NAME

Bio::Phylo::Util::Exceptions - Errors ($@) that are objects

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 ( my $e = Bio::Phylo::Util::Exceptions::BadNumber->caught ) {
    # print out where the error came from
    print $@->trace->as_string;
    
    # caught() returns $@, so $e and $@ are the 
    # same object in this example. 
    # Therefore, the same thing would be:
    print $e->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 an incorrectly formatted string argument is provided, for example a string that would be split into substrings under NEXUS tokenization rules, a string that isn't an xs:NCName or a string that isn't a binomial CURIE
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

new()

Constructor

 Type    : Constructor
 Title   : new
 Usage   : $class->new( error => 'An exception was thrown!' );
 Function: Constructs exception
 Returns : A Bio::Phylo::Util::Exceptions object
 Args    : error => 'Error message'

throw()

Throws exception.

 Type    : Exception
 Title   : throw
 Usage   : $class->throw( error => 'An exception was thrown!' );
 Function: Throws exception
 Returns : A Bio::Phylo::Util::Exceptions object
 Args    : error => 'Error message'

caught()

Catches an exception by class.

 Type    : Handler
 Title   : caught
 Usage   : my $e = Bio::Phylo::Util::Exceptions->caught;
 Function: Catches an exception
 Returns : A Bio::Phylo::Util::Exceptions object
 Args    : None

rethrow()

Rethrows a caught exception.

 Type    : Exception
 Title   : rethrow
 Usage   : $@->rethrow;
 Function: Rethrows exception
 Returns : A Bio::Phylo::Util::Exceptions object
 Args    : None

as_string()

Serializes exception.

 Type    : Serializer
 Title   : as_string
 Usage   : print $@->as_string;
 Function: Serializes exception with description and stack trace.
 Returns : String
 Args    : None

CITATION

If you use Bio::Phylo in published research, please cite it: