Bio::Root Err
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Summary
Bio::Root::Err - Exception class for Perl 5 objects
Package variables
No package variables defined.
Included modules
Bio::Root::Global qw ( :devel $CGI )
Bio::Root::Object
Bio::Root::Vector ( )
Exporter ( )
Inherit
Bio::Root::Object Bio::Root::Vector Exporter
Synopsis
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.
See also the USAGE section .
Description
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 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 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 Perl itself) may utilize one
of these.
Methods
_add_list_dataDescriptionCode
_add_noteDescriptionCode
_add_techDescriptionCode
_build_from_stringDescriptionCode
_get_list_dataDescriptionCode
_has_errDescriptionCode
_initializeDescriptionCode
_set_cloneDescriptionCode
_set_contextDescriptionCode
_set_list_dataDescriptionCode
_set_typeDescriptionCode
contextDescriptionCode
format_stack_entryDescriptionCode
getDescriptionCode
get_allDescriptionCode
is_fatalDescriptionCode
msgDescriptionCode
noteDescriptionCode
printDescriptionCode
setDescriptionCode
stackDescriptionCode
stringDescriptionCode
techDescriptionCode
throwDescriptionCode
typeDescriptionCode
warningDescriptionCode
Methods description
_add_list_datacode    nextTop
 Usage     : n/a; called by _set_list_data()
 Purpose   : adds a new note or tech note.
See Also : _set_list_data()
_add_notecodeprevnextTop
 Usage     : n/a; internal method called by _add_list_data()
 Purpose   : adds a new note.
See Also : _add_list_data()
_add_tech()codeprevnextTop
 Usage     : n/a; internal method called by _add_list_data()
 Purpose   : adds a new technical note.
See Also : _add_list_data()
_build_from_stringcodeprevnextTop
 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()
_get_list_datacodeprevnextTop
 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()
_has_errcodeprevnextTop
 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()
_initializecodeprevnextTop
 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()
_set_clonecodeprevnextTop
 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.
_set_contextcodeprevnextTop
 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.)
_set_list_datacodeprevnextTop
 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.
_set_typecodeprevnextTop
 Usage     : n/a; internal method
 Purpose   : Sets the type of Err (warning, exception, fatal)
           : Called by _initialize()
 Argument  : string
contextcodeprevnextTop
 Usage     : $context = $err->context;
           : $context = $err->context('<P>');
 Purpose   : Get the containment context of the object which generated the exception.
 Returns   : String
 Argument  : optional string to be used as a delimiter.
See Also : get(), string()
format_stack_entrycodeprevnextTop
 Usage     : &format_stack_entry(<class>,<file>,<line>,<class_method>,<has_args>,<wantarray>)
           : This function is exported.
 Purpose   : Creates a single stack entry given a caller() list.
 Argument  : List of scalars (output of the caller() method).
 Returns   : String = class_method($line)
           : e.g., Bio::Root::Object::name(1234)
getcodeprevnextTop
 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()
get_allcodeprevnextTop
 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())
See Also : get()
is_fatalcodeprevnextTop
 Usage     : $err->is_fatal;
 Purpose   : Determine if the error is of type 'FATAL'
 Returns   : Boolean
 Status    : Experimental, Deprecated
msgcodeprevnextTop
 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()
notecodeprevnextTop
 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.
See Also : get(), string()
printcodeprevnextTop
 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()
setcodeprevnextTop
 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.
stackcodeprevnextTop
 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.
See Also : get(), string()
stringcodeprevnextTop
 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()
techcodeprevnextTop
 Usage     : $tech = $err->tech;
           : $tech = $err->tech('<P>');
 Purpose   : Get any technical note associate with the exception.
 Returns   : String
 Argument  : optional string to be used as a delimiter.
See Also : get(), string()
throwcodeprevnextTop
 Usage     : throw($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()
typecodeprevnextTop
 Usage     : $type = $err->type;
 Purpose   : Get the type of Err (warning, exception, fatal)
 Returns   : String
 Argument  : optional string to be used as a delimiter.
See Also : get(), string()
warningcodeprevnextTop
 Usage     : warning($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()
Methods code
_add_list_datadescriptionprevnextTop
sub _add_list_data {
#--------------------
    my( $self, $member, $data ) = @_;

    local $_ = $member;
    SWITCH: {
	/note/i  && do{ $self->_add_note( $data ); };
	/tech/i  && do{ $self->_add_tech( $data ); };
    }
}
_add_notedescriptionprevnextTop
sub _add_note {
#---------------
    my( $self, $data ) = @_;

    if( defined $self->{'_note'} ) {
	push @{ $self->{'_note'}}, $data;
    } else {
	$self->_set_list_data('note', $data );
    }
}

