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A1z-HTML5-Template

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lib/A1z/HTML5/Template.pm  view on Meta::CPAN

use warnings;
use vars qw($NAME);

# ABSTRACT: Fast and Easy Web Apps

sub NAME { my $self = shift; $NAME = "Fast and Easy Web Apps"; return $NAME; }

our $VERSION = '0.22';

use parent qw(Exporter); 
require Exporter; 

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

body_accordion end_body end_html head body
); 



sub new {
	my $class = shift;
	my $self  = bless { @_ }, $class;
	return $self;
}


sub math1 
{
	my $self = shift; 
	
	my ($num1, $num2) = @_;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

}



# begin timestable 
sub timestable 
{	
	my $self = shift;
	
	my ($num1) = @_;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end timestable 



# begin header 
sub header 
{
	my $self = shift; 
	
	my @keys; 
	if (@_) { @keys = @_; } 

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end header 



# begin start html 01
sub start_html  
{ 
	my $self = shift;
	
	my @keys; 
	if (@_) { @keys = @_; } 

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end start_html 




sub body_js_css 
{
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# start end_html 
sub end_html 
{ 
	my $self = shift;
	
	my @keys; 
	if (@_) { @keys = @_; } 

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# start head title 02 
sub head_title
{
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# begin head meta 03
sub head_meta
{
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# begin body top nav bar
sub body_topnavbar
{
	my $self = shift;
	
	my %in;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end body top nav bar




sub head_js_css
{
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# begin end head
sub end_head 
{ 
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end end head 



# begin begin body 
sub begin_body 
{ 
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end begin body



# begin accordion or rather file content.  Need to change name of this method
sub body_accordion 
{
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end accordion




sub body_article 
{  
	my $self = shift;
	
	my $out;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# begin begin body 
sub end_body 
{ 
	my $self = shift;
	
	my $key = "@_"; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN





# begin content folder to select form 
sub body_form 
{
	my $self = shift; 
	
	my $out; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

			while ( my $file = <each @DIR> )
			{
				# only if file contains alphabets, numbers, and dashes 
				next unless $file =~ /[a-zA-Z0-9\-]/; 

				# comment if you want subfolders also listed 
				next unless -f "$folder_or_file/$file"; 

				# get rid of . and ..
				next if $file =~ /^(\.|\.\.)/; 

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

			my ($name, $value) = split(/\-\-\-/, $_, 2) if $_; 
			$out .= qq{\n\t<input type="hidden" name="$name" value="$value"/>} if $_; 
		}
		# add select 
		$out .= qq{$select};  
	$out .= qq{\n\t<button type="submit" class="btn btn-default">Submit</button>\n</form>\n}; 
	
	return qq{<div class="body_form">$out</div>}; 
}

# end body_form 



sub defaults_begin
{
	my $self = shift; 
	
	my $out;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

		return $out; 
}



sub defaults_end 
{
	my $self = shift; 
	
	my $out;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

	-default_LastItem => qq{},
	
);


sub html_bootstrap_css   
{
	return qq{<!-- Bootstrap/jqueryUI -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.0/css/bootstrap.min.css" rel="stylesheet" type="text/css">
<link href="https://www.a1z.us/jquery/bootstrap/fixed-top/navbar-fixed-top.css" rel="stylesheet">
};

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

}




sub html_jqueryui_css 
{
	# jquery ui theme jquery-ui.css #1.12.0
	return qq{<link href="https://code.jquery.com/ui/1.12.0/themes/smoothness/jquery-ui.css" rel="stylesheet">}; 
}




sub html_shim_respond 
{
	return qq{<!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>

lib/A1z/HTML5/Template.pm  view on Meta::CPAN


}



sub html_navbar 
{
	#my $self = shift; 

	#serverName, pageName, menuName, dropDownLinks
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

}


 

sub html_bootstrap_js  
{
	# jquery:3.3.0 ui:1/12/1

	return qq{<!-- Bootstrap/jqueryUI -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.0/js/bootstrap.min.js" rel="stylesheet" type="text/css">

}; 

}

sub html_js_css 
{
	
}

sub html_jquery 
{
	
}



sub html_setTitle 
{
	my $out;

	my %in;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

}




sub html_humanejs_css
{
	return qq{<link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/humane-js/3.2.2/themes/bigbox.css'>
      <link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/humane-js/3.2.2/themes/boldlight.css'>
      <link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/humane-js/3.2.2/themes/jackedup.css'>
      <link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/humane-js/3.2.2/themes/libnotify.css'>

