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Bio-PrimerDesigner-0.07
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/ Bio::PrimerDesigner::Tables

NAME

Bio::PrimerDesigner::Table -- Draw HTML tables for PCR primer display

DESCRIPTION

Draws simple HTML tables to display Bio::PrimerDesigner PCR primer design and e-PCR results for web applications.

METHODS

info_table

Prints a two-column table for generic, key-value style annotations. Expects to be passed the name of the gene/feature/etc. and a hash of attributes. If there is an 'image' key, the value is assumed to be an image URL, which is printed in a double-wide cell at the bottom of the table.

my $gene       = 'Abc-1';
my %gene_info  = (
    Chromosome => I,
    Start      => 100450,
    Stop       => 102893,
    Strand     => '+'
);

my $page = Bio::PrimerDesigner::Tables->new;
$page->info_table( $gene, %gene_info );

PCR_header

Returns a generic header for the PCR primer table. Does not expect any argumments.

PCR_set

Returns the top row for the PCR primer table. Expects the primer set number as its only argument.

PCR_row

Returns table rows with PCR primer info. Should be called once for each primer pair. Expects to be passed a hash containing the Bio::PrimerDesigner::Result object and the primer set number and an (optional) label.

my $pcr_row =  PCR_row( 
    primers => $result_obj,
    setnum  => $set_number,
    label   => $label
);

ePCR_row

Returns table rows summarizing e-PCR results. Expects to be passed an Bio::PrimerDesigner::Result e-PCR results object and an optional e-PCR label.

render

Renders the image URL. Expects to be passed a hash of the map start and stop, and other features to be mapped (i.e. gene,forward_primer,reverse_primer, label,start and stop of each feature, and gene strand).

my $image =  $page->render( 
    start => $startleft,
    stop  => $startright,
    feat  => $features
);

PCR_map

Returns a 6 column wide table cell with the <IMG ...> info. Will display the image of mapped primers in the browser when passed the image URL.

AUTHOR

Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>.

LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

SEE ALSO

Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::epcr.