#----------------------------------------------------------------------
}
_add_techdescriptionprevnextTop
sub _add_tech {
#-------------
    my( $self, $data ) = @_;

    if( defined $self->{'_tech'} ) {
	push @{ $self->{'_tech'}}, $data;
    } else {
	$self->_set_list_data('Tech', $data );
    }
}
_build_from_stringdescriptionprevnextTop
sub _build_from_string {
#----------------------
    my ($self, $msg, $note, $tech) = @_;
    my @list = split "\n", $msg;
    my ($mode,$line);
    my $rebuilt = 0;

    # print "$ID: Attempting to build from string: $msg";<STDIN>;

    MEMBER:
    foreach $line (@list) {
	if($line =~ /^-+$/) { last MEMBER; }
	if($line =~ /^-+ (\w+) -+$/) { $self->{'_type'} = $1; $rebuilt = 1; next MEMBER; }
	if($line =~ /^MSG: *(\w.*)/) { my $msg = $1;
				       if($self->_has_err($msg)) {
					   die "Duplicate error.";
				       }
				       $self->{'_msg'} = $msg;
				       $mode = 'msg';
				       next MEMBER; }
	if($line =~ /^CONTEXT: *(\w.*)/) { push @{$self->{'_context'}}, $1; $mode = 'context'; next MEMBER; }
	if($line =~ /^NOTE: *(\w.*)/) { push @{$self->{'_note'}}, $1; $mode = 'note'; next MEMBER; }
	if($line =~ /^TECH: *(\w.*)/) { push @{$self->{'_tech'}}, $1; $mode = 'tech'; next MEMBER; }
	if($line =~ /^STACK:/) { $mode = 'stack'; next MEMBER; }
	next MEMBER if !$mode;
	SWITCH: {
	    local $_ = $mode;
	    m/msg/ && do{ $self->{'_msg'} .= "$line\n"; last SWITCH; };
	    m/note/ && do{ push @{$self->{'_note'}}, $line; last SWITCH; };
	    m/context/ && do{ push @{$self->{'_context'}}, $line; last SWITCH; };
	    m/tech/ && do{ push @{$self->{'_tech'}}, $line; last SWITCH; };
	    m/stack/ && do{ push @{$self->{'_stack'}}, $line; last SWITCH; };
	    next MEMBER;
	}
    }
    if($rebuilt) {
	## Optionally add additional notes.
	$self->_set_list_data('note', $note) if defined $note;
	$self->_set_list_data('tech', $tech) if defined $tech;
    }

    $rebuilt;
}
_get_list_datadescriptionprevnextTop
sub _get_list_data {
#-------------------
    my( $self, $member, $delimiter ) = @_;
    $delimiter ||= "\t";
    # Sensitive to data member name changes.
    $member = "_\l$member";
    return if !defined $self->{$member};
    join( $delimiter, @{$self->{$member}} );
}
_has_errdescriptionprevnextTop
sub _has_err {
#-------------
    my ($self, $msg) = @_;

    $msg =~ s/^\s+//;
    $msg =~ s/\s+$//;

    my $err = $self->first;
    my ($existing_msg);
    do {
#	print "checking err object $self\n";
	$existing_msg = $err->msg;
	$existing_msg =~ s/^\s+//;
	$existing_msg =~ s/\s+$//;
#	print "  msg: $existing_msg";<STDIN>;
	return 1 if $existing_msg eq $msg;

    } while($err = $err->next);

    0;
}
_initializedescriptionprevnextTop
sub _initialize {
#----------------
    my( $self, @param ) = @_;

    my $make = $self->Bio::Root::Object::_initialize( @param );

    my( $msg, $note, $tech, $stack, $type, $context, $obj) =
	$self->_rearrange([qw(MSG NOTE TECH STACK TYPE CONTEXT OBJ)], @param);

    ## NOTE: Don't eval {} the construction process for Err objects.

    if($make =~ /clone/i) {
	$self->_set_clone($obj);
    } else {
	if(!$self->_build_from_string($msg, $note, $tech)) {
#	    print "Failed to rebuild: msg = $msg";<STDIN>;
	    $self->set('msg', $msg );
	    $self->_set_type( $type );
	    $self->_set_context($context);
	    $self->_set_list_data('note', $note );
	    $self->_set_list_data('tech', $tech );
	    $self->_set_list_data('stack', $stack );
	}
	$self->set_display();
    }

    $DEBUG and do{ print STDERR "---> Initialized Err (${\ref($self)}).\n\n";
		   # $self->print();
	       };
    $make;
}

##
## Destructor: Not needed currently. Perhaps if and when Vector is used by delegation.
##

#####################################################################################
##                                  ACCESSORS                                      ##
#####################################################################################
}
_set_clonedescriptionprevnextTop
sub _set_clone {
#---------------
    my($self, $obj) = @_;

    ref($obj) || throw($self, "Can't clone $ID object: Not an object ref ($obj)");

    $self->{'_type'}  = $obj->{'_type'};
    $self->{'_msg'}   = $obj->{'_msg'};
    $self->{'_note'}  = $obj->{'_note'};
    $self->{'_tech'}  = $obj->{'_tech'};
    $self->{'_stack'} = $obj->{'_stack'};
    $self->{'_context'} = $obj->{'_context'};
#    $self->clone_vector($obj);
}
_set_contextdescriptionprevnextTop
sub _set_context {
#------------------
    my($self, $aref) = @_;

    eval {
	if (!ref $aref) {
#	    push @{$aref}, sprintf "object %s \"%s\"",ref($self->parent), $self->parent->name;
	    push @{$aref}, "UNKNOWN CONTEXT";
	}
    };
    if($@) { push @{$aref}, 'undefined object'; }

    if($self->type eq 'EXCEPTION') {
	$aref->[0] = "Exception thrown by\l $aref->[0]";
    } else {
	$aref->[0] = "Error in\l $aref->[0]";
    }

    my $script = ($0 =~ /([\w\/\.]+)/, $1);
    push @$aref, "SCRIPT: $script";

    $self->{'_context'} = $aref;

#    print "$ID: _set_context():\n";
#    foreach(@$aref) { print "  $_\n"; }
#    <STDIN>;
}
_set_list_datadescriptionprevnextTop
sub _set_list_data {
#-------------------
    my( $self, $member, $data ) = @_;
	
    # Sensitive to data member name changes.
    $member = "_\l$member";

#    $DEBUG && do {printf STDERR "\n$ID: Setting \"%s\" list data (%s)\n", $member, $data;<STDIN>; };

    defined $self->{$member} and return $self->_add_list_data( $member, $data );

    if( $data ) {
	$self->{$member} = [];
	if( $member =~ /stack/) {
	    foreach (@$data) {
		push @{ $self->{$member}}, format_stack_entry(@$_);
	    }
	} else {
	    my @entries = split "\t", $data;
	    foreach (@entries) {
		next if /^$/;
#		$DEBUG && do {print STDERR "adding $member: $_";<STDIN>;};
		push @{ $self->{$member}}, $_;
	    }
	}
    } else {
	$self->{$member} = undef;
    }
}
_set_typedescriptionprevnextTop
sub _set_type {
#----------------
    my( $self, $data ) = @_;
    $data ||= 'EXCEPTION';

#    printf "\n$ID: Setting type (%s) for err = %s\n", $data, $self->msg;<STDIN>;

    my (@type);
    if( @type = grep /$data/i, @Bio::Root::Err::ERR_TYPES ) {
	$self->{'_type'} = $type[0];
    } else {
	$self->{'_type'} = 'EXCEPTION';
    }

#    print "type = $self->{'_type'} for $self";<STDIN>;
}
contextdescriptionprevnextTop
sub context {
 my($self,$delimiter) = @_; $self->get('context',$delimiter);
}
format_stack_entrydescriptionprevnextTop
sub format_stack_entry {
#------------------------
    my( $class, $file, $line, $classmethod, $hasargs, $wantarray) = @_;

#    if($DEBUG) {
#	print STDERR "format_stack_entry data:\n";
#	foreach(@_) {print STDERR "$_\n"; } <STDIN>;
#    }

    $classmethod ||= 'unknown class/method';
    $line        ||= 'unknown line';
    return "$classmethod($line)";
}

