Bio::Root Exception
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Root::Exception - Generic exception objects for Bioperl
Package variables
Privates (from "my" definitions)
$debug = $Error::Debug
Included modules
    use Bio::Root::Exception;
use Error;
# Set Error::Debug to include stack trace data in the error messages $Error::Debug = 1; $file = shift; open (IN, $file) || throw Bio::Root::FileOpenException ( "Can't open file $file for reading", $!);
     # Here we have an object that ISA Bio::Root::Root, so it inherits throw().
open (IN, $file) || $object->throw(-class => 'Bio::Root::FileOpenException', -text => "Can't open file $file for reading", -value => $!);
    use Bio::Root::Exception;
use Error qw(:try);
# Note that we need to import the 'try' tag from # Set Error::Debug to include stack trace data in the error messages $Error::Debug = 1; $file = shift; try { open (IN, $file) || throw Bio::Root::FileOpenException ( "Can't open file $file for reading", $!); } catch Bio::Root::FileOpenException with { my $err = shift; print STDERR "Using default input file: $default_file\n"; open (IN, $default_file) || die "Can't open $default_file"; } otherwise { my $err = shift; print STDERR "An unexpected exception occurred: \n$err"; # By placing an the error object reference within double quotes, # you're invoking its stringify() method. } finally { # Any code that you want to execute regardless of whether or not # an exception occurred. }; # the ending semicolon is essential!
    @Bio::TestException::ISA = qw( Bio::Root::Exception );
These are generic exceptions for typical problem situations that could arise
in any module or script.
Using defined exception classes like these is a good idea because it
indicates the basic nature of what went wrong in a convenient,
computable way.
If there is a type of exception that you want to throw
that is not covered by the classes listed above, it is easy to define
a new one that fits your needs. Just write a line like the following
in your module or script where you want to use it (or put it somewhere
that is accessible to your code):
    @NoCanDoException::ISA = qw( Bio::Root::Exception );
All of the exceptions defined in this module inherit from a common
base class exception, Bio::Root::Exception. This allows a user to
write a handler for all Bioperl-derived exceptions as follows:
           use Bio::Whatever;
use Error qw(:try);
try { # some code that depends on Bioperl } catch Bio::Root::Exception with { my $err = shift; print "A Bioperl exception occurred:\n$err\n"; };
So if you do create your own exceptions, just be sure they inherit
from Bio::Root::Exception directly, or indirectly by inheriting from a
Bio::Root::Exception subclass.
The exceptions in Bio::Root::Exception are extensions of Graham Barr's
Error module available from CPAN. Despite this dependency, the
Bio::Root::Exception module does not explicitly require Error.
This permits Bio::Root::Exception to be loaded even when is not available. is not part of the Bioperl distibution, and may not be
present within any given perl installation. So, when you want to
throw an exception in a Bioperl module, the safe way to throw it
is to use Bio::Root::Root/throw which can use
when it's available. See documentation in Bio::Root::Root for details.
No description
Methods description
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 Purpose : Guarantees that -value is set properly before
calling Error::new().
Arguments: key-value style arguments same as for Error::new() You can also specify plain arguments as ($message, $value) where $value is optional. -value, if defined, must be non-zero and not an empty string in order for eval{}-based exception handlers to work. These require that if($@) evaluates to true, which will not be the case if the Error has no value (Error overloads numeric operations to the Error::value() method). It is OK to create Bio::Root::Exception objects without specifying -value. In this case, an invisible dummy value is used. If you happen to specify a -value of zero (0), it will be replaced by the string "The number zero (0)". If you happen to specify a -value of empty string (""), it will be replaced by the string "An empty string ("")".
 Purpose : Get a nicely formatted string containing information about the 
exception. Format is similar to that produced by
Bio::Root::Root::throw(), with the addition of the name of
the exception class in the EXCEPTION line and some other
data available via the Error object.
Example : print $error->pretty_format;
 Purpose : Overrides Error::stringify() to call pretty_format(). 
This is called automatically when an exception object
is placed between double quotes.
Example : catch Bio::Root::Exception with {
my $error = shift;
print "$error";
See Also: pretty_format()
Methods code
sub new {
    my ($class, @args) = @_; 
    my ($value, %params);
    if( @args % 2 == 0 && $args[0] =~ /^-/) {
        %params = @args;
        $value = $params{'-value'};
    else {
        $params{-text} = $args[0];
        $value = $args[1];

    if( defined $value ) {
        $value = "The number zero (0)" if $value =~ /^\d+$/ && $value == 0;
        $value = "An empty string (\"\")" if $value eq "";
    else {
	$value ||= $DEFAULT_VALUE;
    $params{-value} = $value;

