Since you are using JGraphT to create your GraphML files, you need to adjust JGraphT's export tool or write your own GraphML export for JGraphT.
Thus, you need to ask the JGraphT community for help. In other words, this forum is the wrong place to ask this question.
If your question is actually, if there is an API to replace JGraphT altogether, then the answer is: "Yes, there is." yEd is built upon the commercial yFiles library which provides a powerful and flexible high-level API for creating, arranging, displaying, and exporting graphs.