package	Bio::Root::Utilities;
use strict;

# $Id: Utilities.pm 16123 2009-09-17 12:57:27Z cjfields $

=head1 NAME

Bio::Root::Utilities - General-purpose utility module

=head1 SYNOPSIS

=head2 Object Creation

    # Using the supplied singleton object:
    use Bio::Root::Utilities qw(:obj);
    $Util->some_method();

    # Create an object manually:
    use Bio::Root::Utilities;
    my $util = Bio::Root::Utilities->new();
    $util->some_method();

    $date_stamp = $Util->date_format('yyy-mm-dd');

    $clean = $Util->untaint($dirty);

    $compressed = $Util->compress('/home/me/myfile.txt')

    my ($mean, $stdev) = $Util->mean_stdev( @data );

    $Util->authority("me@example.com");
    $Util->mail_authority("Something you should know about...");

    ...and a host of other methods. See below.

=head1 DESCRIPTION

Provides general-purpose utilities of potential interest to any Perl script.

The C<:obj> tag is a convenience that imports a $Util symbol into your
namespace representing a Bio::Root::Utilities object. This saves you
from creating your own Bio::Root::Utilities object via
C<Bio::Root::Utilities-E<gt>new()> or from prefixing all method calls with
C<Bio::Root::Utilities>, though feel free to do these things if desired.
Since there should normally not be a need for a script to have more
than one Bio::Root::Utilities object, this module thus comes with it's
own singleton.

=head1 INSTALLATION

This module is included with the central Bioperl distribution:

   http://www.bioperl.org/wiki/Getting_BioPerl
   ftp://bio.perl.org/pub/DIST

Follow the installation instructions included in the README file.

=head1 DEPENDENCIES

Inherits from L<Bio::Root::Root>, and uses L<Bio::Root::IO> 
and L<Bio::Root::Exception>.

Relies on external executables for file compression/uncompression 
and sending mail. No paths to these are hard coded but are located 
as needed.

=head1 SEE ALSO

  http://bioperl.org  - Bioperl Project Homepage

=head1 FEEDBACK

=head2 Mailing Lists

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/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

=head1 AUTHOR

Steve Chervitz E<lt>sac@bioperl.orgE<gt>

See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.


=head1 ACKNOWLEDGEMENTS

This module was originally developed under the auspices of the
Saccharomyces Genome Database: http://www.yeastgenome.org/

=head1 COPYRIGHT

Copyright (c) 1996-2007 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.

=cut

=head1 APPENDIX

Methods beginning with a leading underscore are considered private
and are intended for internal use by this module. They are
B<not> considered part of the public interface and are described here
for documentation purposes only.

=cut

# Let the code begin...

use Bio::Root::IO;
use Bio::Root::Exception;

use vars qw(@EXPORT_OK %EXPORT_TAGS);
use base qw(Bio::Root::Root Exporter);
@EXPORT_OK   = qw($Util);
%EXPORT_TAGS = ( obj => [qw($Util)],
		   std => [qw($Util)],);

use vars qw($ID $Util $GNU_PATH $TIMEOUT_SECS 
            @COMPRESSION_UTILS @UNCOMPRESSION_UTILS
            $DEFAULT_NEWLINE $NEWLINE $AUTHORITY
            @MONTHS @DAYS $BASE_YEAR $DEFAULT_CENTURY
            );

$ID = 'Bio::Root::Utilities';
# Number of seconds to wait before timing out when reading input (taste_file())
$TIMEOUT_SECS  = 30;
$NEWLINE = $ENV{'NEWLINE'} || undef;
$BASE_YEAR = 1900;  # perl's localtime() assumes this for it's year data.
# TODO: update this every hundred years. Y2K-sensitive code.
$DEFAULT_CENTURY = $BASE_YEAR + 100;
@MONTHS = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
@DAYS   = qw(Sun Mon Tue Wed Thu Fri Sat);
# Sets the preference for compression utilities to be used by compress().
# The first executable in this list to be found in the current PATH will be used,
# unless overridden in the call to that function. See docs for details.
@COMPRESSION_UTILS = qw(gzip bzip2 zip compress);
@UNCOMPRESSION_UTILS = qw(gunzip bunzip2 unzip uncompress);

# Default person to receive feedback from users and possibly automatic error messages.
$AUTHORITY = '';

# Note: $GNU_PATH is now deprecated, shouldn't be needed since now this module
# will automatically locate the compression utility in the current PATH.
# Retaining $GNU_PATH for backward compatibility.
#
# $GNU_PATH points to the directory containing the gzip and gunzip
# executables. It may be required for executing gzip/gunzip
# in some situations (e.g., when $ENV{PATH} doesn't contain this dir.
# Customize $GNU_PATH for your site if the compress() or
# uncompress() functions are generating exceptions.
$GNU_PATH  = '';
#$GNU_PATH  = '/tools/gnu/bin/';

$DEFAULT_NEWLINE = "\012";  # \n  (used if get_newline() fails for some reason)