    my $self = $class->SUPER::new( %params );
    return $self;
sub pretty_format {
    my $self = shift;
    my $msg = $self->text;
    my $stack = '';
    if( $Error::Debug ) {
      $stack = $self->_reformat_stacktrace();
    my $value_string = $self->value ne $DEFAULT_VALUE ? "VALUE: ".$self->value."\n" : "";
    my $class = ref($self);

    my $title = "------------- EXCEPTION: $class -------------";
    my $footer = "\n" . '-' x CORE::length($title);
    my $out = "\n$title\n" .
       "MSG: $msg\n". $value_string. $stack. $footer . "\n";
    return $out;

# Reformatting of the stack performed by  _reformat_stacktrace:
# 1. Shift the file:line data in line i to line i+1.
# 2. change xxx::__ANON__() to "try{} block"
# 3. skip the "require" and "Error::subs::try" stack entries (boring)
# This means that the first line in the stack won't have any file:line data
# But this isn't a big issue since it's for a Bio::Root::-based method
# that doesn't vary from exception to exception.
sub _reformat_stacktrace {
    my $self = shift;
    my $msg = $self->text;
    my $stack = $self->stacktrace();
    $stack =~ s/\Q$msg//;
    my @stack = split( /\n/, $stack);
    my @new_stack = ();
    my ($method, $file, $linenum, $prev_file, $prev_linenum);
    my $stack_count = 0;
    foreach my $i( 0..$#stack ) {
        # print "STACK-ORIG: $stack[$i]\n";
if( ($stack[$i] =~ /^\s*([^(]+)\s*\(.*\) called at (\S+) line (\d+)/) || ($stack[$i] =~ /^\s*(require 0) called at (\S+) line (\d+)/)) { ($method, $file, $linenum) = ($1, $2, $3); $stack_count++; } else{ next; } if( $stack_count == 1 ) { push @new_stack, "STACK: $method"; ($prev_file, $prev_linenum) = ($file, $linenum); next; } if( $method =~ /__ANON__/ ) { $method = "try{} block"; } if( ($method =~ /^require/ and $file =~ /Error\.pm/ ) || ($method =~ /^Error::subs::try/ ) ) { last; } push @new_stack, "STACK: $method $prev_file:$prev_linenum"; ($prev_file, $prev_linenum) = ($file, $linenum); } push @new_stack, "STACK: $prev_file:$prev_linenum"; return join "\n", @new_stack;
sub stringify {
    my ($self, @args) = @_;
    return $self->pretty_format( @args );
General documentation
See the examples/exceptions directory of the Bioperl distribution for
working demo code.
Bio::Root::Root/throw for information about throwing
Bio::Root::Exception-based exceptions.
Error (available from CPAN, author: GBARR) is helping to guide the design of exception handling in Perl 6.
See these RFC's:
Steve Chervitz <>
Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
This software is provided "as is" without warranty of any kind.
 Purpose : A generic base class for all BioPerl exceptions.
By including a "catch Bio::Root::Exception" block, you
should be able to trap all BioPerl exceptions.
Example : throw Bio::Root::Exception("A generic exception", $!);
Methods defined by Bio::Root::ExceptionTop
Subclasses of Bio::Root::Exception Top
 Purpose : Indicates that a method has not been implemented.
Example : throw Bio::Root::NotImplemented(
-text => "Method \"foo\" not implemented in module FooBar.",
-value => "foo" );
 Purpose : Indicates that some input/output-related trouble has occurred.
Example : throw Bio::Root::IOException(
-text => "Can't save data to file $file.",
-value => $! );
 Purpose : Indicates that a file could not be opened.
Example : throw Bio::Root::FileOpenException(
-text => "Can't open file $file for reading.",
-value => $! );
 Purpose : Indicates that a system call failed.
Example : unlink($file) or throw Bio::Root::SystemException(
-text => "Can't unlink file $file.",
-value => $! );
 Purpose : Indicates that one or more parameters supplied to a method 
are invalid, unspecified, or conflicting.
Example : throw Bio::Root::BadParameter(
-text => "Required parameter \"-foo\" was not specified",
-value => "-foo" );
 Purpose : Indicates that a specified (start,end) range or 
an index to an array is outside the permitted range.
Example : throw Bio::Root::OutOfRange(
-text => "Start coordinate ($start) cannot be less than zero.",
-value => $start );
 Purpose : Indicates that a requested thing cannot be located 
and therefore could possibly be bogus.
Example : throw Bio::Root::NoSuchThing(
-text => "Accession M000001 could not be found.",
-value => "M000001" );