about_textpresso

#!/usr/bin/perl

# CGI script provides the aboutpage of Textpresso system
#
# Copyright (c) Hans-Michael Muller 2007.

use strict;
# The following line needs adjustments for each implementation
use lib "/usr/local/lib/textpresso/displaying/ecoli/";
# end line that needs adjustments
use CGI;
use TextpressoDisplayTasks;
use TextpressoDisplayGlobals;
use TextpressoDatabaseGlobals;
use TextpressoTable;

my $query = new CGI;
my $myself = $query->url(-absolute => 1);

PrintTop($query, $myself, 1);

my $about_textpresso = new TextpressoTable;
$about_textpresso->init;
$about_textpresso->addtablerow("About Textpresso");
my $text = "Textpresso is an information extracting and processing package for biological literature. ";
$text .= "It was initially developed by Hans-Michael Muller, Eimear Kenny and Paul W. Sternberg, ";
$text .= "with contributions from Juancarlos Chan and David Chen. ";
$text .= "This new version was developed by Hans-Michael Muller with contributions from Arun Rangarajan. ";
$text .= "Textpresso is part of " . $query->a({href=>"http://www.wormbase.org", target=>"_blank"}, "WormBase");
$text .= " at the " . $query->a({href=>"http://www.caltech.edu/", target=>"_blank"}, "California Institute of Technology");
$text .= ", California.";
$text .= " Textpresso is supported by a grant from the ";
$text .= $query->a({href=>"http://www.genome.gov", target=>"_blank"}, "National Human Genome Research Institute");
$text .= " at the US National Institutes of Health # HG004090. ";
$about_textpresso->addtablerow($text);
#print $about_textpresso->maketable($query, tablestyle => 'borderless', width => "60%");
#print $query->br;

my $copyright = new TextpressoTable;
$copyright->init;
$copyright->addtablerow("Copyright");
my $text = "Copyright © 2001-2007 California Institute of Technology. All rights reserved. ";
$copyright->addtablerow($text);
$text = "The " . $query->a({href=>"http://www.geneontology.org", target=>"_blank"}, "Gene Ontology Consortium");
$text .= " holds a copyright for most of the contents of the \'Biological Process\', \'Molecular Function\' and \'Cellular Component\' ";
$text .= "ontologies used on this site. ";
$text .= "All other material in this web site are copyrighted by the authors of the Textpresso Project at the California Institute of Technology. ";
$text .= "All materials appearing on this server may not be reproduced or stored in a retrieval system without prior written permission of the publisher and in no case for profit. ";
$text .= "Documents from this server are provided \"AS-IS\" without any warranty, expressed or implied. ";
$copyright->addtablerow($text);
$text = "Any results and output obtained from the Textpresso";
$text .= $query->span({style => "vertical-align:super;font-size:60%"}, "TM");
$text .= " server shall not be used for any purpose other than private study, scholarship or academic research. ";
$text .= " Anybody using Textpresso";
$text .= " in excess of \"fair use\" may be liable for copyright infringement. ";
$copyright->addtablerow($text);
$text = "Hans-Michael Müller, Eimear E. Kenny and Paul W. Sternberg claim all rights in the word \"Textpresso\" as a trademark. ";
$copyright->addtablerow($text);
#print $copyright->maketable($query, tablestyle => 'borderless', width => "60%");
#print $query->br;

my $database_description = new TextpressoTable;
$database_description->init;
$database_description->addtablerow("Database Description");
$database_description->addtablerow("Currently, this site contains information about the following literatures and data types (data count in parenthesis):");
my %count = ();
foreach my $lit (keys % {(DB_LITERATURE)}) {
    my $fn = DB_ROOT . (DB_LITERATURE)->{$lit} . DB_TEXT;
    my @types = @{(DB_SEARCH_TARGETS_DEFAULTS)};
    my @content = ();
    foreach my $type (sort @types) {
	opendir (DIR,"$fn/$type/");
	my @fl = readdir (DIR);
	closedir (DIR);
	my $nu = @fl;
	$nu -= 2;
	$count{total} += $nu;
	(my $nice = $type) =~ s/$fn\///; 
	$count{$nice} += $nu;
	push @content, "$nice ($nu)" if ($nu);
    }
    $database_description->addtablerow($query->span({-style=>"text-decoration:underline"}, $lit) . ": " . join(", ", @content)) if (@content);
}

my @aux = ();
foreach my $t (sort keys % count) {
    push @aux, "$t : $count{$t}";
}

