Bioinformatics Core API
Introduction
This package is a core library of APIs:
- to model Rich Search Results objects (e.g. annotated NCBI BLAST results)
- to model DNA and protein sequences
- to model features / annotations
- to provide readers and writers for these objects
In turn, these object-oriented data models form the basic foundation of the Bioinformatics Core UI components
All in all, Core and Core-UI APIs are the building blocks to make bioinformatics tools; e.g. BLAST Filter, BioDocumentViewer and BlastViewer
Requirements
Use a Java Virtual Machine 1.8 (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
Since this package is a library, its primary purpose targets a use within other softwares. You can see how to use the library by having a look at:
- "test" package in this project: it contains sample sources codes; "TestSerialSystem.java" and "TestSFeatureSystem.java" are of particular interest
- Blast Filter Tool source code: a full example of a running application relying on this library
- Bioinformatics Core UI components: a set of viewers of sequence/feature/etc objects
Added in release 6.2.0 (Sept. 2020), there is a tool available:
- ImportIprScanPredictions: import Iprscan predicted domains and adds that information into a BLAST or PLAST result file.
See also Wiki.
License and dependencies
Bioinformatics Core API itself is released under the GNU Affero General Public License, Version 3.0. AGPL
It depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.
-- (c) 2003-2020 - Patrick G. Durand