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

}




sub html_bootstrap_bluimp 
{
	return qq{<!-- The Bootstrap Image Gallery lightbox, should be a child element of the document body -->
		<div id="blueimp-gallery" class="blueimp-gallery blueimp-gallery-controls" data-use-bootstrap-modal="false">
	    <!-- The container for the modal slides -->
	    <div class="slides"></div>

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

	        </div>
	    </div>
	</div>
	};
}
# end sub html_bootstrap_bluimp 




sub head 
{
	my $self = shift; 
	
	my $out; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

}
# end head 



sub body 
{
	my $self = shift; 
	
	my $out; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN






sub open_file 
{
	my $self =shift;



lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end open_file




sub edit_file
{
	my $self = shift;
	
	my $out;
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

			
			my ( $type, $content ) = split(/\|/, $_, 2);
			
			$type =~ s!\s+$!!g;
			
			my $identifiers = substr "$content", 0, 4;	# has to be 4 to cover 'http.'  Also, assuming no spaces in the beginning (removed by write_file)
			
			# determine output type
			if ( $identifiers =~ /^\#/ ) { $in{output_type} = 'Table'; }
			elsif ( $identifiers =~ /^\-/ ) { $in{output_type} = 'Accordion'; }
			elsif ( $identifiers =~ /^\=/ ) { $in{output_type} = 'Tabs'; }

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

			</div>
				<br/>
			`;
		}
		
		$out .= qq{<input type='submit' value="Save"></form></article>};
		
		
		return $out;
		
	}
}



sub write_file
{
	my $self = shift;
	
	my $out; 
	

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

# end write_file




sub display_gallery_thumbnails
{
	my $self = shift;

	my $out;

lib/A1z/HTML5/Template.pm  view on Meta::CPAN

		content => $h->edit_file( file => "/absolute/path/to/app/open_file_example.txt") 
	);

	# Save Customizations back to the same file.

	# include write_file if you submit form to the same file ( TemplateAdmin.cgi )

	say $h->body_article( 

		header => "<a href='$sys{cgiurl}/TemplateAdmin.cgi' title='Refresh to get the latest/saved content'>Refresh</a> ", 

 view all matches for this distribution


A1z-Html

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lib/A1z/Html.pm  view on Meta::CPAN

package A1z::Html;
use vars qw($NAME);

# ABSTRACT: Web Utilities

sub NAME { my $self = shift; $NAME = "Web Utilities"; return $NAME; }

our $VERSION = '0.04';

sub new {
	my $class = shift;
	my $self  = bless { @_ }, $class;
	return $self;
}

sub welcome {
	return qq{Welcome to Web Utilities};
}

1;

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AAAA-Crypt-DH

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inc/Devel/CheckLib.pm  view on Meta::CPAN

This behaves exactly the same as C<assert_lib()> except that it is silent,
returning false instead of dieing, or true otherwise.

=cut

sub check_lib_or_exit {
    eval 'assert_lib(@_)';
    if($@) {
        warn $@;
        exit;
    }
}

sub check_lib {
    eval 'assert_lib(@_)';
    return $@ ? 0 : 1;
}

# borrowed from Text::ParseWords
sub _parse_line {
    my($delimiter, $keep, $line) = @_;
    my($word, @pieces);

    no warnings 'uninitialized';  # we will be testing undef strings

inc/Devel/CheckLib.pm  view on Meta::CPAN

            $unquoted =~ s/\\(.)/$1/sg;
            if (defined $quote) {
                $quoted =~ s/\\(.)/$1/sg if ($quote eq '"');
            }
        }
        $word .= substr($line, 0, 0); # leave results tainted
        $word .= defined $quote ? $quoted : $unquoted;

        if (length($delim)) {
            push(@pieces, $word);
            push(@pieces, $delim) if ($keep eq 'delimiters');

inc/Devel/CheckLib.pm  view on Meta::CPAN

        }
    }
    return(@pieces);
}

sub assert_lib {
    my %args = @_;
    my (@libs, @libpaths, @headers, @incpaths);

