User manual, GOTaxExplorer, Version 1.0

Configuration file

GOTaxExplorer uses a configuration file to configure parameters for the database access and for important files. The configuration file is given with the command line option "-c". The following options are available:

url
The database uniform resource locator (url).
user
The username for the database.
password
The password for the database access.
driver
Determines the database driver class, this class has to be in the classpath, default:
com.mysql.jdbc.Driver.
default-browser
Command to open the browser that should be used to access online databases on Unix systems. On other systems, the system default browser is used. Either the absolute path is required or the browser has to be in the user's path, default: firefox.
term-matcher
Determines the number of threads to be used for a comparison of sets of GO terms, default: 1.
funeqs
The number of functionally most similar gene products that are displayed for each entity. If a single gene product is compared to a set of gene products, all members of the set are shown with the scores. If two sets are compared this number defaults to 10.
protein-matcher
The number of threads to be used for a functional equivalence comparison.
bp-graph
The file with the WilmaScope graph for biological process, the absolute path is required, default: ./bp.xwg.
mf-graph
The file with the WilmaScope graph for molecular function, the absolute path is required, default: ./mf.xwg.
cc-graph
The file with the WilmaScope graph for cellular process, the absolute path is required, default: ./cc.xwg.
tax-graph
The file with the WilmaScope graph for the taxonomy, the absolute path is required, default: ./tax.xwg.
bp-tree
The file with the tree representation for biological process, the absolute path is required, default: ./bp.root.
mf-tree
The file with the tree representation for molecular function, the absolute path is required, default: ./mf.root.
cc-tree
The file with the tree representation for cellular process, the absolute path is required, default: ./cc.root.
tax-tree
The file with the tree representation for the taxonomy, the absolute path is required, default: ./tax.root.

The default-browser option as well as all parameters for graphs and trees are not needed by the command line interface version of GOTaxExplorer and thus skipped.

All options can also be given on the command line as parameters. The command line parameters override the options in the configuration file. The parameter name is composed of 1#1 and the key name. Exceptions are: url is replaced by "-u", user is replaced by "-l", password is replaced by "-p".

Syntax of the configuration file

A sample configuration file is given below. The parameters are written as key-value-pairs with a "=" in between. Whitespaces around the "=" are ignored. Comments can be included by adding a "#" at the beginning of a line.


   driver = com.mysql.jdbc.Driver
   #driver=com.p6spy.engine.spy.P6SpyDriver
   url = jdbc:mysql://server:3306/completed_genomes
   user=me
   password=passwd
   bp-tree=/path/to/bp.root
   protein-matcher=5