## Static UTIL object.
$Util = Bio::Root::Root->new();


=head2 date_format

 Title     : date_format
 Usage     : $Util->date_format( [FMT], [DATE])
 Purpose   : -- Get a string containing the formated date or time
           :    taken when this routine is invoked.
           : -- Provides a way to avoid using `date`.
	   : -- Provides an interface to localtime().
           : -- Interconverts some date formats.
           :
           : (For additional functionality, use Date::Manip or
           :  Date::DateCalc available from CPAN).
 Example   : $Util->date_format();
           : $date = $Util->date_format('yyyy-mmm-dd', '11/22/92');
 Returns   : String (unless 'list' is provided as argument, see below)
           :
           :   'yyyy-mm-dd'  = 1996-05-03    # default format.
           :   'yyyy-dd-mm'  = 1996-03-05
           :   'yyyy-mmm-dd' = 1996-May-03
           :   'd-m-y'       = 3-May-1996
           :   'd m y'       = 3 May 1996
           :   'dmy'         = 3may96
           :   'mdy'         = May 3, 1996
           :   'ymd'         = 96may3
           :   'md'          = may3
           :   'year'        = 1996
           :   'hms'         = 23:01:59  # when not converting a format, 'hms' can be 
           :                             # tacked on to any of the above options
           :                             # to add the time stamp: eg 'dmyhms'
           :   'full' | 'unix' = UNIX-style date: Tue May  5 22:00:00 1998
           :   'list'          = the contents of localtime(time) in an array.
 Argument  : (all are optional)
           : FMT  = yyyy-mm-dd | yyyy-dd-mm | yyyy-mmm-dd |
           :        mdy | ymd | md | d-m-y | hms | hm
           :        ('hms' may be appended to any of these to
	   :        add a time stamp)
           :
           : DATE = String containing date to be converted.
           :        Acceptable input formats:
           :           12/1/97 (for 1 December 1997)
           :           1997-12-01
           :           1997-Dec-01
 Throws    :
 Comments  : If you don't care about formatting or using backticks, you can
           : always use: $date = `date`;
           :
           : For more features, use Date::Manip.pm, (which I should
           : probably switch to...)

See Also   : L<file_date()|file_date>, L<month2num()|month2num>

=cut

#---------------'
sub date_format {
#---------------
    my $self   = shift;
    my $option = shift;
    my $date   = shift;  # optional date to be converted.

    my($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst);

    $option ||= 'yyyy-mm-dd';

    my ($month_txt, $day_txt, $month_num, $fullYear);
    my ($converting, @date);

    # Load a supplied date for conversion:
    if(defined($date) && ($date =~ /[\D-]+/)) {
        $converting = 1;
	if( $date =~ m{/}) {
	    ($mon,$mday,$year) = split(m{/}, $date);
	} elsif($date =~ /(\d{4})-(\d{1,2})-(\d{1,2})/) {
	    ($year,$mon,$mday) = ($1, $2, $3);
	} elsif($date =~ /(\d{4})-(\w{3,})-(\d{1,2})/) {
	    ($year,$mon,$mday) = ($1, $2, $3);
	    $mon = $self->month2num($2);
	} else {
	    print STDERR "\n*** Unsupported input date format: $date\n";
	}
	if(length($year) == 4) { 
            $fullYear = $year;
            $year = substr $year, 2; 
        } else {
            # Heuristics to guess what century was intended when a 2-digit year is given
            # If number is over 50, assume it's for prev century; under 50 = default century.
            # TODO: keep an eye on this Y2K-sensitive code
            if ($year > 50) {
                $fullYear = $DEFAULT_CENTURY + $year - 100;
            } else {
                $fullYear = $DEFAULT_CENTURY + $year;
            }
        }
	$mon -= 1;
    } else {
	($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = @date =
	    localtime(($date ? $date : time()));
	return @date if $option =~ /list/i;
        $fullYear = $BASE_YEAR+$year;
    }
    $month_txt = $MONTHS[$mon];
    $day_txt   = $DAYS[$wday] if defined $wday;
    $month_num = $mon+1;

#    print "sec: $sec, min: $min, hour: $hour, month: $mon, m-day: $mday, year: $year\nwday: $wday, yday: $yday, dst: $isdst";<STDIN>;

    if( $option =~ /yyyy-mm-dd/i ) {
	$date = sprintf "%4d-%02d-%02d",$fullYear,$month_num,$mday;
    } elsif( $option =~ /yyyy-dd-mm/i ) {
	$date = sprintf "%4d-%02d-%02d",$fullYear,$mday,$month_num;
    } elsif( $option =~ /yyyy-mmm-dd/i ) {
	$date = sprintf "%4d-%3s-%02d",$fullYear,$month_txt,$mday;
    } elsif( $option =~ /full|unix/i ) {
	$date = sprintf "%3s %3s %2d %02d:%02d:%02d %d",$day_txt, $month_txt, $mday, $hour, $min, $sec, $fullYear;
    } elsif( $option =~ /mdy/i ) {
	$date = "$month_txt $mday, $fullYear";
    } elsif( $option =~ /ymd/i ) {
	$date = $year."\l$month_txt$mday";
    } elsif( $option =~ /dmy/i ) {
	$date = $mday."\l$month_txt$year";
    } elsif( $option =~ /md/i ) {
	$date = "\l$month_txt$mday";
    } elsif( $option =~ /d-m-y/i ) {
	$date = "$mday-$month_txt-$fullYear";
    } elsif( $option =~ /d m y/i ) {
	$date = "$mday $month_txt $fullYear";
    } elsif( $option =~ /year/i ) {
	$date = $fullYear;
    } elsif( $option =~ /dmy/i ) {
	$date = $mday.'-'.$month_txt.'-'.$fullYear;
    } elsif($option and $option !~ /hms/i) {
	print STDERR "\n*** Unrecognized date format request: $option\n";
    }

    if( $option =~ /hms/i and not $converting) {
	$date .= " $hour:$min:$sec" if $date;
	$date ||= "$hour:$min:$sec";
    }

    return $date || join(" ", @date);
}


=head2 month2num

 Title      : month2num
 Purpose    : Converts a string containing a name of a month to integer
            : representing the number of the month in the year.
 Example    : $Util->month2num("march");  # returns 3
 Argument   : The string argument must contain at least the first
            : three characters of the month's name. Case insensitive.
 Throws     : Exception if the conversion fails.

