Bioinformatics Filtering Engine - Core API

What is a filter?

A filter is made of some rules, each of them being a constraint applied on the data contained in a BLAST result file. This library is capable of reading legacy NCBI XML file (-outfmt 5 argument from BLAST+; -m 7 for legacy BLAST) and creating an object-based data model in memory. This model lets you access the many data fields (Hit ID, alignment length, e-value, scores, etc.) of a BLAST result. So, you use a filter to select relevant hits using your own constraints.

About this project

This package contains the data filtering library of BLAST Filter Tool. It contains the data models to represent NCBI BLAST results and Filters (e.g. queries) using hyper-graphs. Indeed, this filtering tool is a concrete implementation of the Hyper-Graph Explorer applied on BLAST data.

Requirements

Use a Java Virtual Machine 1.7 (or above) from Oracle.

Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.

Library uses

See Wiki.

License and dependencies

"Bioinformatics Filtering Engine - Core API" itself is released under the GNU Affero General Public License, Version 3.0. AGPL