GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Bio::Phylo::Util::Exceptions(3) User Contributed Perl Documentation Bio::Phylo::Util::Exceptions(3)

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.

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.

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
    

There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.
Bio::Phylo::Manual
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>

2017-10-30 perl v5.32.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.