=cut

#--------------'
sub month2num {
#--------------

    my ($self, $str) = @_;

    # Get string in proper format for conversion.
    $str = substr($str, 0, 3);
    for(0..$#MONTHS) {
	return $_+1 if $str =~ /$MONTHS[$_]/i;
    }
    $self->throw("Invalid month name: $str");
}

=head2 num2month

 Title   : num2month
 Purpose : Does the opposite of month2num.
         : Converts a number into a string containing a name of a month.
 Example : $Util->num2month(3);  # returns 'Mar'
 Throws  : Exception if supplied number is out of range.

=cut

#-------------
sub num2month {
#-------------
    my ($self, $num) = @_;

    $self->throw("Month out of range: $num") if $num < 1 or $num > 12;
    return $MONTHS[$num-1];
}

=head2 compress

 Title     : compress
 Usage     : $Util->compress(full-path-filename);
           : $Util->compress(<named parameters>);
 Purpose   : Compress a file.
 Example   : $Util->compress("/usr/people/me/data.txt");
           : $Util->compress(-file=>"/usr/people/me/data.txt",
           :                 -tmp=>1,
           :                 -outfile=>"/usr/people/share/data.txt.gz",
           :                 -exe=>"/usr/local/bin/fancyzip");
 Returns   : String containing full, absolute path to compressed file
 Argument  : Named parameters (case-insensitive):
           :   -FILE => String (name of file to be compressed, full path).
           :            If the supplied filename ends with '.gz' or '.Z',
           :            that extension will be removed before attempting to compress.
           : Optional:
           :   -TMP  => boolean. If true, (or if user is not the owner of the file)
           :            the file is compressed to a temp file. If false, file may be
           :            clobbered with the compressed version (if using a utility like
           :            gzip, which is the default)
           :   -OUTFILE => String (name of the output compressed file, full path).
           :   -EXE  => Name of executable for compression utility to use.
           :            Will supercede those in @COMPRESSION_UTILS defined by 
           :            this module. If the absolute path to the executable is not provided,
           :            it will be searched in the PATH env variable.
 Throws    : Exception if file cannot be compressed.
           : If user is not owner of the file, generates a warning and compresses to
           : a tmp file. To avoid this warning, use the -o file test operator 
           : and call this function with -TMP=>1.
 Comments  : Attempts to compress using utilities defined in the @COMPRESSION_UTILS 
           : defined by this module, in the order defined. The first utility that is 
           : found to be executable will be used. Any utility defined in optional -EXE param
           : will be tested for executability first. 
           : To minimize security risks, the -EXE parameter value is untained using
           : the untaint() method of this module (in 'relaxed' mode to permit path separators).

See Also   : L<uncompress()|uncompress>

=cut

#------------'
sub compress {
#------------
    my ($self, @args) = @_;
    # This method formerly didn't use named params and expected fileName, tmp
    # in that order. This should be backward compatibile.
    my ($fileName, $tmp, $outfile, $exe) = $self->_rearrange([qw(FILE TMP OUTFILE EXE)], @args);
    my ($file, $get, $fmt);

    # in case the supplied name already has a compressed extension
    if($fileName =~ /(\.gz|\.Z|\.bz2|\.zip)$/) { $fileName =~ s/$1$//; };
    $self->debug("compressing file $fileName");

    my @util_to_use = @COMPRESSION_UTILS;

    if (defined $exe){
        $exe = $self->untaint($exe, 1);
        unshift @util_to_use, $exe;
    }

    my @checked = @util_to_use;
    $exe ||= '';
    while (not -x $exe and scalar(@util_to_use)) {
        $exe = $self->find_exe(shift @util_to_use);
    }

    unless (-x $exe) {
        $self->throw("Can't find compression utility. Looked for @checked");
    }

    my ($compressed, @cmd, $handle);

    if(defined($outfile) or $tmp or not -o $fileName) {
        if (defined $outfile) {
            $compressed = $outfile;
        } else {
            # obtain a temporary file name (not using the handle)
            # and insert some special text to flag it as a bioperl-based temp file
            my $io = Bio::Root::IO->new();
            ($handle, $compressed) = $io->tempfile();
            $compressed .= '.tmp.bioperl.gz';
        }

        if ($exe =~ /gzip|bzip2|compress/) {
            @cmd = ("$exe -f < \"$fileName\" > \"$compressed\"");
        } elsif ($exe eq 'zip') {
            @cmd = ("$exe -r \"$fileName.zip\" \"$fileName\"");
        }
	not $tmp and
	    $self->warn("Not owner of file $fileName. Compressing to temp file $compressed.");
	$tmp = 1;
    } else {
        # Need to compute the compressed name based on exe since we're returning it.
        $compressed = $fileName;
        if ($exe =~ /gzip/) {
            $compressed .= '.gz';
        } elsif ($exe =~ /bzip2/) {
            $compressed .= '.bz2';
        } elsif ($exe =~ /zip/) {
            $compressed .= '.zip';
        } elsif ($exe =~ /compress/) {
            $compressed .= '.Z';
        }
        if ($exe =~ /gzip|bzip2|compress/) {
            @cmd = ($exe, '-f', $fileName);
        } elsif ($exe eq 'zip') {
            @cmd = ($exe, '-r', "$compressed", $fileName);
        }
    }

    if(system(@cmd) != 0) {
        $self->throw( -class => 'Bio::Root::SystemException',
                      -text => "Failed to compress file $fileName using $exe: $!");
    }

