Toolbar

Summary

Bio::Root::Global - Global variables and utility functions

Package variables

Included modules

Inherit

Exporter

Synopsis

    # no real synopsis - see Bio::Root::Object

Description

The Bio::Root::Global file contains all the global flags
about erro warning etc, and also utility functions, eg
to map numbers to roman numerals.
These functions are generally called by Bio::Root::Object
or somewhere similar, and not directly

Methods

Methods description

None available.

Methods code

BEGIN {

    use vars qw($CGI $TIMEOUT_SECS);

    # $CGI is a boolean to indicate if the script is running as a CGI.
    # Useful for conditionally producing HTML-formatted messages
    # or suppressing messages appropriate only for interactive sessions.

    $CGI = 1 if $ENV{REMOTE_ADDR} || $ENV{REMOTE_HOST};

}

sub debug {

    my $level = shift;
    if( defined $level) { $DEBUG = $level }
    else { $DEBUG = 0 }
#    $MONITOR and do{ print STDERR $DEBUG ? "Debug on ($DEBUG).\n\n" : "Debug off.\n\n"; };
    $MONITOR and do{ print STDERR $DEBUG ? "Debug on ($DEBUG).\n\n" : ""; };
    $DEBUG;

}

sub dont_warn {

    my $arg = shift;
    !$CGI and print STDERR "\n$0: Deprecated method dont_warn() called. Use verbosity(-1) instead\n";
    if( $arg) { verbosity(-1)}
    else { verbosity(0); }

}

sub fatal_on_warn {

    my $arg = shift;
    !$CGI and print STDERR "\n$0: Deprecated method fatal_on_warn() called. Use strictness(2) instead\n";
    if( $arg) { strictness(2)}
    else { strictness(0); }
}

#####################################################################################
#                            END OF PACKAGE 
#####################################################################################

1;

}

sub monitor {

    my $level = shift;
    if( defined $level) { $MONITOR = $level }
    else { $MONITOR = 0 }
    $DEBUG and (print STDERR "Monitor on ($MONITOR).\n\n");
    $MONITOR;

}

sub record_err {

    if( defined shift) { $RECORD_ERR = 1}
    else { $RECORD_ERR = 0 }
    $RECORD_ERR ? ($DEBUG && print STDERR "\n*** RECORD_ERR on. ***\n\n") : ($DEBUG && print STDERR "RECORD_ERR off.\n\n");
    $RECORD_ERR;
}

##
## The following methods are deprecated and will eventually be removed.
##

}

sub roman2int {

    my $roman = uc(shift);
    foreach (keys %ROMAN_NUMS) {
	return $_ if $ROMAN_NUMS{$_} eq $roman;
    }
# Alternatively:
#    my @int = grep $ROMAN_NUMS{$_} eq $roman, keys %ROMAN_NUMS;
#    return $int[0];
    undef;

}

sub strictness {

# Values can integers from -2 to 2
# See Bio::Root::Object::strict() for more explanation.
    my $arg = shift;
    if( defined $arg) { $STRICTNESS = $arg}
    $DEBUG && print STDERR "\n*** STRICTNESS: $arg ***\n\n";
    $STRICTNESS;

}

sub testing {

    my $level = shift;
    if( defined $level) { $TESTING = $level }
    else { $TESTING = 0 }
    $TESTING ? ($MONITOR && print STDERR "Testing on ($TESTING).\n\n") : ($MONITOR && print STDERR "Testing off.\n\n");
    $TESTING;

}

sub verbosity {

# Values can integers from -1 to 1
# See Bio::Root::Object::verbose() for more explanation.
    my $arg = shift;
    if( defined $arg) { $VERBOSITY = $arg}
    $DEBUG && print STDERR "\n*** VERBOSITY: $arg ***\n\n";
    $VERBOSITY;

}

sub warn_on_fatal {

    my $arg = shift;
    !$CGI and print STDERR "\n$0: Deprecated method warn_on_fatal() called. Use strictness(-2) instead\n";
    if( $arg) { strictness(-2)}
    else { strictness(0); }

}

General documentation

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.