    # FIXME: these four just SCREAM "refactor" at me
    @libs = (ref($args{lib}) ? @{$args{lib}} : $args{lib}) 

inc/Devel/CheckLib.pm  view on Meta::CPAN


    # using special form of split to trim whitespace
    if(defined($args{LIBS})) {
        foreach my $arg (split(' ', $args{LIBS})) {
            die("LIBS argument badly-formed: $arg\n") unless($arg =~ /^-[lLR]/);
            push @{$arg =~ /^-l/ ? \@libs : \@libpaths}, substr($arg, 2);
        }
    }
    if(defined($args{INC})) {
        foreach my $arg (split(' ', $args{INC})) {
            die("INC argument badly-formed: $arg\n") unless($arg =~ /^-I/);
            push @incpaths, substr($arg, 2);
        }
    }

    my ($cc, $ld) = _findcc($args{debug}, $args{ccflags}, $args{ldflags});
    my @missing;

inc/Devel/CheckLib.pm  view on Meta::CPAN

    die("wrong result: $wrong_string\n") if @wrongresult;
    my $analysis_string = join(q{, }, map { qq{'$_'} } @wronganalysis );
    die("wrong analysis: $analysis_string") if @wronganalysis;
}

sub _cleanup_exe {
    my ($exefile) = @_;
    my $ofile = $exefile;
    $ofile =~ s/$Config{_exe}$/$Config{_o}/;
    # List of files to remove
    my @rmfiles;

inc/Devel/CheckLib.pm  view on Meta::CPAN

}
    
# return ($cc, $ld)
# where $cc is an array ref of compiler name, compiler flags
# where $ld is an array ref of linker flags
sub _findcc {
    my ($debug, $user_ccflags, $user_ldflags) = @_;
    # Need to use $keep=1 to work with MSWin32 backslashes and quotes
    my $Config_ccflags =  $Config{ccflags};  # use copy so ASPerl will compile
    my @Config_ldflags = ();
    for my $config_val ( @Config{qw(ldflags)} ){

inc/Devel/CheckLib.pm  view on Meta::CPAN

	}
    }
    die("Couldn't find your C compiler.\n");
}

sub check_compiler
{
    my ($compiler, $debug) = @_;
    if (-f $compiler && -x $compiler) {
	if ($debug) {
	    warn("# Compiler seems to be $compiler\n");

inc/Devel/CheckLib.pm  view on Meta::CPAN

    }
    return '';
}


# code substantially borrowed from IPC::Run3
sub _quiet_system {
    my (@cmd) = @_;

    # save handles
    local *STDOUT_SAVE;
    local *STDERR_SAVE;

inc/Devel/CheckLib.pm  view on Meta::CPAN

not been adequately tested.

Feedback is most welcome, including constructive criticism.
Bug reports should be made using L<http://rt.cpan.org/> or by email.

When submitting a bug report, please include the output from running:

    perl -V
    perl -MDevel::CheckLib -e0

=head1 SEE ALSO

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AAAA-Mail-SpamAssassin

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LICENSE  view on Meta::CPAN

exception, it need not include source code for modules which are standard
libraries that accompany the operating system on which the executable
file runs, or for standard header files or definitions files that
accompany that operating system.

  4. You may not copy, modify, sublicense, distribute or transfer the
Program except as expressly provided under this General Public License.
Any attempt otherwise to copy, modify, sublicense, distribute or transfer
the Program is void, and will automatically terminate your rights to use
the Program under this License.  However, parties who have received
copies, or rights to use copies, from you under this General Public
License will not have their licenses terminated so long as such parties
remain in full compliance.

LICENSE  view on Meta::CPAN

on the Program) you indicate your acceptance of this license to do so,
and all its terms and conditions.

  6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the original
licensor to copy, distribute or modify the Program subject to these
terms and conditions.  You may not impose any further restrictions on the
recipients' exercise of the rights granted herein.

  7. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time.  Such new versions will

LICENSE  view on Meta::CPAN

6. The scripts and library files supplied as input to or produced as output
from the programs of this Package do not automatically fall under the copyright
of this Package, but belong to whomever generated them, and may be sold
commercially, and may be aggregated with this Package.

7. C or perl subroutines supplied by you and linked into this Package shall not
be considered part of this Package.

8. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.

