Bio::Root::Err.pm - Exception class for Perl 5 objects
Bio::Root::Object.pm is a wrapper for Bio::Root::Err.pm objects so clients do not have to create these objects directly. Please see Bio::Root::Object::throw() as well as _initialize() for a more complete treatment of how to create Bio::Root::Err.pm objects.
use Bio::Root::Err; $err = Bio::Root::Err->new(-MSG =>"Bad data: $data", -STACK =>[\caller(0), \caller(1), ...], );
To use the throw() method directly:
use Bio::Root::Err (:std); throw( $object_ref, 'Error message', 'additional note', 'technical note');
The $object_ref argument should be a reference to a Bio::Root::Object.pm.
$object_ref
See also USAGE.
This module is included with the central Bioperl distribution:
http://bio.perl.org/Core/Latest ftp://bio.perl.org/pub/DIST
Follow the installation instructions included in the README file.
A Bio::Root::Err.pm object encapsulates data and methods that facilitate working with errors and exceptional conditions that arise in Perl objects. There are no biological semantics in this module, as one may suspect from its location in the Bio:: hierarchy. The location of this module serves to separate it from the namespaces of other Perl Error modules. It also makes it convenient for use by Bio:: objects.
The motivation for having an error object is to allow Perl 5 objects to deal with errors or exceptional conditions that can arise during their construction or manipulation. For example:
(1) A complex object can break in many ways. (2) Tracking errors within a set of nested objects can be difficult. (3) The way an error is reported should be context-sensitive: a web-user needs different information than does the software engineer.
Bio::Root::Err.pm, along with Bio::Root::Object.pm, attempt to make such problems tractable. Please see the Bio::Root::Object.pm documentation for more about my error handling philosophy.
A Bio::Root::Err.pm object is an example of a Vector-Object: This module inherits both from Bio::Root::Object.pm and Bio::Root::Vector.pm. This permits a single Err object to exist within a linked list of Err objects OR alone. See the Bio::Root::Vector.pm documentation for more about Vector-Objects.
The API for this module is not complete since the module is under development.
Exception handling with Perl 5 objects is currently not as evolved as one would like. The error handling used by Bio::Root::Object.pm and Bio::Root::Err.pm relies on Perl's built-in error/exception handling with eval/die, which is not very object-aware. What I've attempted to do with these modules is to make eval/die more object-savvy, as well as make Perl 5 objects more eval/die-savvy (but the current strategy is basically a hack).
It would be great if Perl could throw an object reference with die(). This would permit more intelligent and easy to write exception handlers. For now the Err.pm object is reconstructed from the output of string().
There are some other third-party Exception classes such as Torsten Ekedahl's Experimental::Exception.pm or Ken Steven's Throwable.pm or Graham Barr's Error.pm (see "Other Exception Modules"). These modules attempt to introduce a traditional "try-catch-throw" exception handling mechanism into Perl. Future version of my modules (and perhaps erl itself) may utilize one of these.
A demo script that illustrates working with Bio::Root::Err objects is available at:
http://bio.perl.org/Core/Examples/Root_object/error.pl
Bio::Root::Err.pm inherits from Bio::Root::Object.pm and Bio::Root::Vector.pm.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/
Steve A. Chervitz, sac@genome.stanford.edu
See the FEEDBACK section for where to send bug reports and comments.
Bio::Root::Err.pm, 0.041
Bio::Root::Object.pm - Core object Bio::Root::Vector.pm - Vector object Bio::Root::Global.pm - Manages global variables/constants http://bio.perl.org/Projects/modules.html - Online module documentation http://bio.perl.org/ - Bioperl Project Homepage
Experimental::Exception.pm - ftp://ftp.matematik.su.se/pub/teke/ Error.pm - http://www.cpan.org/authors/id/GBARR/ Throwable.pm - mailto:kstevens@globeandmail.ca http://genome-www.stanford.edu/perlOOP/exceptions.html
This module was developed under the auspices of the Saccharomyces Genome Database: http://genome-www.stanford.edu/Saccharomyces
Other Bioperl developers contributed ideas including Ewan Birney, Ian Korf, Chris Dagdigian, Georg Fuellen, and Steven Brenner.