$database_description->addtablerow($query->span({-style=>"text-decoration:underline"}, "Summary") . ": " . join(", ", @aux)) if (@aux);

my $textpresso_sites = new TextpressoTable;
$textpresso_sites->init;
$textpresso_sites->addtablerow("Textpresso Sites");
$textpresso_sites->addtablerow(
		 $query->a({-href=>'http://www.textpresso.org/celegans', -target=>'_blank'}, "<b><em>C. elegans</em></b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.org/fly', -target=>'_blank'}, "<b><em>D. melanogaster</em></b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.org/neuroscience', -target=>'_blank'}, "<b>Neuroscience</b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.org/master', -target=>'_blank'}, "<b>Master <em>(under construction)</em></b>")
		 );
$textpresso_sites->addtablerow($query->a({-href=>'http://www.yeastgenome.org/textpresso', -target => '_blank'}, "<b><em>Yeast</em></b>") . ", " .
		 $query->a({-href=>'http://www.ciliate.org/textpresso', -target => '_blank'}, "<b><em>Tetrahymena</em></b>") . ", " .
		 $query->a({-href=>'http://ashbya.genome.duke.edu/textpresso/index.html', -target => '_blank'}, "<b><em>Ashbya gossypii</em></b>") . ", " .
		 $query->a({-href=>'http://helab.bioinformatics.med.umich.edu/bbp/textpresso/cgi-bin/simpleretrieval.cgi', -target => '_blank'},
			   "<b><em>Brucella</em></b>")
		 );
$textpresso_sites->addtablerow($query->a({-href=>'http://www.textpresso.ebs.ogi.edu/index.html', -target => '_blank'}, "<b>OHSU Fungal Textpresso</b>") . ": " .
		 $query->a({-href=>'http://www.textpresso.ebs.ogi.edu/ncrassa/index.html', -target => '_blank'}, "<b><em>N. crassa</em></b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.ebs.ogi.edu/anidulans/index.html', -target => '_blank'}, "<b><em>A. nidulans</em></b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.ebs.ogi.edu/mgrisea/index.html', -target => '_blank'}, "<b><em>M. grisea</em></b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.ebs.ogi.edu/cryptococcus/index.html', -target => '_blank'}, "<b><em>Cryptococcus</em></b>") . ", " .
		 $query->a({-href=>'http://www.textpresso.ebs.ogi.edu/grandfungal/index.html', -target => '_blank'}, "<b><em>Filamentous Fungi (Beta)</em></b>")
		 );

my $maintable = new TextpressoTable;
$maintable->init;
$maintable->addtablerow();
$maintable->addtablerow( $about_textpresso->maketable ($query,
					tablestyle => 'borderless-headerbackground',
					width => '100%'),
			 $copyright->maketable ($query,
					tablestyle => 'borderless-headerbackground',
					width => '100%')

			);
print $maintable->maketable ($query,
                             tablestyle => 'borderless-headerbackground',
                             width => '100%');

my $maintable2 = new TextpressoTable;
$maintable2->init;
$maintable2->addtablerow();
$maintable2->addtablerow($database_description->maketable ($query,
					tablestyle => 'borderless-headerbackground',
					width => '100%'),
			$textpresso_sites->maketable ($query,
					tablestyle => 'borderless-headerbackground',
					width => '100%')
			);
print $maintable2->maketable ($query,
                             tablestyle => 'borderless-headerbackground',
                             width => '100%');


PrintBottom($query);