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Free software programmed in Java

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JrMan
jrMan renderer is an open-source version of the Reyes rendering algorithm used by Pixar's PhotoRealistic RenderMan and implemented in Java by Gerardo Horvilleur, Jorge Vargas, Elmer Garduno, and Alessandro Falappa.
JFLAP
JFLAP (Java Formal Languages and Automata Package) is interactive educational software written in Java for experimenting with topics in the computer science area of formal languages and automata theory, primarily intended for use at the undergraduate level or as an advanced topic for high school. JFLAP allows one to create and simulate structures, such as programming a finite-state machine, and experiment with proofs, such as converting a nondeterministic finite automaton (NFA) to a deterministic finite automaton (DFA).
Flyway
database migration tool
Apache PDFBox
open-source PDF library
Apache Aries
Blueprint container software
JMulTi
JMulTi is an open-source interactive software for econometric analysis, specialised in univariate and multivariate time series analysis. It has a Java graphical user interface.
CommaFeed
CommaFeed is a free and open source feed reader. It is a web application which can be self hosted on a web server or used through commafeed.com. It has responsive design supporting desktop, tablet and mobile browser simultaneously. An Android News+ client was available but discontinued. It supports right-to-left feeds.
Archimedes
free CAD software
OpenAM
OpenAM is an open-source access management, entitlements and federation server platform. Now it is supported by Open Identity Platform Community.
Mifos
American financial software nonprofit
Eclipse Che
open-source IDE
uDig
uDig is a GIS software program produced by a community led by Canadian-based consulting company Refractions Research.
Red5
media server