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DefaultJ is a powerful Java library that provides default values for any class, offering multiple strategies for obtaining those values. It can be used as a dependency injection utility, similar to Guice. With 14 built-in strategies, DefaultJ can obtain default values through various means such as explicit bindings, annotations, enum values, factory methods, and more. It also supports custom annotations and offers annotation processors for validation. Available on Maven Central, DefaultJ can be easily integrated into Gradle and Maven projects. Contributions and selective usage of the library are encouraged.

This package contains several example programs of the usage of the JavaPermutationTools (JPT) library. JPT is a Java library that enables representing and generating permutations and sequences, as well as performing computation on permutations and sequences. It includes implementations of a variety of permutation distance metrics as well as distance metrics on sequences (i.e., Strings, arrays, and other ordered data types). In addition to programs demonstrating the usage of the JPT library, the jpt-examples package also contains programs for replicating the experiments from a few published papers that utilized the library or implementations on which the library is based. JPT's source code is maintained on GitHub, and the prebuilt jars of the library can be imported from Maven Central using maven or other build tools. The purpose of the package jpt-examples is to demonstrate usage of the major functionality of the JPT library. You can find out more about the JPT library itself from its website: https://jpt.cicirello.org/.

This is a Java library which provides a flexible and customizable way to bind command line arguments to Java objects, in a similar manner to how JSON, XML, and YAML can be bound to Java objects. You can easily define Java classes that represent the data structure of your command line arguments, and use annotations to specify how those arguments should be parsed and bound to the corresponding fields in your Java object. This allows you to write command line interfaces that are more intuitive and easier to use, while also reducing the amount of boilerplate code that is needed to parse and validate command line arguments.

This open source software is a reference implementation, consisting of software and related files, for the OMG specification called the Semantics of a Foundational Subset for Executable UML Models (fUML). The reference implementation is intended to implement the execution semantics of UML activity models, accepting an XMI file from a conformant UML model as its input and providing an execution trace of the selected activity model(s) as its output. The core execution engine, which is directly generated from the normative syntactic and semantic models for fUML, may also be used as a library implementation of fUML in other software.

DynamicJasper (DJ) is an API that hides the complexity of Jasper Reports, it helps developers to save time when designing simple/medium complexity reports generating the layout of the report elements automatically. It creates reports dynamically, defining at runtime the columns, column width (auto width), groups, variables, fonts, charts, crosstabs, sub reports (that can also be dynamic), page size and everything else that you can define at design time. This dependency provides basic ttf font files to be used along with DynamicJasper This packages requires JasperReports 6.3.1 or newer http://dynamicjasper.com

fastutil extends the Java Collections Framework by providing type-specific maps, sets, lists, and queues with a small memory footprint and fast operations; it provides also big (64-bit) arrays, sets, and lists, sorting algorithms, fast, practical I/O classes for binary and text files, and facilities for memory mapping large files. This jar (fastutil-core.jar) contains data structures based on integers, longs, doubles, and objects, only; fastutil.jar contains all classes. If you have both jars in your dependencies, this jar should be excluded.

This project is a resource for the JCoRe Linnaeus Annotator. The dictionaries contained herein are used for the recognition of concrete species names in text, e.g. "human", "mouse", "n. furzeri", "c. elegans" etc as well as species hints, i.e. indirect clues to a species like the word "patient" which most likely refers to a human. Additionally to such rather clear proxies, this project also includes a small dictionary containing maximum-frequency-proxies for genus expressions like "Drosophila" which will be mapped to "D. melanogaster". For the task of only finding concrete species names in text, there is the project jcore-linnaeus-species-ae-species-dict.

This project has a lot of business classes to work with genes and related named entities. Genes are part of a GeneDocument and may have gold IDs as well as mapped/predicted IDs. Another large part are species because most (all?) gene ID databases are species specific. So there are also classes or members to represent species mentions and the assignment of species IDs (taxonomy IDs) to genes. There is little to no business logic herein. This project is only useful as building block in other projects dealing with species assignment, gene ID mapping or similar efforts.

Java implementation of the Ziggurat algorithm for generating Gaussian distributed pseudorandom numbers. The Ziggurat algorithm is significantly faster than the more commonly encountered Polar method, and has some other desirable statistical properties. The ZigguratGaussian class is a Java port of the GNU Scientific Library's C implementation (Voss, 2005) of the Ziggurat method. In porting to Java, we have made several optimizations, the details of which can be found in the source code comments, which highlights any differences between this Java implementation and the C implementation on which it is based. This package also includes an implementation of the Polar Method, included to enable comparing speed advantage of the Ziggurat algorithm.