jqcML

About jqcML

jqcML is a Java application programming interface (API) for the qcML standard.

Firstly, jqcML provides a complete object model to represent qcML data. Secondly, jqcML provides the ability to read, write and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA).

jqcML is made available under the permissive Apache 2.0 open-source license. If you use jqcML as part of your work, please cite the following publication:

• Bittremieux, W., Kelchtermans, P., Valkenborg, D., Martens, L. & Laukens, K. jqcML: An open-source Java API for mass spectrometry quality control data in the qcML format. Journal of Proteome Research (2014). doi:10.1021/pr401274z

For more information about how to use jqcML, see the how to for some examples. The jqcML documentation is available here.

News

jqcML v1.0.5 (16 April 2015)

• BUGFIX: Fix error while validating an embedded stylesheet

jqcML v1.0.4 (30 March 2015)

• ENHANCEMENT: Enforce valid required elements
• ENHANCEMENT: Unified toString() behavior

jqcML v1.0.3 (27 March 2015)

• ENHANCEMENT: Parameterizable custom qcDB queries
• ENHANCEMENT: General code style improvements, cyclic dependency fixes, code duplication removals, and vulnerability fixes
• BUGFIX: Fix an issue where a qcML with only SetQualities and no RunQualities was not written to the qcDB properly
• BUGFIX: Remove obsolete tests, add additional tests, and optimize unit test execution

For more information see the release notes.

Getting jqcML

The Downloads section contains the jqcML jar executables. Furthermore, the source code is available from this repository through git.

Attention: the jqcML version numbers are independent from the qcML version numbers. Instead jqcML works with the latest qcML version; currently this is qcML v0.0.8. Furthermore, version changes are indicated in the release notes.

Getting Help

If you have questions or need additional help, you can contact us by creating an issue.

Please let us know your feedback, including error reports, improvement suggestions, new feature requests and any other things you might want to suggest.

When reporting a bug, please remember to include the detailed log file generated by jqcML and the JPA log file (if applicable).

About qcML

qcML implements a data exchange format geared towards capturing quality control (QC) data from mass spectrometry experiments. For more information, see the qcML website.

jqcML is supported by the InSPECtor project.