AUTHOR

Luke McCarthy <[email protected]>

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.

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.