Copyright (c) 1996-8 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
Improve documentation.
Experiment with other Exception modules.
Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only.
Usage : n/a; automatically called by Bio::Root::Object::new() Purpose : Initializes key Bio::Root::Err.pm data. Returns : String (the -MAKE constructor option.) Argument : Named parameters passed from new() : (PARAMETER TAGS CAN BE UPPER OR LOWER CASE). : -MSG => basic description of the exception. : -NOTE => additional note to indicate cause of exception : or provide information about how to fix/report it : -TECH => addition note with technical information : of interest to developer. : -STACK => array reference containing caller() data : -TYPE => string, one of @Bio::Root::Err::ERR_TYPES : (default = exception). : -CONTEXT => array reference : -OBJ => Err object to be cloned.
See Also : Bio::Root::Object::_set_err()
Usage : n/a; internal method used by _initialize() Purpose : Copy all Bio::Root::Err.pm data members into a new object reference. Argument : object ref for object to be cloned. Comments : Does not cloning the vector since this method is : typically used to extract a single Err object from its vector.
Usage : n/a; called by _initialize() Purpose : Re-create an Err.pm object from a string containing Err data. Returns : boolean, (was the Err.pm object rebuilt?) Argument : message, note, tech passed from _initialize() : The message is examined to see if it contains a stringified error.
See Also : _initialize(), string(), _has_err()
Usage : n/a; internal method called by _build_from_string() Purpose : Deterimine if an Err has already been set to prevent duplicate Errs. Returns : boolean
See Also : _build_from_string()
Usage : n/a; internal method Purpose : Sets the type of Err (warning, exception, fatal) : Called by _initialize() Argument : string
Usage : n/a; internal method used by set(). : $err->_set_list_data( $member, $data); Purpose : For data members which are anonymous arrays: note, tech, stack, : adds the given data to the list. Arguments : $member = any of qw(note tech stack) : $data = string Comments : Splits $data on tab. Each item : of the split is a new entry. : To clobber the current data (unusual situation), you must first : call set() with no data then call again with desired data.
Usage : n/a; internal method used by set(). Purpose : Sets the object containment context for the exception. : (this is the hierarchy of objects in which the : exception occurred.)
Usage : $err->set( $member, $data ); Purpose : General accessor for setting any Err.pm data member. Example : $err->set('note', 'this is an additional note.'); Returns : n/a Argument : $member = string, any of qw(msg type note tech stack) : $data = string Throws : n/a Comments : Note, tech, and stack items are appended to any existing : notes, tech notes, and stack. : There should be no need to mess with the stack.
Usage : $message = $err->msg; Purpose : Get the main message associated with the exception. Returns : String Argument : optional string to be used as a delimiter.
See Also : get(), string()
Usage : $type = $err->type; Purpose : Get the type of Err (warning, exception, fatal) Returns : String Argument : optional string to be used as a delimiter.
Usage : $note = $err->note; : $note = $err->note('<P>'); Purpose : Get any general note associated with the exception. Returns : String Argument : optional string to be used as a delimiter.
Usage : $tech = $err->tech; : $tech = $err->tech('<P>'); Purpose : Get any technical note associate with the exception. Returns : String Argument : optional string to be used as a delimiter.
Usage : $stack = $err->stack; : $stack = $err->stack('<P>'); Purpose : Get the call stack for the exception. Returns : String Argument : optional string to be used as a delimiter.
Usage : $context = $err->context; : $context = $err->context('<P>'); Purpose : Get the containment context of the object which generated the exception. Returns : String Argument : optional string to be used as a delimiter.