1;
__END__

#####################################################################################
#                                  END OF CLASS                                     #
#####################################################################################
}
getdescriptionprevnextTop
sub get {
#---------
    my( $self, $member, $delimiter ) = @_;

    my $outer_delim = $delimiter || "\n";
#   my $outer_delim = ($CGI ? "\n<P>" : $delimiter);  ## Subtle bug here.

    my (@out);
    local $_ = $member;
    SWITCH: {
	/type/i  && do{ push (@out, $self->{'_type'},$outer_delim) };
#	/msg/i   && do{ print "getting msg";<STDIN>; push (@out, (defined $self->{'_msg'} ? $self->{'_msg'} : ''),$outer_delim); print "msg: @out<---";<STDIN>; };
	/msg/i   && do{ push (@out, (defined $self->{'_msg'} ? $self->{'_msg'} : ''),$outer_delim); };
	/note/i  && do{ push (@out, $self->_get_list_data('note', $delimiter ),$outer_delim) };
	/tech/i  && do{ push (@out, $self->_get_list_data('tech', $delimiter ),$outer_delim) };
	/stack/i && do{ push (@out, $self->_get_list_data('stack', $delimiter ),$outer_delim) };
	/context/i && do{ push (@out, $self->_get_list_data('context', $delimiter ),$outer_delim) };

	## CAN'T USE THE FOLLOWING FORM SINCE IT FAILS WHEN $member EQUALS 'msgnote'.
#	/note|tech|stack/ && do{ push @out, $self->_get_list_data( $_, $delimiter ); };

	 last SWITCH;
	$self->warn("Invalid or undefined Err data member ($member).");
    }
#    $DEBUG && do{ print STDERR "OUTER DELIM = $outer_delim \nOUT: \n  @out <---";<STDIN>;};
    wantarray ? @out : join('',@out);
}
get_alldescriptionprevnextTop
sub get_all {
#------------
    my( $self, $member, $delimiter ) = @_;

    if( $self->size() == 1) {
	return $self->get( $member, $delimiter);
    } else {
	my $err = $self;

	### Return data from multiple errors in a list.
	if(wantarray) {
	    my @out;
	    do{ push @out, $err->get( $member);
	    } while($err = $err->prev());
	    return @out;

	} else {
	    ### Return data from multiple errors in a string with each error's data
	    ### bracketed by a "Error #n\n" line and two delimiters.
	    my $out = '';
	    if($err->size() == 1) {
		$out = $err->get( $member, $delimiter);
	    } else {
		do{ #$out .= "Error #${\$err->rank()}$delimiter";
		    $out .= $err->get( $member, $delimiter);
		    $out .= $delimiter.$delimiter;
		} while($err = $err->prev());
	    }
	    return $out;
	}
    }
}

#####################################################################################
##                              INSTANCE METHODS                                   ##
#####################################################################################
}
is_fataldescriptionprevnextTop
sub is_fatal {
 my $self = shift; $self->{'_type'} eq 'FATAL';
}
msgdescriptionprevnextTop
sub msg {
 my($self,$delimiter) = @_; $self->get('msg',$delimiter);
}
notedescriptionprevnextTop
sub note {
 my($self,$delimiter) = @_; $self->get('note',$delimiter);
}
printdescriptionprevnextTop
sub print {
#-----------
    my( $self, %param ) = @_;
#    my $OUT = $self->parent->fh();
#    print $OUT $self->string(%param);
    print $self->string(%param);
}
setdescriptionprevnextTop
sub set {
#---------
    my( $self, $member, $data ) = @_;

    local $_ = "\u$member";
    SWITCH: {
	/msg/i && do{ $self->{'_msg'} = (defined $data ? $data : 'Unknown error'); last SWITCH; };
	/type/i && do{ $self->_set_type( $data ); last SWITCH; };
	/note|tech|stack/i && do{ $self->_set_list_data( $member, $data); last SWITCH};
	warn "\n*** Invalid or unspecified Err data member: $member\n\n";
    }
}
stackdescriptionprevnextTop
sub stack {
 my($self,$delimiter) = @_; $self->get('stack',$delimiter);
}
stringdescriptionprevnextTop
sub string {
#-----------
    my( $self, @param ) = @_;

    my %param = @param;
    $self->set_display( @param );
    my $show = $self->show;
    my $out  = $param{-BEEP} ? "\a" : '';

    my $err = $param{-CURRENT} ? $self->last : $self->first;

