Sight cross platform 3.0.0 alpha (jar)

Release notes:

Sight 3.0.0 alpha is developed by Audrius Meškauskas as a subsequent stage of the GPL-based Sight project, initially started in Ulm university. This release has several important new features:

1. Sight now supports workflows, containing loops and confluences. This allows to implement much more variable strategies of the bioinformatical research.
2. Built – in Smith and Waterman search allows searching the local database for the related sequences.
3. Cross platform implementation of WSDL compatible protocol allows to integrate web services using this way of communication.
4. The whole Sight workflow now can be converted into a single Sight agent. Such combined agents are valuable not just as an “elementary units” in more complicated workflows, but also as a simply usable modules for java programmer.
5. Sight now has agents for reading and writing in SwissProt and FASTA formats an can be used as a system to search or classify data in flat files having these formats.
6. Sight provides a “mini environment” to test and create data filters, based on java regular expressions.
7. Improved user environment (for example, possibility to copy/paste a part of workflow) makes creating of workflows easier.
8. XML agent generator supports namespaces.
9. Table agent generator supports turned tables and some cases when the response must be composed from the several tables in the document.
10. Manual landmark marking agent generator now uses regular expressions to specify landmarks.
11. Sight now can work with workflows where the final result is a graph rather than a table. The annotation event listener accepts registers events when two named nodes must be connected by the named link. Generated graphs can be viewed using CytoScape (see http://www.cytoscape.org/).
12. The new version has a large number of the other small improvements and fixed bugs.

This alpha-pre release is still not properly documented. While the user manual is in preparation, we suggest to read the button tool tips and try to understand the general logic of the program. Audrius Meškauskas will also be glad to answer all questions.

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Changelog: