EMBOSS::GUI::Conf3pm

Usage

  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;
                        ...
                }
        }
  }

Overview

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.