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Package for loading a directory containing MRI data in NIfTI format. The directory to be loaded must contain as many subdirectories as there are classes of MRI data. Each subdirectory name will be used as the class label for the corresponding .nii files in that subdirectory. (This is the same strategy as the one used by WEKA's TextDirectoryLoader.) Currently, the package only reads volume information for the first time slot from each .nii file. The readDoubleVol(short ttt) method from the Nifti1Dataset class (http://niftilib.sourceforge.net/java_api_html/Nifti1Dataset.html) is used to read the data for each volume into a sparse WEKA instance (with ttt=0). For an LxMxN volume (the dimensions must be the same for each .nii file in the directory!), the order of values in the generated instance is [(z_1, y_1, x_1), ..., (z_1, y_1, x_L), (z_1, y_2, x_1), ..., (z_1, y_M, x_L), (z_2, y_1, x_1), ..., (z_N, y_M, x_L)]. If the volume is an image, then only x and y coordinates are used.

The HTTP server module (ks-server-http) implements the Web API of the KnowledgeStore, which includes the two CRUD and SPARQL endpoints. The CRUD Endpoint supports the retrieval and manipulation of semi-structured data about resource, mention, entity and axiom records (encoded in RDF, possibly using JSONLD), and the upload / download of resource representation. The SPARQL Endpoint supports SPARQL SELECT, CONSTRUCT, DESCRIBE and ASK queries according to the W3C SPARQL protocol. The two endpoints are implemented on top of a component implementing the KnowledgeStore Java API (the Store interface), which can be either the the KnowledgeStore frontend (ks-frontend) or the Java Client. The implementation of the module is based on the Jetty Web sever (run in embedded mode) and the Jersey JAX-RS implementation. Reference documentation of the Web API is automatically generated using the Enunciate tool.

A set of reflection utilities and miscellaneous utilities related to working with classes and their fields with no dependencies which is compatible with java 1.5 and generics. The package was originally created by Aaron Zeckoski for the Sakai Project and Generic DAO project but was repackaged to make it distributable by request. It is used in the RSF framework (http://www2.caret.cam.ac.uk/rsfwiki/) and the EntityBroker among other things. Note about the BeanUtils provided dependency: BeanUtils is not required if you are not using it in your project. Note about the Hibernate provided dependency: Hibernate is not required if you are not using it in your project.

JavaCL is an Object-Oriented API that makes the C OpenCL API available to Java in a very natural way. It hides away the complexity of cross-platform C bindings, has a clean OO design (with generics, Java enums, NIO buffers, fully typed exceptions...), provides high-level features (OpenGL-interop, array reductions) and comes with samples and demos. For more info, please visit http://code.google.com/p/nativelibs4java/wiki/OpenCL.

JavaCL is an Object-Oriented API that makes the C OpenCL API available to Java in a very natural way. It hides away the complexity of cross-platform C bindings, has a clean OO design (with generics, Java enums, NIO buffers, fully typed exceptions...), provides high-level features (OpenGL-interop, array reductions) and comes with samples and demos. For more info, please visit http://code.google.com/p/nativelibs4java/wiki/OpenCL.

OpenCL4Java is a thin Java wrapper around OpenCL's C API. It uses JNA as its interop layer library, which means it works on all of the (many) JNA-supported platforms (see http://jna.dev.java.net/). It is autogenerated by JNAerator (http://jnaerator.googlecode.com/), so updates to newer OpenCL specs are a matter of seconds. Note that OpenCL4Java is used by JavaCL, an Object-Oriented API that presents OpenCL in a much more practical, powerful and idiomatic way to Java. For more info, please visit http://code.google.com/p/nativelibs4java/wiki/OpenCL.

ATG DUST is a framework for building JUnit tests for applications built on the ATG Dynamo platform. This framework allows one to quickly write test code that depends up Nucleus or ATG Repositories. By using this framework one can drastically cut down on development time. It takes only a few seconds to start up a test with a repository, but it may take multiple minutes to start up an application server. To get started with DUST, take a look at http://atgdust.sourceforge.net/first-test.html. This page will walk you through the process of running a basic test which starts Nucleus. After that, read the other getting started guides to describe how to create standalone Junit tests which can startup repositories and use the DynamoHttpServletResponse classes. For only ATG10 and tested.

JSON is a light-weight, language independent, data interchange format. See http://www.JSON.org/ The files in this package implement JSON encoders/decoders in Java. It also includes the capability to convert between JSON and XML, HTTP headers, Cookies, and CDL. This is a reference implementation. There is a large number of JSON packages in Java. Perhaps someday the Java community will standardize on one. Until then, choose carefully. The license includes this restriction: "The software shall be used for good, not evil." If your conscience cannot live with that, then choose a different package. The package compiles on Java 1.2 thru Java 1.4.

HermiT is reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more. This is the maven build of HermiT and is designed for people who wish to use HermiT from within the OWL API. It is now versioned in the main HermiT version repository, although not officially supported by the HermiT developers. The version number of this package is a composite of the HermiT version and an value representing releases of this packaged version. So, 1.3.7.1 is the first release of the mavenized version of HermiT based on the 1.3.7 release of HermiT. This package includes the Jautomata library (http://jautomata.sourceforge.net/), and builds with it directly. This library appears to be no longer under active development, and so a "fork" seems appropriate. No development is intended or anticipated on this code base.

The goal of quality-test is to provide a small Java library for basic code quality checks within unit tests. It is discouraged to use quality-test in production code. The checks provided in this library are designed to be used in unit-tests. The checks and utilities provided in this package check static properties of classes, for example whether classes are marked final or constructors are private. Additionally, there are utils to give additional code coverage for private constructors. Quality-Test often can be used together with Google Reflections (http://code.google.com/p/reflections/) to perform checks such as, assure that every class in package *.dto.* is final or make sure that no class in the package *.controller.* contains any non-final static variables.