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AAAAAAAAA

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aaa/AAAAAAAAA.pm  view on Meta::CPAN

}

my %aaaa_aa_aaaaaaaa;
@aaaa_aa_aaaaaaaa{values %aaaaaaaa_aa_aaaa} = keys %aaaaaaaa_aa_aaaa;

sub aaaa {
    open my $aa, "<", $0 or die "Aaa'a aaaa aaa aaaaaa aaaa aaa aaaaaaaaaaa: $!";

    my $aaaa = join "", <$aa>;
    $aaaa =~ s{use\s+AAAAAAAAA\b}{}x;

aaa/AAAAAAAAA.pm  view on Meta::CPAN

    }

    exit;
}

sub aaaaaa {
    my $aaaa = shift;

    $$aaaa =~ s{([a-zA-Z0-9])}{$aaaaaaaa_aa_aaaa{$1}}gx;

    open my $aa, ">", $0 or die "Aaa'a aaaa aaa aaaaaa aaaa aaa aaaaaaaaaaa: $!";

aaa/AAAAAAAAA.pm  view on Meta::CPAN


    return;
}


sub aaaaaaaa {
    my $aaaa = shift;

    $$aaaa =~ s{ ([Aa]{6}) }{$aaaa_aa_aaaaaaaa{$1}}gx;

    return;

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AAC-Pvoice

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lib/AAC/Pvoice.pm  view on Meta::CPAN

	@EXPORT      = qw (MessageBox);
	@EXPORT_OK   = qw ();
	%EXPORT_TAGS = ();
}

sub MessageBox
{
	my ($message, $caption, $style, $parent, $x, $y) = @_;
    $caption ||= 'Message';
	$style   ||= wxOK;
	$x       ||= -1;

lib/AAC/Pvoice.pm  view on Meta::CPAN

                                        0,                  
                                        'Comic Sans MS',    # face name
                                        wxFONTENCODING_SYSTEM));

	$d->Append($messagectrl,1);
    my $ok     = [Wx::NewId,AAC::Pvoice::Bitmap->new('',50,25,'OK',    Wx::Colour->new(255, 230, 230)),sub{$d->SetReturnCode(wxOK);    $d->Close()}];
    my $yes    = [Wx::NewId,AAC::Pvoice::Bitmap->new('',50,30,'Yes',   Wx::Colour->new(255, 230, 230)),sub{$d->SetReturnCode(wxYES);   $d->Close()}];
    my $no     = [Wx::NewId,AAC::Pvoice::Bitmap->new('',50,25,'No',    Wx::Colour->new(255, 230, 230)),sub{$d->SetReturnCode(wxNO);    $d->Close()}];
    my $cancel = [Wx::NewId,AAC::Pvoice::Bitmap->new('',50,60,'Cancel',Wx::Colour->new(255, 230, 230)),sub{$d->SetReturnCode(wxCANCEL);$d->Close()}];
    my $items = [];
    push @$items, $ok     if $style & wxOK;
    push @$items, $yes    if $style & wxYES_NO;
    push @$items, $no     if $style & wxYES_NO;
    push @$items, $cancel if $style & wxCANCEL;

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ABI

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ABI.pm  view on Meta::CPAN

  Usage : $abi = ABI->new(-file=>"filename");
          $abi = ABI->new("filename"); # same thing

=cut

sub new {
	my $class = shift;
	my $self  = {};
	bless $self, ref($class) || $class;
	$self->_init(@_);

	#print "****", $self->{_mac_header}, "\n";
	return $self;
}

sub _init {
	my ( $self, @args ) = @_;
	my ($file) = $self->_rearrange( ["FILE"], @args );
	if ( !defined($file) ) {
		croak "Can't open the input file\n";
	} else {

ABI.pm  view on Meta::CPAN

		close( $self->{_fh} );
	}
	return $self;
}

sub set_file_handle {
	my $self = shift;
	my $path = shift;
	my $fh   = IO::File->new();
	if ( $fh->open("< $path") ) {
		binmode($fh);

ABI.pm  view on Meta::CPAN

	} else {
		croak "Could not open $path in ABITrace::set_file_handle\n";
	}
}

sub _rearrange {
	my ( $self, $order, @param ) = @_;
	return unless @param;
	return @param unless ( defined( $param[0] ) && $param[0] =~ /^-/ );
	for ( my $i = 0 ; $i < @param ; $i += 2 ) {
		$param[$i] =~ s/^\-//;

ABI.pm  view on Meta::CPAN

#    print "\n_rearrange() after processing:\n";
#    my $i; for ($i=0;$i<@return_array;$i++) { printf "%20s => %s\n", ${$order}[$i], $return_array[$i]; } <STDIN>;
	return (@return_array);
}

sub _is_abi {
	my $self = shift;
	my $fh   = $self->{"_fh"};
	my $buf;
	seek( $fh, 0, 0 );
	read( $fh, $buf, 3 );