    return $compressed;
}

=head2 uncompress

 Title     : uncompress
 Usage     : $Util->uncompress(full-path-filename);
           : $Util->uncompress(<named parameters>);
 Purpose   : Uncompress a file.
 Example   : $Util->uncompress("/usr/people/me/data.txt");
           : $Util->uncompress(-file=>"/usr/people/me/data.txt.gz",
           :                   -tmp=>1,
           :                   -outfile=>"/usr/people/share/data.txt",
           :                   -exe=>"/usr/local/bin/fancyzip");
 Returns   : String containing full, absolute path to uncompressed file
 Argument  : Named parameters (case-insensitive):
           :   -FILE => String (name of file to be uncompressed, full path).
           :            If the supplied filename ends with '.gz' or '.Z',
           :            that extension will be removed before attempting to uncompress.
           : Optional:
           :   -TMP  => boolean. If true, (or if user is not the owner of the file)
           :            the file is uncompressed to a temp file. If false, file may be
           :            clobbered with the uncompressed version (if using a utility like
           :            gzip, which is the default)
           :   -OUTFILE => String (name of the output uncompressed file, full path).
           :   -EXE  => Name of executable for uncompression utility to use.
           :            Will supercede those in @UNCOMPRESSION_UTILS defined by 
           :            this module. If the absolute path to the executable is not provided,
           :            it will be searched in the PATH env variable.
 Throws    : Exception if file cannot be uncompressed.
           : If user is not owner of the file, generates a warning and uncompresses to
           : a tmp file. To avoid this warning, use the -o file test operator 
           : and call this function with -TMP=>1.
 Comments  : Attempts to uncompress using utilities defined in the @UNCOMPRESSION_UTILS 
           : defined by this module, in the order defined. The first utility that is 
           : found to be executable will be used. Any utility defined in optional -EXE param
           : will be tested for executability first. 
           : To minimize security risks, the -EXE parameter value is untained using
           : the untaint() method of this module (in 'relaxed' mode to permit path separators).

See Also   : L<compress()|compress>

=cut

#------------'
sub uncompress {
#------------
    my ($self, @args) = @_;
    # This method formerly didn't use named params and expected fileName, tmp
    # in that order. This should be backward compatibile.
    my ($fileName, $tmp, $outfile, $exe) = $self->_rearrange([qw(FILE TMP OUTFILE EXE)], @args);
    my ($file, $get, $fmt);

    # in case the supplied name lacks a compressed extension
    if(not $fileName =~ /(\.gz|\.Z|\.bz2|\.zip)$/) { $fileName .= $1; };
    $self->debug("uncompressing file $fileName");

    my @util_to_use = @UNCOMPRESSION_UTILS;

    if (defined $exe){
        $exe = $self->untaint($exe, 1);
        unshift @util_to_use, $exe;
    }

    $exe ||= '';
    while (not -x $exe and scalar(@util_to_use)) {
        $exe = $self->find_exe(shift @util_to_use);
    }

    unless (-x $exe) {
        $self->throw("Can't find compression utility. Looked for @util_to_use");
    }

    my ($uncompressed, @cmd, $handle);

    $uncompressed = $fileName;
    $uncompressed =~ s/\.\w+$//;

    if(defined($outfile) or $tmp or not -o $fileName) {
        if (defined $outfile) {
            $uncompressed = $outfile;
        } else {
            # obtain a temporary file name (not using the handle)
            my $io = Bio::Root::IO->new();
            ($handle, $uncompressed) = $io->tempfile();
            # insert some special text to flag it as a bioperl-based temp file
            $uncompressed .= '.tmp.bioperl';
        }

        if ($exe =~ /gunzip|bunzip2|uncompress/) {
            @cmd = ("$exe -f < \"$fileName\" > \"$uncompressed\"");
        } elsif ($exe eq 'unzip') {
            @cmd = ("$exe -p \"$fileName\" > \"$uncompressed\"");
        }
	not $tmp and
	    $self->warn("Not owner of file $fileName. Uncompressing to temp file $uncompressed.");
	$tmp = 1;
    } else {
        if ($exe =~ /gunzip|bunzip2|uncompress/) {
            @cmd = ($exe, '-f', $fileName);
        } elsif ($exe eq 'zip') {
            @cmd = ($exe, $fileName);
        }
    }

    if(system(@cmd) != 0) {
        $self->throw( -class => 'Bio::Root::SystemException',
                      -text => "Failed to uncompress file $fileName using $exe: $!");
    }

    return $uncompressed;
}


=head2 file_date

 Title    : file_date
 Usage    : $Util->file_date( filename [,date_format])
 Purpose  : Obtains the date of a given file.
          : Provides flexible formatting via date_format().
 Returns  : String = date of the file as: yyyy-mm-dd (e.g., 1997-10-15)
 Argument : filename = string, full path name for file
          : date_format = string, desired format for date (see date_format()).
          :               Default = yyyy-mm-dd
 Thows    : Exception if no file is provided or does not exist.
 Comments : Uses the mtime field as obtained by stat().

=cut

#--------------
sub file_date {
#--------------
    my ($self, $file, $fmt) = @_;

    $self->throw("No such file: $file") if not $file or not -e $file;

    $fmt ||= 'yyyy-mm-dd';

    my @file_data = stat($file);
    return $self->date_format($fmt, $file_data[9]); # mtime field
}


=head2 untaint

 Title   : untaint
 Purpose : To remove nasty shell characters from untrusted data
         : and allow a script to run with the -T switch.
         : Potentially dangerous shell meta characters:  &;`'\"|*?!~<>^()[]{}$\n\r
         : Accept only the first block of contiguous characters:
         :  Default allowed chars = "-\w.', ()"
         :  If $relax is true  = "-\w.', ()\/=%:^<>*"
 Usage   : $Util->untaint($value, $relax)
 Returns : String containing the untained data.
 Argument: $value = string
         : $relax = boolean
 Comments:
     This general untaint() function may not be appropriate for every situation.
     To allow only a more restricted subset of special characters
     (for example, untainting a regular expression), then using a custom
     untainting mechanism would permit more control.

     Note that special trusted vars (like $0) require untainting.

