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 CLASSES

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.

METHODS

throw()

Serializes invocant to XML.

 Type    : Exception
 Title   : throw
 Usage   : $class->throw( error => 'An exception was thrown!' );
 Function: Throws exception
 Returns : A Bio::Phylo::Util::Exceptions object
 Args    : None

SEE ALSO

Bio::Phylo::Manual

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

REVISION

 $Id: Exceptions.pm 4224 2007-07-16 03:16:05Z rvosa $