign.model.utils |
Contains utility classes to be used with implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.utils.indextranslation | |
| info.bioinfweb.libralign.multiplealignments |
Contains classes used in the implementation of
MultipleAlignmentsContainer
which allow to combine several AlignmentAreas. |
| info.bioinfweb.libralign.pherogram |
Contains classes related to storing and displaying a trace file from Sanger sequencing.
|
| info.bioinfweb.libralign.pherogram.distortion | |
| info.bioinfweb.libralign.pherogram.model |
Contains
PherogramProvider and its implementations. |
| info.bioinfweb.libralign.pherogram.provider |
Contains
PherogramProvider and its implementations. |
| info.bioinfweb.libralign.pherogram.view |
Contains classes to display an undistorted pherogram.
|