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LibrAlign is a Java library providing powerful GUI components that allow displaying multiple sequence alignments or single sequences including any type of attached raw or metadata.

• Alignment GUI components display one or multiple related multiple sequence alignments or also a single sequence.
• Data areas display any type of raw or meta data attached to a sequence or a whole alignment. For new data types additional custom data areas can easily be created.
• Alignment and data models store the data displayed in the alignment components and data areas.

Note that this documentation may still undergo changes before the release of LibrAlign 1.0, since API changes may happen during that time.

Demo application

Have a look at the Swing demo application showing how a simple alignment editor based on LibrAlign can be implemented. It illustrates the usage of the available GUI components and the I/O functionality. Implementing a respective application in SWT would follow the same principles.

API documentation

This wiki gives an introduction and overview on LibrAlign. A detailed documentation of all LibrAlignclasses can be found in the API documentation:

• JavaDoc on the latest version of LibrAlign
• Overview on the available JavaDocs on previous LibrAlign versions

Supported GUI toolkits

LibrAlign makes use of the bioinfweb library TIC, which allows to provide all GUI components in a Swing and a SWT version. Therefore LibrAlign integrates into the look and feel of any Swing or SWT/Eclipse RCP application, while still offering identical functionality. See Working with toolkits for details.

Components

LibrAlign is separated into several components for different purposes.

• core is the main component, containing the model classes, GUI component main classes and data areas. All other modules depend on core.
• io provides functionality for reading and writing sequence and alignment formats to and from LibrAlign models. It makes use of the event based IO library JPhyloIO. See Reading and writing data for details.
• swing contains the Swing specific implementations of the LibrAlign GUI components. See Working with toolkits for details.
• swt contains the SWT specific implementations of the LibrAlign GUI components. See Working with toolkits for details.
• biojava1 and biojava4 contain classes that provide an interoperability with the different versions of BioJava. See Working with BioJava for details.