=cut

#------------`
sub untaint {
#------------
    my($self,$value,$relax) = @_;
    $relax ||= 0;
    my $untainted;

    $self->debug("\nUNTAINT: $value\n");

    unless (defined $value and $value ne '') {
        return $value;
    }

    if( $relax ) {
	$value =~ /([-\w.\', ()\/=%:^<>*]+)/;
	$untainted = $1
#    } elsif( $relax == 2 ) {  # Could have several degrees of relax.
#	$value =~ /([-\w.\', ()\/=%:^<>*]+)/;
#	$untainted = $1
    } else {
	$value =~ /([-\w.\', ()]+)/;
	$untainted = $1
    }

    $self->debug("UNTAINTED: $untainted\n");

    $untainted;
}


=head2 mean_stdev

 Title    : mean_stdev
 Usage    : ($mean, $stdev) = $Util->mean_stdev( @data )
 Purpose  : Calculates the mean and standard deviation given a list of numbers.
 Returns  : 2-element list (mean, stdev)
 Argument : list of numbers (ints or floats)
 Thows    : n/a

=cut

#---------------
sub mean_stdev {
#---------------
    my ($self, @data) = @_;
    return (undef,undef) if not @data; # case of empty @data list
    my $mean = 0;
    my $N = 0;
    foreach (@data) { $mean += $_; $N++ }
    $mean /= $N;
    my $sum_diff_sqd = 0;
    foreach (@data) { $sum_diff_sqd += ($mean - $_) * ($mean - $_); }
    # if only one element in @data list, unbiased stdev is undefined
    my $stdev = $N <= 1 ? undef : sqrt( $sum_diff_sqd / ($N-1) );
    return ($mean, $stdev);
}


=head2 count_files

 Title    : count_files
 Purpose  : Counts the number of files/directories within a given directory.
          : Also reports the number of text and binary files in the dir
          : as well as names of these files and directories.
 Usage    : count_files(\%data)
          :   $data{-DIR} is the directory to be analyzed. Default is ./
          :   $data{-PRINT} = 0|1; if 1, prints results to STDOUT, (default=0).
 Argument : Hash reference (empty)
 Returns  : n/a;
          : Modifies the hash ref passed in as the sole argument.
          :  $$href{-TOTAL}            scalar
          :  $$href{-NUM_TEXT_FILES}   scalar
          :  $$href{-NUM_BINARY_FILES} scalar
          :  $$href{-NUM_DIRS}         scalar
          :  $$href{-T_FILE_NAMES}     array ref
          :  $$href{-B_FILE_NAMES}     array ref
          :  $$href{-DIRNAMES}         array ref

=cut

#----------------
sub count_files {
#----------------
    my $self = shift;
    my $href = shift;   # Reference to an empty hash.
    my( $name, @fileLine);
    my $dir = $$href{-DIR} || './'; # THIS IS UNIX SPECIFIC? FIXME/TODO
    my $print = $$href{-PRINT} || 0;

    ### Make sure $dir ends with /
    $dir !~ m{/$} and do{ $dir .=  '/'; $$href{-DIR} = $dir; };

    open ( my $PIPE, "ls -1 $dir |" ) || $self->throw("Can't open input pipe: $!");

    ### Initialize the hash data.
    $$href{-TOTAL} = 0;
    $$href{-NUM_TEXT_FILES} = $$href{-NUM_BINARY_FILES} = $$href{-NUM_DIRS} = 0;
    $$href{-T_FILE_NAMES} = [];
    $$href{-B_FILE_NAMES} = [];
    $$href{-DIR_NAMES} = [];
    while( <$PIPE> ) {
	chomp();
	$$href{-TOTAL}++;
	if( -T $dir.$_ ) {
	    $$href{-NUM_TEXT_FILES}++; push @{$$href{-T_FILE_NAMES}}, $_; }
	if( -B $dir.$_ and not -d $dir.$_) {
	    $$href{-NUM_BINARY_FILES}++; push @{$$href{-B_FILE_NAMES}}, $_; }
	if( -d $dir.$_ ) {
	    $$href{-NUM_DIRS}++; push @{$$href{-DIR_NAMES}}, $_; }
    }
    close $PIPE;

    if( $print) {
	printf( "\n%4d %s\n", $$href{-TOTAL}, "total files+dirs in $dir");
	printf( "%4d %s\n", $$href{-NUM_TEXT_FILES}, "text files");
	printf( "%4d %s\n", $$href{-NUM_BINARY_FILES}, "binary files");
	printf( "%4d %s\n", $$href{-NUM_DIRS}, "directories");
    }
}


#=head2 file_info
#
# Title   : file_info
# Purpose : Obtains a variety of date for a given file.
#	  : Provides an interface to Perl's stat().
# Status  : Under development. Not ready. Don't use!
#
#=cut

#--------------
sub file_info {
#--------------
    my ($self, %param) = @_;
    my ($file, $get, $fmt) = $self->_rearrange([qw(FILE GET FMT)], %param);
    $get ||= 'all';
    $fmt ||= 'yyyy-mm-dd';

    my($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size,
       $atime, $mtime, $ctime, $blksize, $blocks) = stat $file;

    if($get =~ /date/i) {
	## I can  get the elapsed time since the file was modified but
	## it's not so straightforward to get the date in a nice format...
        ## Think about using a standard CPAN module for this, like
        ## Date::Manip or Date::DateCalc.

	my $date = $mtime;
	my $elsec = time - $mtime;
	printf "\nFile age: %.0f sec %.0f hrs %.0f days", $elsec, $elsec/3600, $elsec/(3600*24);<STDIN>;
	my $days = sprintf "%.0f", $elsec/(3600*24);
    } elsif($get eq 'all') {
	return stat $file;
    }
}


