The Gephi Toolkit project package essential modules (Graph, Layout, Filters, IO...) in a standard Java library, which any Java project can use for getting things done.
The toolkit is just a single JAR that anyone could reuse in a Java program. This tutorial aims to introduce the project, show possibilities and start write some code.
mvn exec:java -Dexec.mainClass="org.gephi.toolkit.demos.Main"
.Consult the Gephi Toolkit Javadoc for help.