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LibrAlign
 
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LibrAlign 0.9.0 alpha

Packages 
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.
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