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__NOTOC__
= Java implementation =
 
== Requirements ==
== Requirements ==
Alida requires Java 1.6 or later.  
Alida's implementation in Java requires Java 1.6 or later.  


The following external jars are needed to use Alida:
The following external jars are needed to use Alida:
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== Current release (v1.2)==
== Current release (v1.2)==
* Alida Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Java Binaries [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin.zip zip] (includes Alida binaries, license information and the file ''aldgraphml.jar'' with Alida's extensions of graphml)
* Alida Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida Java Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src.zip zip] (includes only the sources, license files and some READMEs on how to use and compile Alida)
* Alida API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api.zip zip] (includes Javadocs of Alida's API)
* Alida Java API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api.zip zip] (includes Javadocs of Alida's API)
<br/>
<br/>


== All versions of Alida ==
== Archive of Alida's Java releases ==


{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
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|-
|-
| 1.2
| 1.2
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.2.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]
| March 2nd, 2012
| March 2nd, 2012
|-
|-
| 1.1
| 1.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.1.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]
| Sep 14th, 2011
| Sep 14th, 2011
|-
|-
| 1.0
| 1.0
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_api-1.0.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]
| May 9th, 2011
| May 9th, 2011
|}
|}
<br/>
<br/>


== Manual ==
= C++ implementation =
 
Alida's implementation in C++ requires Linux as operating system.
 
The following external libraries are needed:
 
* [http://loki-lib.sourceforge.net/index.php?n=Main.HomePage Loki], Version 0.17
 
Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:
* [http://opencv.willowgarage.com/wiki/ OpenCV], Version 2.1 or higher (refer to the [[Installation]] section for details on compiling the OpenCV wrapper)
 
== Current release (v0.1)==
* Alida C++ Sources [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_src.zip zip] (includes the sources, license files and some READMEs on how to use and compile Alida)
* Alida C++ API [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/cpp/Alida-Cpp_api.zip zip] (includes Doxygen documentation of Alida's C++ API)
<br/>
 
== Archive of Alida's C++ releases ==
 
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Sources
! API
! Date
|-
| 0.1
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip coming soon...][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip coming soon...]
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.tgz coming soon...][http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.tgz coming soon...]
| March 12th, 2012
|}
<br/>
 
= Manual =


Detailed information about Alida, its API and usage, can be found in the user and programmer manual.  
Detailed information about Alida, its API and usage, can be found in the user and programmer manual.  
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<br/>
<br/>


== Additional resources ==
= Additional resources =


* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
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<br/>
<br/>


== Logo ==
= Logo =


* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]

Revision as of 17:10, 9 March 2012

Java implementation

Requirements

Alida's implementation in Java requires Java 1.6 or later.

The following external jars are needed to use Alida:

In addition, Alida requires some more libraries which are either in-house developments or result from modifications of other libraries:

  • We use a slightly modified version of SezPoz for annotation indexing. You can get the modified version here.
  • Alida also requires some graphml extensions to be found in aldgraphml.jar jar.
  • The graphical operator runner features an online help system based on JavaHelp System, the corresponding Alida-Help.jar can be found here.

If you download the Alida binary zipfile you will find these two libraries in the subdirectory intjars of the zipfile.
Make sure that all of them are in the classpath when executing the operator runners.

Current release (v1.2)

  • Alida Java Binaries zip (includes Alida binaries, license information and the file aldgraphml.jar with Alida's extensions of graphml)
  • Alida Java Sources zip (includes only the sources, license files and some READMEs on how to use and compile Alida)
  • Alida Java API zip (includes Javadocs of Alida's API)


Archive of Alida's Java releases

Version Binaries Sources API Date
1.2 zip zip zip March 2nd, 2012
1.1 zip zip zip Sep 14th, 2011
1.0 zip zip zip May 9th, 2011


C++ implementation

Alida's implementation in C++ requires Linux as operating system.

The following external libraries are needed:

Optionally a prototypical implementation of an OpenCV wrapper is included for which the OpenCV library is required:

  • OpenCV, Version 2.1 or higher (refer to the Installation section for details on compiling the OpenCV wrapper)

Current release (v0.1)

  • Alida C++ Sources zip (includes the sources, license files and some READMEs on how to use and compile Alida)
  • Alida C++ API zip (includes Doxygen documentation of Alida's C++ API)


Archive of Alida's C++ releases

Version Sources API Date
0.1 coming soon...coming soon... coming soon...coming soon... March 12th, 2012


Manual

Detailed information about Alida, its API and usage, can be found in the user and programmer manual.

  • Alida-Manual, Version 1.0 pdf


Additional resources

  • Chipory - a graph visualization tool for displaying MiToBo history graphs
    Chipory is an extended version of the Chisio software developed at the Bilkent University in Turkey.


The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

  • To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.
  • In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.
  • For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.


Download the current release: [http

Source code for Chipory is available upon request.

  • Alida logo as PDF