User manual, GOTaxExplorer, Version 1.0
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".
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