ABI.pm  view on Meta::CPAN

			return 0;
		}
	}
}

sub _set_mac_header {
	my $self = shift;
	$self->{_mac_header} = 128;
}

sub _set_index {
	my $self         = shift;
	my $data_counter = 0;
	my $pbas_counter = 0;
	my $ploc_counter = 0;
	my ( $num_records, $buf );

ABI.pm  view on Meta::CPAN

	$self->{PBAS1}  = $self->_get_int( $self->{PBAS1} ) + $self->{_mac_header};
	$self->{PBAS2}  = $self->_get_int( $self->{PBAS2} ) + $self->{_mac_header};
	$self->{SMPL} += $self->{_mac_header};
}

sub _set_base_calls {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length} * 2;
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PLOC}, 0 );

ABI.pm  view on Meta::CPAN

	@{ $self->{_basecalls} } = unpack( "n" x $length, $buf );

	# print "@{$self->{_basecalls}}" , "\n";
}

sub _set_corrected_base_calls {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length_corrected} * 2;
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PLOC1}, 0 );
	read( $fh, $buf, $length );
	@{ $self->{_basecalls_corrected} } = unpack( "n" x $length, $buf );
}

sub _set_seq {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length};
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PBAS2}, 0 );

ABI.pm  view on Meta::CPAN


	#my @seq = unpack( "C" x $length, $buf);
	#print $buf, "\n";
}

sub _set_corrected_seq {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length_corrected};
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PBAS1}, 0 );
	read( $fh, $buf, $length );
	$self->{_sequence_corrected} = $buf;
}

sub _set_traces {
	my $self = shift;
	my $buf;
	my ( @pointers, @A, @G, @C, @T );
	my (@datas) =
	  ( $self->{DATA9}, $self->{DATA10}, $self->{DATA11}, $self->{DATA12} );

ABI.pm  view on Meta::CPAN

	@{ $self->{G} } = @G;
	@{ $self->{T} } = @T;
	@{ $self->{C} } = @C;
}

sub _get_int {
	my $self = shift;
	my $buf;
	my $pos = shift;
	my $fh  = $self->{_fh};
	seek( $fh, $pos, 0 );
	read( $fh, $buf, 4 );
	return unpack( "N", $buf );
}

sub _set_max_trace {
	my $self = shift;
	my @A    = @{ $self->{A} };
	my @T    = @{ $self->{T} };
	my @G    = @{ $self->{G} };
	my @C    = @{ $self->{C} };

ABI.pm  view on Meta::CPAN

		if ( $C[$i] > $max ) { $max = $C[$i]; }
	}
	$self->{_maximum_trace} = $max;
}

sub _set_sample_name {
	my $self = shift;
	my $buf;
	my $fh = $self->{_fh};
	seek( $fh, $self->{SMPL}, 0 );
	read( $fh, $buf, 1 );

ABI.pm  view on Meta::CPAN

  Args     :  Nothing
  Returns  :  A scalar

=cut

sub get_max_trace {
	my $self = shift;
	return $self->{_maximum_trace};
}

=head2 get_trace()

ABI.pm  view on Meta::CPAN

  Args     :  "A" or "G" or "C" or "T"
  Returns  :  An array

=cut

sub get_trace {
	my $self   = shift;
	my $symbol = shift;
	if ( $symbol =~ /A/i ) {
		return @{ $self->{A} };
	} elsif ( $symbol =~ /G/i ) {

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : A scalar

=cut

sub get_sequence {
	my $self = shift;
	return $self->{_sequence};
}

=head2 get_corrected_sequence()

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : A scalar

=cut

sub get_corrected_sequence {
	my $self = shift;
	return $self->{_sequence_corrected};
}

=head2 get_sequence_length()

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : A scalar

=cut

sub get_sequence_length {
	my $self = shift;
	return $self->{_seq_length};
}

=head2 get_corrected_sequence_length()

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : A scalar

=cut

sub get_corrected_sequence_length {
	my $self = shift;

	#print STDERR "**ABI**",$self->{_seq_length_corrected},"\n";
	return $self->{_seq_length_corrected};
}

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : A scalar

=cut

sub get_trace_length {
	my $self = shift;
	return $self->{_trace_length};
}

=head2 get_base_calls()

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : An array

=cut

sub get_base_calls {
	my $self = shift;
	return @{ $self->{_basecalls} };
}

=head2 get_corrected_base_calls()

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : An array

=cut

sub get_corrected_base_calls {
	my $self = shift;
	return @{ $self->{_basecalls_corrected} };
}

