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Version 1.0.2
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LexBIG Software User Agreement
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Convention | Description | Example | |||||||
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Bold & Capitalized Command | Indicates a Menu command |
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Capitalized command>Capitalized command | Indicates Sequential Menu commands | Admin > Refresh | |||||||
| Used for filenames, directory names, commands, file listings, source code examples and anything that would appear in a Java program, such as methods, variables, and classes. |
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Boldface type | Options that you select in dialog boxes or drop-down menus. Buttons or icons that you click. | Select the file and click the Open button. | |||||||
Italics | Used to reference other documents, sections, figures, and tables. | caCORE Software Development Kit 1.0 Programmer's Guide | |||||||
Italic boldface type | Text that you type | In the New Subset text box, enter Proprietary Proteins. | |||||||
| Highlights a concept of particular interest |
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| Highlights information of which you should be particularly aware. |
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Example source is provided below for a simple program that lists the available coding schemes (containers for vocabulary concepts and relations) registered to a LexBIG server node:
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import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList;
import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering;
import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl;
import org.LexGrid.LexBIG.LexBIGService.LexBIGService;
import org.LexGrid.LexBIG.Utility.ObjectToString;
public class ListCodeSystems {
public static void main(String[] args) {
try {
LexBIGService lbs = new LexBIGServiceImpl();
CodingSchemeRenderingList schemes = lbs.getSupportedCodingSchemes();
for (CodingSchemeRendering csr
: schemes.getCodingSchemeRendering() )
System.out.printIn(
ObjectToString.toString(csr.getCodingSchemeSummary()));
} catch (Exception e) {
e.printStackTrace();
}
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This appendix includes lists and hypertext links, where appropriate, to technical manuals, articles, scientific publications and online resources related to the LexBIG project.
- LexBIG GForge Projectproject Docs archive, Files archive
- LexBIG Project Administration Materials
- LexGrid Home Page for this release
- Vocabulary Knowledge Center
- Sun Java Tools (JDK, JRE, NetBeans)
Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include - Eclipse Project (IDE)
Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include
Appendix B Included Materials
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Redistributable components (e.g. those listed below) and associated license terms are also made available. The redistributable components provide equivalent content and function, but require more extensive configuration for program execution. |
| This archive includes the LexBIG runtime code, excluding all dependencies. | ||||||||||||||||
| The LexBIG graphical user interface runtime code, excluding all dependencies. | ||||||||||||||||
| Provided by Sun's reference implementation of the JavaBeans Activation Framework (JAF)
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Grid infrastructure to support the caBIG® community. Contains tools for creating and deploying caBIG®-compliant grid services. | |||||||||||||||||
| Provides a simple Provides a simple API for working with command line arguments, options, option groups, mandatory options and so forth. | ||||||||||||||||
| Provides implementations of common encoders and decoders such as Base64, Hex, Phonetic and URLs. | ||||||||||||||||
| Provides a suite of classes that extend or augment the Java Collections Framework. | ||||||||||||||||
| Provides a very common set of utility classes that provide extra functionality for classes in the | ||||||||||||||||
| Provides a bridge between different logging libraries. | ||||||||||||||||
| Provides a generic object pooling interface Provides a generic object pooling interface, a toolkit for creating modular object pools and several general purpose pool implementations. | ||||||||||||||||
| Provides a Java language implementation of standard NFA regular expression features. | ||||||||||||||||
| SQL relational database engine written in Java. | ||||||||||||||||
| International components for Unicode processing. | ||||||||||||||||
| Java package for processing regular expressions. | ||||||||||||||||
Java date chooser bean for graphically picking a date. |
| Java date chooser bean for graphically picking a date. | |||||||||||||||
jdom | Java-based solution for accessing, manipulating, and outputting XML data from Java code. | ||||||||||||||||
| Java framework for building Semantic Web
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| Java regression test framework. | ||||||||||||||||
| Runtime logging services. | ||||||||||||||||
| Text search engine library written in Java. | ||||||||||||||||
| Provided by the Sun JavaMail API
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| JDBC drivers for MySQL database. | ||||||||||||||||
* | Used internally by LexBIG load and export extensions to access and manipulate Eclipse Modeling Framework (EMF) LexBIG load and export extensions to access and manipulate Eclipse Modeling Framework (EMF)
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| JDBC drivers for PostgreSQL database. | ||||||||||||||||
| Used for graph representations in the LexBIG GUI. | ||||||||||||||||
( swt .jar) | Provides the underlying widget toolkit used by the LexBIG GUI. | ||||||||||||||||
| XML parsing services. |
Appendix C Additional Terms and Conditions
Refer to the license.pdf and license.txt files (installed to the LexBIG root directory) for the license terms and conditions of included components.
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