#------------
sub delete {
#------------
  my $self = shift;
  my $fileName = shift;
  if(not -e $fileName) {
    $self->throw("Can't delete file $fileName: Does not exist.");
  } elsif(not -o $fileName) {
    $self->throw("Can't delete file $fileName: Not owner.");
  }
  my $ulval = unlink($fileName) > 0 or
    $self->throw("Failed to delete file $fileName: $!");
}


=head2 create_filehandle

 Usage     : $object->create_filehandle(<named parameters>);
 Purpose   : Create a FileHandle object from a file or STDIN.
           : Mainly used as a helper method by read() and get_newline().
 Example   : $data = $object->create_filehandle(-FILE =>'usr/people/me/data.txt')
 Argument  : Named parameters (case-insensitive):
           :  (all optional)
           :    -CLIENT  => object reference for the object submitting
           :                the request. Default = $Util.
           :    -FILE    => string (full path to file) or a reference
           :                to a FileHandle object or typeglob. This is an
           :                optional parameter (if not defined, STDIN is used).
 Returns   : Reference to a FileHandle object.
 Throws    : Exception if cannot open a supplied file or if supplied with a
           : reference that is not a FileHandle ref.
 Comments  : If given a FileHandle reference, this method simply returns it.
           : This method assumes the user wants to read ascii data. So, if
           : the file is binary, it will be treated as a compressed (gzipped)
           : file and access it using gzip -ce. The problem here is that not
           : all binary files are necessarily compressed. Therefore,
           : this method should probably have a -mode parameter to
           : specify ascii or binary.

See Also :  L<get_newline()|get_newline>

=cut

#---------------------
sub create_filehandle {
#---------------------
    my($self, @param) = @_;
    my($client, $file, $handle) =
	$self->_rearrange([qw( CLIENT FILE HANDLE )], @param);

    if(not ref $client) {  $client = $self; }
    $file ||= $handle;
    if( $client->can('file')) {
	$file = $client->file($file);
    }

    my $FH;
    my ($handle_ref);

    if($handle_ref = ref($file)) {
      if($handle_ref eq 'FileHandle') {
	$FH = $file;
	$client->{'_input_type'} = "FileHandle";
      } elsif($handle_ref eq 'GLOB') {
	$FH = $file;
	$client->{'_input_type'} = "Glob";
      } else {
        $self->throw(-class=>'Bio::Root::IOException',
                     -text =>"Can't read from $file: Not a FileHandle or GLOB ref.");
      }
      $self->verbose > 0 and printf STDERR "$ID: reading data from FileHandle\n";

    } elsif($file) {
      $client->{'_input_type'} = "FileHandle for $file";

      # Use gzip -cd to access compressed data.
      if( -B $file ) {
	$client->{'_input_type'} .= " (compressed)";
        my $gzip = $self->find_exe('gzip');
	$file = "$gzip -cd $file |"
      }

      require FileHandle;
      $FH = new FileHandle;
      open ($FH, $file) || $self->throw(-class=>'Bio::Root::FileOpenException',
                                        -text =>"Can't access data file: $file: $!");
      $self->verbose > 0 and printf STDERR "$ID: reading data from file $file\n";

    } else {
      # Read from STDIN.
      $FH = \*STDIN;
      $self->verbose > 0 and printf STDERR "$ID: reading data from STDIN\n";
      $client->{'_input_type'} = "STDIN";
    }

    return $FH;
  }

=head2 get_newline

 Usage     : $object->get_newline(<named parameters>);
 Purpose   : Determine the character(s) used for newlines in a given file or
           : input stream. Delegates to Bio::Root::Utilities::get_newline()
 Example   : $data = $object->get_newline(-CLIENT => $anObj,
           :                                   -FILE =>'usr/people/me/data.txt')
 Argument  : Same arguemnts as for create_filehandle().
 Returns   : Reference to a FileHandle object.
 Throws    : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline().

See Also : L<taste_file()|taste_file>, L<create_filehandle()|create_filehandle>

=cut

#-----------------
sub get_newline {
#-----------------
    my($self, @param) = @_;

    return $NEWLINE if defined $NEWLINE;

    my($client ) =
	$self->_rearrange([qw( CLIENT )], @param);

    my $FH = $self->create_filehandle(@param);

    if(not ref $client) {  $client = $self;   }

    if($client->{'_input_type'} =~ /STDIN|Glob|compressed/) {
      # Can't taste from STDIN since we can't seek 0 on it.
      # Are other non special Glob refs seek-able?
      # Attempt to guess newline based on platform.
      # Not robust since we could be reading Unix files on a Mac, e.g.
      if(defined $ENV{'MACPERL'}) {
	$NEWLINE = "\015";  # \r
      } else {
	$NEWLINE = "\012";  # \n
      }
    } else {
      $NEWLINE = $self->taste_file($FH);
    }

    close ($FH) unless ($client->{'_input_type'} eq 'STDIN' ||
                        $client->{'_input_type'} eq 'FileHandle' ||
                        $client->{'_input_type'} eq 'Glob' );

    delete $client->{'_input_type'};

    return $NEWLINE || $DEFAULT_NEWLINE;
  }


=head2 taste_file

 Usage     : $object->taste_file( <FileHandle> );
           : Mainly a utility method for get_newline().
 Purpose   : Sample a filehandle to determine the character(s) used for a newline.
 Example   : $char = $Util->taste_file($FH)
 Argument  : Reference to a FileHandle object.
 Returns   : String containing an octal represenation of the newline character string.
           :   Unix = "\012"  ("\n")
           :   Win32 = "\012\015" ("\r\n")
           :   Mac = "\015"  ("\r")
 Throws    : Exception if no input is read within $TIMEOUT_SECS seconds.
           : Exception if argument is not FileHandle object reference.
           : Warning if cannot determine neewline char(s).
 Comments  : Based on code submitted by Vicki Brown (vlb@deltagen.com).

