jAffy

jAffy is a Java library for accessing Affy file formats, written by Steven Eschrich

This code was developed out of a need to have Java-based access to the various Affy file formats. It was done partially via looking at the example files, but more recently was rewritten using the official documentation of the file formats.

Documentation

I do not have extensive documentation yet outside of the javadocs and some example programs (as part of jAffyApps package). The javadocs are here.

Origins

This code was developed using three different sources:

• The Affymetrix detailed documentation on file formats. See Affymetrix for details.

• Affymetrix C++ code for accessing files, licensed using LGPL. See Affymetrix for details.

• Local work on a C library for accessing file formats, libaffy.

In all three cases there do not appear to be any limitations more severe than LGPL, hence this library is released under that licensing.