the BiVeS framework
The BiVeS Framework is probably the resource you want to use in your project. It is executable from command line (it contains a Main) and combines all /BiVeS modules (see right hand side dependency graph):
In addition, we provide a web service which uses BiVeS to provide all functionalities through JSON calls, and a web service client library which is able to communicate with the web service.
All these modules utilize the xmlutils project, which provides advanced features for handling XML trees.
Include the BiVeS Framework via Maven:
<dependency>
<groupId>de.uni-rostock.sbi</groupId>
<artifactId>BiVeS</artifactId>
<version>$VERSION</version>
</dependency>
(see all versions at Maven Central)