See Also : L<get_newline()|get_newline>

=cut

#---------------
sub taste_file {
#---------------
  my ($self, $FH) = @_;
  my $BUFSIZ = 256;   # Number of bytes read from the file handle.
  my ($buffer, $octal, $str, $irs, $i);

  ref($FH) eq 'FileHandle' or $self->throw("Can't taste file: not a FileHandle ref");

  $buffer = '';

  # this is a quick hack to check for availability of alarm(); just copied
  # from Bio/Root/IOManager.pm HL 02/19/01
  my $alarm_available = 1;
  eval {
      alarm(0);
  };
  if($@) {
      # alarm() not available (ActiveState perl for win32 doesn't have it.
      # See jitterbug PR#98)
      $alarm_available = 0;
  }
  $SIG{ALRM} = sub { die "Timed out!"; };
  my $result;
  eval {
    $alarm_available && alarm( $TIMEOUT_SECS );
    $result = read($FH, $buffer, $BUFSIZ); # read the $BUFSIZ characters of file
    $alarm_available && alarm(0);
  };
  if($@ =~ /Timed out!/) {
    $self->throw("Timed out while waiting for input.",
		 "Timeout period = $TIMEOUT_SECS seconds.\nFor longer time before timing out, edit \$TIMEOUT_SECS in Bio::Root::Utilities.pm.");

  } elsif(not $result) {
    my $err = $@;
    $self->throw("read taste failed to read from FileHandle.", $err);

  } elsif($@ =~ /\S/) {
    my $err = $@;
    $self->throw("Unexpected error during read: $err");
  }

  seek($FH, 0, 0) or $self->throw("seek failed to seek 0 on FileHandle.");

  my @chars = split(//, $buffer);
  my $flavor;

  for ($i = 0; $i <$BUFSIZ; $i++) {
    if (($chars[$i] eq "\012")) {
      unless ($chars[$i-1] eq "\015") {
	$flavor='Unix';
	$octal = "\012";
	$str = '\n';
	$irs = "^J";
	last;
      }
    } elsif (($chars[$i] eq "\015") && ($chars[$i+1] eq "\012")) {
      $flavor='DOS';
      $octal = "\015\012";
      $str = '\r\n';
      $irs = "^M^J";
      last;
    } elsif (($chars[$i] eq "\015")) {
      $flavor='Mac';
      $octal = "\015";
      $str = '\r';
      $irs = "^M";
      last;
    }
  }
  if (not $octal) {
    $self->warn("Could not determine newline char. Using '\012'");
    $octal = "\012";
  } else {
#    print STDERR "FLAVOR=$flavor, NEWLINE CHAR = $irs\n";
  }
  return($octal);
}

=head2 file_flavor

 Usage     : $object->file_flavor( <filename> );
 Purpose   : Returns the 'flavor' of a given file (unix, dos, mac)
 Example   : print "$file has flavor: ", $Util->file_flavor($file);
 Argument  : filename = string, full path name for file
 Returns   : String describing flavor of file and handy info about line endings.
           : One of these is returned:
           :   unix (\n or 012 or ^J)
           :   dos (\r\n or 015,012 or ^M^J)
           :   mac (\r or 015 or ^M)
           :   unknown
 Throws    : Exception if argument is not a file
           : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline().

See Also : L<get_newline()|get_newline>,  L<taste_file()|taste_file>

=cut

#---------------
sub file_flavor {
#---------------
    my ($self, $file) = @_;
    my %flavors=("\012"    =>'unix (\n or 012 or ^J)',
                 "\015\012" =>'dos (\r\n or 015,012 or ^M^J)',
                 "\015"     =>'mac (\r or 015 or ^M)'
                );

    -f $file or $self->throw("Can't determine flavor: arg '$file' is either non existant or is not a file.\n");
    my $octal = $self->get_newline($file);
    my $flavor = $flavors{$octal} || "unknown";
    return $flavor;
}

######################################
#####     Mail Functions      ########
######################################

=head2 mail_authority

 Title    : mail_authority
 Usage    : $Util->mail_authority( $message )
 Purpose  : Syntactic sugar to send email to $Bio::Root::Global::AUTHORITY

See Also  : L<send_mail()|send_mail>

=cut

sub mail_authority {

    my( $self, $message ) = @_;
    my $script = $self->untaint($0,1);

    my $email = $self->{'_auth_email'} || $AUTHORITY;
    if (defined $email) {
        $self->send_mail( -TO=>$AUTHORITY, -SUBJ=>$script, -MSG=>$message);
    } else {
        $self->throw("Can't email authority. No email defined.");
    }
}

=head2 authority

 Title    : authority
 Usage    : $Util->authority('admin@example.com');
 Purpose  : Set/get the email address that should be notified by mail_authority()

See Also  : L<mail_authority()|mail_authority>

=cut

sub authority {

    my( $self, $email ) = @_;
    $self->{'_auth_email'} = $email if defined $email;
    return $self->{'_auth_email'};
}


=head2 send_mail

 Title    : send_mail
 Usage    : $Util->send_mail( named_parameters )
 Purpose  : Provides an interface to mail or sendmail, if available
 Returns  : n/a
 Argument : Named parameters:  (case-insensitive)
          :  -TO   => e-mail address to send to
          :  -SUBJ => subject for message  (optional)
          :  -MSG  => message to be sent   (optional)
          :  -CC   => cc: e-mail address   (optional)
 Thows    : Exception if TO: address appears bad or is missing.
          : Exception if mail cannot be sent.
 Comments : Based on  TomC's tip at:
          :   http://www.perl.com/CPAN/doc/FMTEYEWTK/safe_shellings
          :
          : Using default 'From:' information.
          :   sendmail options used:
          :      -t: ignore the address given on the command line and
          :          get To:address from the e-mail header.
          :     -oi: prevents send_mail from ending the message if it
          :          finds a period at the start of a line.

