EMBOSS::GUI::Conf(3) repository for EMBOSS::GUI site-specific configuration

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.

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.