NAME¶
EMBOSS::GUI::Conf - repository for EMBOSS::GUI site-specific configuration
AUTHOR¶
Luke McCarthy <lukem@gene.pbi.nrc.ca>
SYNOPSIS¶
use EMBOSS::GUI::Conf;
$conf = EMBOSS::GUI::Conf->new();
foreach $app ($conf->apps) {
($name, $doc) = @$app;
if (!$conf->is_excluded($name)) {
...
}
}
foreach $group ($conf->groups) {
$group_name = shift @$group;
if (!conf->is_excluded($group_name) {
foreach $app (@$group) {
($name, $doc) = @$app;
...
}
}
}
DESCRIPTION¶
EMBOSS::GUI::Conf contains site-specific configuration information for
EMBOSS::GUI. Consult the source for a description of the variables that can be
set.
Public methods are described below:
- new()
- Returns a new EMBOSS::GUI::Conf object. This method stores
the EMBOSS::GUI::Conf package variables in the object hash, ensures that
the specified output path is writeable and adds the EMBOSS binaries to the
path.
- apps()
- Returns a list of available EMBOSS applications. Each
element of the list is a reference to an array containing the name and
description of an application.
- groups()
- Returns a list of application groups. Each element of the
list is a reference to an array containing the name of the group and a
list of applications belonging to that group (each application is in turn
a reference to an array as described in apps() above.) Note that an
individual application can appear in multiple groups.
- is_excluded($subject)
- Returns true if the subject is being excluded from public
display, false otherwise.
$subject is the name of an application or application group as it appears in
the output from wossname.
- databases()
- Returns a list of available databases. Each element of the
list is the name of a database, suitable for use in a USA.
- matrices()
- Returns a list of available alignment scoring matrices.
Each element of the list is a reference to an array containing the
filename of the scoring matrix, suitable for use as the value of a matrix
or matrixf argument, and a description of the matrix.
- codon_usage_tables()
- Returns a list of available codon usage tables. Each
element of the list is a reference to an array containing the filename of
the codon usage table, suitable for use as the value of a codon argument,
and the name of the species from which it is derived.
BUGS¶
None that I know of.
COPYRIGHT¶
Copyright (c) 2004 Luke McCarthy. All rights reserved. This program is free
software. You may copy or redistribute it under the same terms as Perl
itself.