NAME

deob_interface.cgi - a WWW user interface to the BioPerl Deobfuscator

VERSION

This document describes deob_interface.cgi version 0.0.3

SYNOPSIS

    This program is designed to be used through a web browser. To install
    deob_interface.cgi and the rest of the Deobfuscator package, see the
    README.

DESCRIPTION

Deob_interface.cgi provides a web-based front-end to the BioPerl Deobfuscator. It uses the Deobfuscator package to open the Berkeley databases storing the BioPerl documentation and then display a list of the available modules. A search box is also provided if the user wants to pare down the list.

When a user clicks on the name of a class, deob_interface.cgi looks up the stored documentation on the methods in that class, and all of the classes that class inherits from, and displays a list of those methods. The list shows the class, return values, and usage statement for each method. A user can see more extensive documentation for a method by clicking on its name or its class's name.

DIAGNOSTICS

Can't open list of Perl module names

deob_interface.cgi can't locate the textfile package_list.txt containing the full list of BioPerl packages. By default this file should be in the same directory as deob_interface.cgi. See "CONFIGURATION AND ENVIRONMENT" for more information.

Can't close list of Perl module names

deob_interface.cgi was unsuccessful in closing the package_list.txt file after reading it. This is most likely a transient filesystem error.

Unknown sort option selected in deob_interface.cgi

In the event a sort parameter other than sort by class or sort by method was sent to the sorting subroutine, deob_interface.cgi will exit with a fatal error.

CONFIGURATION AND ENVIRONMENT

See the README for installation instructions.

There are four hardcoded variables you may need to set. Look in deob_interface.cgi for a section labeled 'SET HARDCODED VALUES HERE'.

$deob_detail_path

The URL of the deob_detail.cgi program. Set to http://localhost/cgi-bin/deob_detail.cgi by default. deob_detail.cgi needs to be in your webserver's cgi-bin directory or some location where you are allowed to serve executable code to the web.

If you are setting up the Deobfuscator package on your own machine, the default URL will probably work. Otherwise, you will need to change the URL, replacing the localhost portion with the hostname of your webserver, and replacing cgi-bin with the path to deob_detail.cgi (starting at your webserver's root directory).

$PERLMODULES

The textfile containing a list of the BioPerl modules. Set to package_list.txt by default. package_list.txt is automatically generated by the deob_index.pl script and its name is a hardcoded value.

If your copy of package_list.txt has a different name or is not in the same directory as deob_detail.cgi, set $PERLMODULES to the full path of package_list.txt's location.

$BerkeleyDB_packages

The Berkeley DB file storing documentation on BioPerl packages. Set to packages.db by default. packages.db is automatically generated by the deob_index.pl script and its name is a hardcoded value.

If your copy of packages.db has a different name or is not in the same directory as deob_detail.cgi, set $BerkeleyDB_packages to the full path of packages.db's location.

$BerkeleyDB_methods

The Berkeley DB file storing documentation on BioPerl methods. Set to methods.db by default. methods.db is automatically generated by the deob_index.pl script and its name is a hardcoded value.

If your copy of methods.db has a different name or is not in the same directory as deob_detail.cgi, set $BerkeleyDB_methods to the full path of methods.db's location.

DEPENDENCIES

version, CGI, Deobfuscator

INCOMPATIBILITIES

None reported.

BUGS AND LIMITATIONS

Selecting a class name returns no methods

Clicking on Bio::Tools::dpAlign or Bio::Tools::AlignFactory in the upper class selection pane produces an empty lower methods pane. There are undoubtedly other modules that will display this behavior. Reported by Laura Kavanaugh 2006-04-18.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                       - General discussion
  http://www.bioperl.org/wiki/Mailing_lists   - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

SEE ALSO

Deobfuscator, deob_detail.cgi, deob_index.pl

AUTHOR

Laura Kavanaugh

CONTRIBUTORS

Dave Messina <dave-pause@davemessina.net>

David Curiel

ACKNOWLEDGMENTS

This software was developed originally at the Cold Spring Harbor Laboratory's Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David Curiel, who provided much-needed guidance and assistance on this project. Also, special thanks to Todd Wylie for his help with CGI.

LICENSE AND COPYRIGHT

Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved.

You may use modify or redistribute this software under the same terms as Perl itself.

DISCLAIMER

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq