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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.
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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.