Getting started: Difference between revisions
From Jstacs
Jump to navigationJump to search
No edit summary |
|||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
We recommend to use a [ | We recommend to use a [https://en.wikipedia.org/wiki/Integrated_development_environment integrated development environment] (IDE) as for instance [http://www.eclipse.org eclipse]. | ||
== Basic Requirements == | == Basic Requirements == | ||
* Make sure that you have installed [http://java.sun.com/javase/downloads/index.jsp Java] 1. | * Make sure that you have installed [http://java.sun.com/javase/downloads/index.jsp Java] 1.7 or later. | ||
* Download latest version of [http://www.jstacs.de/index.php/Downloads Jstacs]. | * Download latest version of [http://www.jstacs.de/index.php/Downloads Jstacs]. | ||
* Include all <code>jar</code>s (<code>jstacs-<version>.jar</code> and further potentially required <code>jar</code>s from the <code>lib</code> directory of Jstacs) into your classpath: | * Include all <code>jar</code>s (<code>jstacs-<version>.jar</code> and further potentially required <code>jar</code>s from the <code>lib</code> directory of Jstacs) into your classpath: | ||
** Using a | ** Using a IDE, you have to add the <code>jar</code>s to the Java build path by changing the properties of your project. | ||
** Using command line, you have to compile your program using: <code>javac -cp <JARs> <YourClass>.java</code> where <code><JARs></code> contains the path to all your jar-files. | ** Using command line, you have to compile your program using: <code>javac -cp <JARs> <YourClass>.java</code> where <code><JARs></code> contains the path to all your jar-files. | ||
* Run your program: | * Run your program: | ||
** Using a | ** Using a IDE, running jobs depends on the IDE and is often linked with some button. | ||
** Using command line, you have to use <code>java -cp <JARs> <YourClass></code>. | ** Using command line, you have to use <code>java -cp <JARs> <YourClass></code>. | ||
| Line 16: | Line 16: | ||
* If you want to use [http://www.jstacs.de/api/de/jstacs/utils/UserTime.html UserTime], you must compile <code>de_jstacs_utils_UserTime.c</code> and you must set the library-path (<code>-Djava.library.path</code>) to the directory where the dynamic library resides. For details see the documentation of [http://www.jstacs.de/api/de/jstacs/utils/UserTime.html UserTime]. | * If you want to use [http://www.jstacs.de/api/de/jstacs/utils/UserTime.html UserTime], you must compile <code>de_jstacs_utils_UserTime.c</code> and you must set the library-path (<code>-Djava.library.path</code>) to the directory where the dynamic library resides. For details see the documentation of [http://www.jstacs.de/api/de/jstacs/utils/UserTime.html UserTime]. | ||
* Some parts of Jstacs require additional libraries. For instance, [http://www.jstacs.de/api/de/jstacs/utils/REnvironment.html REnvironment] requires <code>RServe-<version>.jar</code> or [http://www.jstacs.de/api/de/jstacs/data/bioJava/BioJavaAdapter.html BioJavaAdapter] requires <code>biojava-live.jar</code> and <code>bytecode.jar</code>. Such libraries can be found in the <code>lib</code> directory of the [[Downloads|binary version]] of Jstacs. | |||
* We use LaTeX to include formulas in our javadoc-comments. To render these as images, you need [http://users.informatik.uni-halle.de/~grau/LaTeXlet/ LaTeXlet]. | * We use LaTeX to include formulas in our javadoc-comments. To render these as images, you need [http://users.informatik.uni-halle.de/~grau/LaTeXlet/ LaTeXlet]. | ||
Latest revision as of 14:45, 12 February 2016
We recommend to use a integrated development environment (IDE) as for instance eclipse.
Basic Requirements
- Make sure that you have installed Java 1.7 or later.
- Download latest version of Jstacs.
- Include all
jars (jstacs-<version>.jarand further potentially requiredjars from thelibdirectory of Jstacs) into your classpath:- Using a IDE, you have to add the
jars to the Java build path by changing the properties of your project. - Using command line, you have to compile your program using:
javac -cp <JARs> <YourClass>.javawhere<JARs>contains the path to all your jar-files.
- Using a IDE, you have to add the
- Run your program:
- Using a IDE, running jobs depends on the IDE and is often linked with some button.
- Using command line, you have to use
java -cp <JARs> <YourClass>.
Additional Requirements
- If you want to use REnvironment, you must have a server with a running instance of R and Rserve.
- If you want to use UserTime, you must compile
de_jstacs_utils_UserTime.cand you must set the library-path (-Djava.library.path) to the directory where the dynamic library resides. For details see the documentation of UserTime.
- Some parts of Jstacs require additional libraries. For instance, REnvironment requires
RServe-<version>.jaror BioJavaAdapter requiresbiojava-live.jarandbytecode.jar. Such libraries can be found in thelibdirectory of the binary version of Jstacs.
- We use LaTeX to include formulas in our javadoc-comments. To render these as images, you need LaTeXlet.
First steps
For your first steps with Jstacs, we recommend to download the Recipes of the Jstacs Cookbook and start with compiling and running one of the simpler code examples, for instance the Creation of user-specfic alphabet. If you could compile and run this example successfully, you might want to have a look at the other Code examples and choose one of them as the starting point of your own application. If you want to extend Jstacs by your own model, classifier, or learning principle, we recommend to read the Jstacs Cookbook and use the API documentation for an overview of current implementation and abstract classes you could possibly make use of.
