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 );
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.