jmzML

Screenshot from jmzML

jmzML provides a portable and lightweight JAXB-based implementation of the full mzML 1.1 standard format, with considerable tweaks to make the processing of files memory efficient. In particular, mzML files are effectively indexed on the fly and used as swap files, with only requested snippets of data loaded from a file when accessing it. Additionally, internal references in the mzML XML are resolved automatically by jmzML, giving you direct access in the object model to entities that are only referenced by ID in the actual XML file.

Apart from reading indexed and non-indexed mzML files, jmzML also allows writing of non-indexed mzML files.

jmzML is written in 100% pure Java, and is made available under the permissive Apache2 open source license.

Download here: http://jmzml.googlecode.com