NAME

Bio::Phylo::Util::Exceptions - Exception classes for Bio::Phylo.

SYNOPSIS

use Bio::Phylo::Forest::Node;
my $node = Bio::Phylo::Forest::Node->new;

# now let's try something illegal
eval {
   $node->set_branch_length( 'non-numerical value' );
};

# have an error
if ( $@ && UNIVERSAL::isa( $@, 'Bio::Phylo::Util::Exception' ) ) {

   # print out where the error came from
   print $@->trace->as_string;
}

DESCRIPTION

Sometimes, Bio::Phylo dies. If this happens because you did something that brought Bio::Phylo into an undefined and dangerous state (such as might happen if you provide a non-numerical value for a setter that needs numbers), Bio::Phylo will throw an "exception", a special form of the $@ variable that is a blessed object with useful methods to help you diagnose the problem.

This package defines the exceptions that can be thrown by Bio::Phylo. There are no serviceable parts inside. Refer to the Exception::Class perldoc for more examples on how to catch exceptions and show traces.

EXCEPTION TYPES

Bio::Phylo::Util::Exceptions::BadNumber

Thrown when anything other than a number that passes Scalar::Util's looks_like_number test is given as an argument to a method that expects a number.

Bio::Phylo::Util::Exceptions::BadString

Thrown when a string that contains any of the characters ():;, is given as an argument to a method that expects a name.

Bio::Phylo::Util::Exceptions::BadFormat

Thrown when a non-existing parser or unparser format is requested, in calls such as parse( -format => 'newik', -string => $string ), where 'newik' doesn't exist.

Bio::Phylo::Util::Exceptions::OddHash

Thrown when an odd number of arguments has been specified. This might happen if you call a method that requires named arguments and the key/value pairs don't seem to match up.

Bio::Phylo::Util::Exceptions::ObjectMismatch

Thrown when a method is called that requires an object as an argument, and the wrong type of object is specified.

Bio::Phylo::Util::Exceptions::UnknownMethod

Trown when an indirect method call is attempted through the $obj->get('unknown_method') interface, and the object doesn't seem to implement the requested method.

Bio::Phylo::Util::Exceptions::BadArgs

Thrown when something undefined is wrong with the supplied arguments.

Bio::Phylo::Util::Exceptions::FileError

Thrown when a file specified as an argument does not exist or is not readable.

Bio::Phylo::Util::Exceptions::ExtensionError

Thrown when there is an error loading a requested extension.

Bio::Phylo::Util::Exceptions::OutOfBounds

Thrown when an entity is requested that falls outside of the range of objects contained by a Bio::Phylo::Listable subclass, probably through the $obj->get_by_index($i) method call.

Bio::Phylo::Util::Exceptions::NotImplemented

Thrown when an interface method is called instead of the implementation by the child class.

Bio::Phylo::Util::Exceptions::Deprecated

Thrown when a deprecated method is called.

SEE ALSO

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Exceptions.pm 3395 2007-03-26 17:49:02Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.