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This plugin provides a registered action, toolbar button and menu actions which can clear the REUSE flag <b>preventing a file from being replaced</b>. <br/><br/> The toolbar button, which looks like a "push pin", provides a visual indication that the currently active editor is REUSEable; the button is only enabled when the active editor is REUSEable. <br/><br/> In some situations the IDE/platform opens a file with the REUSE flag (see NetBeans API doc Line.ShowOpenType); files opened like this can be automatically replaced in an editor window by other files. <br/><br/> IDE REUSE examples: single stepping into a file, clicking on a stacktrace for goto source, jVi tag-stack operations.

JPA Security is an Access Control Solution for the Java Persistence API (JPA). With JPA Security your access control can be performed in the database. You may query the database for all objects of a certain type and will receive only the objects you have read access for. This filtering is performed in the database. Unaccessible queried objects will not be loaded into memory. JPA Security enables you to completely remove security-related code from your code-base. All access control may be configured via Annotations or XML. With JPA Security you do not have to change your access control paradigm (but maybe you want to, when you see the great capability of JPA Security). You even can mix access control paradigms easily. JPA Security is not designed to replace current security solutions, but to extend them. It integrates smoothly into the security mechanisms of the Java EE Platform, but may be used with third-party frameworks like Spring Security or in Java SE, too. With the extensibility of JPA Security it is easy to provide your own access control paradigm, access rules storage or login mechanism.

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.