bio::primerdesigner::remote(3pm) [debian man page]

Bio::PrimerDesigner::Remote(3pm)			User Contributed Perl Documentation			  Bio::PrimerDesigner::Remote(3pm)

NAME

       Bio::PrimerDesigner::Remote - A class for remote access to Bio::PrimerDesigner

SYNOPSIS

	 use Bio::PrimerDesigner::Remote;

DESCRIPTION

       Interface to the server-side binaries.  Passes the primer design paramaters to a remote CGI, which uses a server-side installation of
       Bio::PrimerDesigner to process the request.

METHODS

   CGI_request
       Passes arguments to the URL of the remote Bio::PrimerDesigner CGI and returns the raw output for further processing by local design
       classes.

   check
       Tests the URL to make sure the host is live and the CGI returns the expected results.

AUTHOR

       Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

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, primer_designer.cgi.

perl v5.10.0							    2009-08-04					  Bio::PrimerDesigner::Remote(3pm)

Bio::PrimerDesigner::Tables(3pm)			User Contributed Perl Documentation			  Bio::PrimerDesigner::Tables(3pm)

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.

perl v5.10.0							    2009-08-04					  Bio::PrimerDesigner::Tables(3pm)