See Also  : L<mail_authority()|mail_authority>

=cut


#-------------'
sub send_mail {
#-------------
    my( $self, @param) = @_;
    my($recipient,$subj,$message,$cc) = $self->_rearrange([qw(TO SUBJ MSG CC)],@param);

    $self->throw("Invalid or missing e-mail address: $recipient")
	if not $recipient =~ /\S+\@\S+/;

    $subj ||= 'empty subject'; $message ||= '';

    # Best to use mail rather than sendmail. Permissions on sendmail in
    # linux distros have been significantly locked down in recent years,
    # due to the perception that it is insecure.
    my ($exe, $ccinfo);
    if ($exe = $self->find_exe('mail')) {
        if (defined $cc) {
            $ccinfo = "-c $cc";
        }
        $self->debug("send_mail: $exe -s '$subj' $ccinfo $recipient\n");
        open (MAIL, "| $exe -s '$subj' $ccinfo $recipient") ||
            $self->throw("Can't send email: mail cannot fork: $!");
        print MAIL <<QQ_EOFM_QQ;
$message
QQ_EOFM_QQ
        $? and $self->warn("mail didn't exit nicely: $?");
        close(MAIL);
    } elsif ($exe = $self->find_exe('sendmail')) {
        open (SENDMAIL, "| $exe -oi -t") ||
            $self->throw("Can't send email: sendmail cannot fork: $!");
        print SENDMAIL <<QQ_EOFSM_QQ;
To: $recipient
Subject: $subj
Cc: $cc

$message

QQ_EOFSM_QQ
        $? and $self->warn("sendmail didn't exit nicely: $?");

        close(SENDMAIL);
    } else {
        $self->throw("Can't find executable for mail or sendmail.");
    }
}


=head2 find_exe

 Title     : find_exe
 Usage     : $Util->find_exe(name);
 Purpose   : Locate an executable (for use in a system() call, e.g.))
 Example   : $Util->find_exe("gzip");
 Returns   : String containing executable that passes the -x test.
             Returns undef if an executable of the supplied name cannot be found.
 Argument  : Name of executable to be found.
           : Can be a full path. If supplied name is not executable, an executable
           : of that name will be searched in all directories in the currently
           : defined PATH environment variable.
 Throws    : No exceptions, but issues a warning if multiple paths are found
           : for a given name. The first one is used.
 Comments  : TODO: Confirm functionality on all bioperl-supported platforms.
             May get tripped up by variation in path separator character used
             for splitting ENV{PATH}.
See Also   :

=cut

sub find_exe {
    my ($self, $name) = @_;
    my @bindirs = split (':', $ENV{'PATH'});
    my $exe = $name;
    unless (-x $exe) {
        undef $exe;
        my @exes;
        foreach my $d (@bindirs) {
            push(@exes, "$d/$name") if -x "$d/$name";
        }
        if (scalar @exes) {
            $exe = $exes[0];
            if (defined $exes[1]) {
                $self->warn("find_exe: Multiple paths to '$name' found. Using $exe.");
            }
        }
    }
    return $exe;
}


######################################
###   Interactive Functions      #####
######################################


=head2 yes_reply

 Title   : yes_reply()
 Usage   : $Util->yes_reply( [query_string]);
 Purpose : To test an STDIN input value for affirmation.
 Example : print +( $Util->yes_reply('Are you ok') ? "great!\n" : "sorry.\n" );
         : $Util->yes_reply('Continue') || die;
 Returns : Boolean, true (1) if input string begins with 'y' or 'Y'
 Argument: query_string = string to be used to prompt user (optional)
         : If not provided, 'Yes or no' will be used.
         : Question mark is automatically appended.

=cut

#-------------
sub yes_reply {
#-------------
    my $self = shift;
    my $query = shift;
    my $reply;
    $query ||= 'Yes or no';
    print "\n$query? (y/n) [n] ";
    chomp( $reply = <STDIN> );
    $reply =~ /^y/i;
}



=head2 request_data

 Title   : request_data()
 Usage   : $Util->request_data( [value_name]);
 Purpose : To request data from a user to be entered via keyboard (STDIN).
 Example : $name = $Util->request_data('Name');
         : # User will see: % Enter Name:
 Returns : String, (data entered from keyboard, sans terminal newline.)
 Argument: value_name = string to be used to prompt user.
         : If not provided, 'data' will be used, (not very helpful).
         : Question mark is automatically appended.

=cut

#----------------
sub request_data {
#----------------
    my $self = shift;
    my $data = shift || 'data';
    print "Enter $data: ";
    # Remove the terminal newline char.
    chomp($data = <STDIN>);
    $data;
}

sub quit_reply {
# Not much used since you can use request_data()
# and test for an empty string.
    my $self = shift;
    my $reply;
    chop( $reply = <STDIN> );
    $reply =~ /^q.*/i;
}


=head2 verify_version

 Purpose : Checks the version of Perl used to invoke the script.
         : Aborts program if version is less than the given argument.
 Usage   : verify_version('5.000')

=cut

#------------------
sub verify_version {
#------------------
    my $self = shift;
    my $reqVersion  = shift;

    $] < $reqVersion and do {
	printf STDERR ( "\a\n%s %0.3f.\n", "** Sorry. This Perl script requires at least version", $reqVersion);
	printf STDERR ( "%s %0.3f %s\n\n", "You are running Perl version", $], "Please update your Perl!\n\n" );
	exit(1);
    }
}


1;


__END__