Usage : $err->get($member, $delimiter); Purpose : Get specific data from the Err.pm object. Returns : String in scalar context. : Array in list context. Argument : $member = any of qw(msg type note tech stack context) or combination. : $delimiter = optional string to be used as a delimiter : between member data.
See Also : string(), msg(), note(), tech(), type(), context(), stack()
Usage : n/a; internal method used by get() Purpose : Gets data for members which are list refs (note, tech, stack, context) Returns : Array Argument : ($member, $delimiter)
See Also : get()
Usage : (same as get()) Purpose : Get specific data from all errors in an Err.pm object. Returns : Array in list context. : String in scalar context. Argument : (same as get())
Usage : n/a; internal method called by _add_list_data() Purpose : adds a new note.
See Also : _add_list_data()
Usage : n/a; internal method called by _add_list_data() Purpose : adds a new technical note.
Usage : n/a; called by _set_list_data() Purpose : adds a new note or tech note.
See Also : _set_list_data()
Usage : $err->print; Purpose : Prints Err data to STDOUT or a FileHandle. Returns : Call to print Argument : Named parameters for string() Comments : Uses string() to get data.
See Also : string()
Usage : $err->string( %named_parameters); Purpose : Stringify the data contained in the Err.pm object. Example : print STDERR $err->string; Returns : String Argument : Named parameters (optional) passed to : Bio::Root::IOManager::set_display().
See Also : print(), _build_from_string(), Bio::Root::IOManager::set_display()
Usage : $err->is_fatal; Purpose : Determine if the error is of type 'FATAL' Returns : Boolean Status : Experimental, Deprecated
Usage : throw($object, [message], [note], [technical note]); : This method is exported. Purpose : Class method version of Bio::Root::Object::throw(). Returns : die()s with the contents of the Err object in a string. : If the global strictness is less than -1, die is not called and : the error is printed to STDERR. Argument : [0] = object throwing the error. : [1] = optional message about the error. : [2] = optional note about the error. : [3] = optional technical note about the error. Comments : The glogal verbosity level is not used. For verbosity-sensitive : behavior, use Bio::Root::Object::throw(). Status : Experimental : This method is an alternative to Bio::Root::Object::throw() : and is not as well developed or documented as that method.
See Also : warning(), Bio::Root::Object::throw() Bio::Root::Global::strictness()
Usage : warning($object, [message], [note], [technical note]); : This method is exported. Purpose : Class method version of Bio::Root::Object::warn(). Returns : Prints the contents of the error to STDERR and returns false (0). : If the global strictness() is > 1, warn() calls are converted : into throw() calls. Argument : [0] = object producing the warning. : [1] = optional message about the error. : [2] = optional note about the error. : [3] = optional technical note about the error. : Comments : The glogal verbosity level is not used. For verbosity-sensitive : behavior, use Bio::Root::Object::warn(). Status : Experimental : This method is an alternative to Bio::Root::Object::warn() : and is not as well developed or documented as that method.
See Also : throw, Bio::Root::Object::warn(), Bio::Root::Global::strictness()
Usage : &format_stack_entry(<class>,<file>,<line>,<class_method>,<has_args>,<wantarray>) : This function is exported. Purpose : Creates a single stack entry given a caller() list. Argument : List of scalars (output of the caller() method). Returns : String = class_method($line) : e.g., Bio::Root::Object::name(1234)
Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind:
All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!).
It is easy for this documentation to become obsolete as this module is still evolving. Always double check this info and search for members not described here.
An instance of Bio::Root::Err.pm is a blessed reference to a hash containing all or some of the following fields:
FIELD VALUE ------------------------------------------------------------------------ _type fatal | warning | exception (one of @Bio::Root::Err::ERR_TYPES). _msg Terse description: Main cause of error. _note List reference. Verbose description: probable cause & troubleshooting for user. _tech List reference. Technical notes of interest to programmer. _stack List reference. Stack trace: list of "class::method(line number)" strings.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.