Bio::Grep::Root - Superclass for all Bio::Grep* packages
This superclass adds some useful methods to all Bio::Grep packages.
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' ")
_check_variable( variable => $var_to_check, regex => $regex, desc => 'Description')
Checks $var_to_check if it matches $regex, which is one of the four predefined regular expressions: int, word, path or sentence. Throws an exception if not, otherwise it returns the untainted value of $var_to_check. Don't use this method, instead use the public methods is_integer(), is_word() ... .
$var_to_check
int
word
path
sentence
... looks not valid.
Some variable does not match the specified regular expression. Bio::Root::BadParameter.
Bio::Root::BadParameter
Missing arguments: require hash with keys "regex" ...
You called _check_variable() without a valid hashref. See "INTERNAL METHODS". Bio::Root::BadParameter.
Unknown regex.
You called _check_variable() with an invalid regex. See "INTERNAL METHODS". Bio::Root::BadParameter.
Markus Riester, <mriester@gmx.de>
Based on Weigel::Seach 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.
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 LICENCE, 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.
To install Bio::Grep, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Grep
CPAN shell
perl -MCPAN -e shell install Bio::Grep
For more information on module installation, please visit the detailed CPAN module installation guide.