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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
Aqueduct is a simple state machine library written in Java. Some programs can be described naturally as a state machine or a flowchart; this library is intended to simplify the development of such programs.
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
FAST(Flowchart Abstract Syntax Tree) SDK is a development toolkit built upon Eclipse RCP and GEF to visualize the process of converting unstructured flowcharts in to structured ones.
jPatchwork is a graphical user interface written in Java which allows the user to create Csound instruments (i.e., to design synthesis algorithms in the Csound language) by creating a flowchart.