Bio::Phylo::Util::Exceptions - Errors ($@) that are objects
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; }
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.
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.
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
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.
parse( -format => 'newik', -string => $string )
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.
Thrown when a method is called that requires an object as an argument, and the wrong type of object is specified.
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.
$obj->get('unknown_method')
Thrown when something undefined is wrong with the supplied arguments.
Thrown when a file specified as an argument does not exist or is not readable.
Thrown when there is an error loading a requested extension.
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.
$obj->get_by_index($i)
Thrown when an interface method is called instead of the implementation by the child class.
Thrown when a deprecated method is called.
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'
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'
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
Rethrows a caught exception.
Type : Exception Title : rethrow Usage : $@->rethrow; Function: Rethrows exception Returns : A Bio::Phylo::Util::Exceptions object Args : None
Serializes exception.
Type : Serializer Title : as_string Usage : print $@->as_string; Function: Serializes exception with description and stack trace. Returns : String Args : None
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.