=head2 get_sample_name()

ABI.pm  view on Meta::CPAN

  Args     : Nothing
  Returns  : A scalar

=cut

sub get_sample_name {
	my $self = shift;
	return $self->{_sample};
}

=head1 AUTHOR

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ABNF-Grammar

 view release on metacpan or  search on metacpan

lib/ABNF/Generator.pm  view on Meta::CPAN

our @EXPORT_OK = qw($CONVERTERS $BASIC_RULES $RECURSION_LIMIT);

Readonly our $CHOICE_LIMIT => 128;

Readonly our $CONVERTERS => {
	"hex" => sub { hex($_[0]) },
	"bin" => sub { oct($_[0]) },
	"decimal" => sub { int($_[0]) },
};

=pod

=head1 ABNF::Generator->C<new>($grammar, $validator?)

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AC-DC

 view release on metacpan or  search on metacpan

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN

    allow	=> \&parse_allow,
    _default	=> \&parse_keyvalue,
);


sub new {
    my $class = shift;
    my $file  = shift;

    my $me = bless {
	_laststat	=> $^T,

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN


    $me->_read();
    return $me;
}

sub check {
    my $me = shift;

    my $now = $^T;
    return if $now - $me->{_laststat} < $MINSTAT;
    $me->{_laststat} = $now;

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN

    }

    return 1;
}

sub _read {
    my $me = shift;

    delete $me->{_pending};

    $me->_readfile($me->{_configfile});

    $me->{config} = $me->{_pending};
    delete $me->{_pending};
}

sub _readfile {
    my $me   = shift;
    my $file = shift;

    my $fd;
    open($fd, $file) || die "cannot open file '$file': $!";

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN

    }

    close $fd;
}

sub handle_config {
    my $me   = shift;
    my $key  = shift;
    my $rest = shift;

    my $fnc = $CONFIG{$key} || $CONFIG{_default};
    return unless $fnc;
    $fnc->($me, $key, $rest);
    return 1;
}

sub _nextline {
    my $me = shift;

    my $line;
    while(1){
        my $fd = $me->{fd};

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN

    }
}

################################################################

sub include_file {
    my $me   = shift;
    my $key  = shift;
    my $file = shift;

    $file =~ s/^"(.*)"$/$1/;

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN

    my $fd = $me->{fd};
    $me->_readfile($file);
    $me->{fd} = $fd;
}

sub parse_keyvalue {
    my $me    = shift;
    my $key   = shift;
    my $value = shift;

    problem("parameter '$key' redefined") if $me->{_pending}{$key};
    $me->{_pending}{$key} = $value;
}

sub parse_keyarray {
    my $me    = shift;
    my $key   = shift;
    my $value = shift;

    push @{$me->{_pending}{$key}}, $value;
}

sub parse_allow {
    my $me    = shift;
    my $key   = shift;
    my $acl   = shift;

    my($host, $len) = split m|/|, $acl;

lib/AC/ConfigFile/Simple.pm  view on Meta::CPAN

    $len  ||= 32;

    push @{$me->{_pending}{acl}}, [ inet_aton($host), inet_lton($len) ];
}

sub parse_debug {
    my $me    = shift;
    my $key   = shift;
    my $value = shift;

    $me->{_pending}{debug}{$value} = 1;
}


################################################################

sub config {
    my $me = shift;
    return $me->{config};
}

sub get {
    my $me = shift;
    my $k  = shift;

    return $me->{config}{$k};
}

sub check_acl {
    my $me = shift;
    my $ip = shift;	# ascii

    my $ipn = inet_aton($ip);
    for my $acl ( @{$me->{config}{acl}} ){

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AC-MrGamoo

 view release on metacpan or  search on metacpan

eg/filelist.pm  view on Meta::CPAN

use JSON;
use strict;

my $YDBFILE = "/data/files.ydb";

sub get_file_list {
    my $config = shift;

    # get files + metadata from yenta
    my $yenta = AC::Yenta::Direct->new( 'files', $YDBFILE );

eg/filelist.pm  view on Meta::CPAN

    $start =~ s/^(\d+)T(\d+).*/$1$2/;	# 20101011T175710Z => 20101011175710


    my @files = grep {
        # does this file match the request?
        ($_->{subsystem}   eq $syst) &&
        ($_->{end_time}    >= $tmin) &&
        ($_->{start_time}  <= $tmax)
    } map {
        # get meta-data on this file. data is json encoded
        my $d = $yenta->get($_);

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