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Each of these packages is accessed via a plugin class which will only be functional if the extra software it needs can be found in the local file system. Note: As of version 0.9.1 there is no longer any need to set the -classpath argument for the additional packages. They are now located as required by the plugins when they are launched. If you have previously defined a batch or script file
to start maxdView you should alter the classpath so that it only
points to the 'current directory' (represented by a single dot),
The XML parser...A package called Xerces is used by the Read Native to parse XML syntax. Xerces was developed by IBM and donated to the Apache Software Foundation. A version of Xerces is now distributed as part of maxdView. The files (and copyright notices) can be found in the external/xml4j subdirectory. By default, the RegExp filter plugin should find these file automatically. Where the software comes from: The JDBC driver...The JDBC is used in the same way as for maxdLoad, it provides the link between the application and the database. The Database Loader plugin is used to browse and retrieve Measurements into maxdView. When this plugin starts, you need specify the location and name of a suitable JDBC driver for the database that you wish to connect to. Consult your database's documentation to find the the correct
driver to use.
Where to get the extra software: The JDBC drivers are normally provided as part of your database distribution. Sometimes they are optional downloads which can be found via the database's website. The Java3D media extension...Java3D is an optional extension of the Java Media Framework (JMF). Java3D can take advantage of the special purpose graphics hardware found in some machines to speed up rendering, but also works on machines without such hardware. The SpacePlot plugin uses these classes to provide 3d visualisation. To activate it, the Java3D extension must be installed in the correct place. The installation tool that comes with Java3D takes care of this for you. Because Java3D is an extension you will have no option as to where the files will be installed. For this reason, maxdView will be able to find the files without any assistance. Where to get the extra software: The WEKA machine learning package...WEKA is a open source package from Waikato University in New Zealand. It provides Java implementations of machine learning algorithms. The Weka Clustering plugin provides an interface to the two
clustering algorithms found in Where to get the extra software: http://www.cs.waikato.ac.nz/~ml/weka/ How to install: Download the JAR file weka-3-1-6.jar. Unpack this file as per the supplied instructions. Start the Weka Clustering plugin. When prompted for the location, specify the weka.jar file that you have unpacked. The XCluster clustering application...XCluster is clustering program written by Gavin Sherlock at Stanford Univeristy. It offers fast hierarchical clustering with optional k-means or self-organising-map partitions. See the XCluster website for details on how to get this software. Where to get the extra software: http://genome-www.stanford.edu/~sherlock/cluster.html How to install: XCluster is written in C not Java. You will need to get the correct XCluster binary for your architecture, e.g. Mac, Windows, Linux. Once you have a suitable XCluster binary, use the "Options" panel on the XCluster plugin to specify the location of the file. The OROMatcher regular-expression package...OROMatcher is a freely available commercial implementation of Perl 5 regular expression matching. This is a powerful syntax used for matching patterns in text strings. The RegExp Filter plugin provides a way to use regular expressions to isolate data points based on their name(s) or associated annotations. A version of this package is now included with maxdView in the external subdirectory. By default, the RegExp Filter plugin should find the required files automatically. Where the extra software comes from: Please be sure to read the copyright notice in the external/OROMatcher-1.1.0a/ directory of the maxdView distribution. Document changes: v1.0, 6 June 2000: new document v1.1, 27 May 2001: changed to reflect the new class finding feature & JNL classes v1.2, 14 June 2001: URLs checked and fixed v1.3, 02 Oct 2002: revised layout v1.4, 15 March 2005: removed JNL material |