#    my $err1 = $err;
#    my $errL = $self->last;
#    print "\n\nERR 1: ${\$err1->msg}";
#    print "\nERR L: ${\$errL->msg}";<STDIN>;

    my $numerate = $err->size() >1;
    my $count = 0;
    my ($title);
    my $hasnote = defined $self->{'_note'};
    my $hastech = defined $self->{'_tech'};

    while (ref $err)  {
	$count++;
#	$out .= sprintf "\nERROR #%d:", $count;

	if(not $title = $err->{'_type'}) {
	    $err = $err->next();
	    next;
	}
	if( $numerate) {
	    ## The rank data is a bit screwy at present.
	    $out .= sprintf "\n%s %s %s\n", '-'x 20, $title,'-'x 20;
	} else {
	    $out .= sprintf "\n%s %s %s\n", '-'x20, $title,'-'x20;
	}
	$show =~ /msg|default/i   and $out .= "MSG: " . $err->msg("\n");
	$show =~ /note|default/i  and $hasnote and $out .= "NOTE: ".$err->note("\n");
	$show =~ /tech|default/i  and $hastech and $out .= "TECH: ".$err->tech("\n");
	$show =~ /context|default/i  and $out .= "CONTEXT: ".$err->context("\n");
	$show =~ /stack|default/i and $out .= "STACK:\n ".$err->stack("\n");
	$out .= sprintf "%s%s%s\n",'-'x 20, '-'x (length($title)+2), '-'x 20;

#	print "$ID: string: cumulative err:\n$out\n";<STDIN>;

	$err = $err->next();
    }

    $out;
}
techdescriptionprevnextTop
sub tech {
 my($self,$delimiter) = @_; $self->get('tech',$delimiter);
}
throwdescriptionprevnextTop
sub throw {
#----------
    my($obj, @param) = @_;

#    print "Throwing exception for object ${\ref $self} \"${\$self->name}\"\n";
    my $err = new Bio::Root::Err(
			   -MSG     =>$param[0],
			   -NOTE    =>$param[1],
			   -TECH    =>$param[2],
			   -STACK   =>scalar(Bio::Root::Object::stack_trace($obj,2)),
			   -CONTEXT =>Bio::Root::Object::containment($obj),
			   -TYPE    =>'EXCEPTION',
		#	    -PARENT =>$obj,
			   );

    if(strictness() < -1) {
	print STDERR $err->string(-BEEP=>1) unless verbosity() < 0;
    } else {
	die $err->string;
    }

    0;
}
typedescriptionprevnextTop
sub type {
 my($self,$delimiter) = @_; $self->get('type',$delimiter);
}
warningdescriptionprevnextTop
sub warning {
#-----------
    my($obj, @param) = @_;

#    print "Throwing exception for object ${\ref $self} \"${\$self->name}\"\n";
    my $err = new Bio::Root::Err(
			   -MSG     =>$param[0],
			   -NOTE    =>$param[1],
			   -TECH    =>$param[2],
			   -STACK   =>scalar(Bio::Root::Object::stack_trace($obj,2)),
			   -CONTEXT =>Bio::Root::Object::containment($obj),
			   -TYPE    =>'WARNING',
			#   -PARENT =>$obj,
			   );

    if(strictness() > 1) {
	die $err->string;

    } else {
	print STDERR $err->string(-BEEP=>1) unless $DONT_WARN;
    }

    0;
}
General documentation
INSTALLATIONTop
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 INSTALL file.
USAGETop
A demo script that illustrates working with Bio::Root::Err objects is
examples/root_object/error.pl.
DEPENDENCIESTop
Bio::Root::Err.pm inherits from Bio::Root::Object.pm and Bio::Root::Vector.pm.
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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://bugzilla.bioperl.org/
AUTHOR Steve ChervitzTop
Email sac@bioperl.org
See the FEEDBACK section section for where to send bug reports and comments.
VERSIONTop
Bio::Root::Err.pm, 0.041
SEE ALSOTop
  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
Other Exception ModulesTop
  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
ACKNOWLEDGEMENTSTop
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.
COPYRIGHTTop
Copyright (c) 1996-8 Steve Chervitz. All Rights Reserved.
This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.
TODOTop
  * Improve documentation.
  * Experiment with other Exception modules.
APPENDIXTop
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.
FOR DEVELOPERS ONLYTop
Data MembersTop
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:
    1 Do NOT rely on these in any code outside of this module.
    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!).
    2 This documentation may be incomplete and out of date.
    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.