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wizard4j offers a java engine that 'runs' flowcharts (written in xml). A 'flowchart run' creates a sequence of user interactions (java api, html forms, rs, ...).The result of a 'run' can be applied to template frameworks like Velocity or Freemarker
JLink lets users author flow charts based on ISO 5807 and IBM standards. Developers can use JLink to add flowcharts to applications, serve a flow chart over the web in PDF or PNG, or dynamically create a flowchart with Javascript, Python or Ruby scripts