/ 
Bio-Grep-v0.10.6
River stage zero No dependents
/ Bio::Grep::Root

NAME

Bio::Grep::Root - Superclass for all Bio::Grep* packages

DESCRIPTION

This superclass adds some useful methods to all Bio::Grep packages.

METHODS

See Bio::Root::Root for inherited methods.

PACKAGE METHODS

is_integer($var_to_check, 'Description')

Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not an integer. If a second argument is passed, it will be used in the exception text.

is_word($var_to_check, 'Description')

Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not a word. If a second argument is passed, it will be used in the exception text.

is_path($var_to_check, 'Description')

Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not a valid path (It is word but accepts also '/'). If a second argument is passed, it will be used in the exception text.

is_sentence($var_to_check, 'Description')

Returns the variable, but it is now not tainted anymore. Throws an exception if the specified variable is not a valid sentence (It is word but accepts also '/:,;|'). If a second argument is passed, it will be used in the exception text.

WARNING: make sure that command line arguments are quoted ( my $command = "... '$sentence' ")

is_arrayref_of_size($a_ref, $size)

Checks if $a_ref is an array reference and the array is of size $size or larger.

DIAGNOSTICS

... looks not valid.

Some variable does not match the specified regular expression. Bio::Root::BadParameter.

Argument is not an array reference.

Method is_arrayref_of_size() is used to check arguments. You probably called a method with wrong arguments.

Missing arguments: require hash with keys "regex" ...

You called the internal method _check_variable() without a valid hashref. Don't use this method. Bio::Root::BadParameter.

Size of argument is too small.

Method is_arrayref_of_size() is used to check arguments. You probably called a method with missing arguments.

Unknown regex.

You called the internal method _check_variable() with an invalid regex. Don't use this method. Bio::Root::BadParameter.

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENSE AND COPYRIGHT

Copyright (C) 2007-2009 by M. Riester.

Based on Weigel::Search v0.13, Copyright (C) 2005-2006 by Max Planck Institute for Developmental Biology, Tuebingen.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.