#!/usr/bin/perl -w
use strict;
use warnings;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
use DBIx::Connector;




#my $dbc = new DBIx::Connector(-realm => 'stellabase');
my $q;
my $cgi;
$cgi = new CGI;
my $dbc;

# set up information to connect to database
my $data_source = "DBI:mysql:stellabase";
my $user = "stellabase";
my $password = "stellabase";
# connect
my $dbh = DBI->connect($data_source, $user, $password)
or die "Can't connect to $dbc: $DBI::errstr";

print $cgi->header('text/html');
print $cgi-> start_html (
             -title=>'Query Results',
             -author=>'jawatson@bu.edu',
             -meta=>{'keywords'=>'DBI',
                     'description'=>"Query Results"},
             -BGCOLOR=>'#ffffff',
             -alink=>'#ff0000',
             -vlink=>'#cc99ff',
             -link=>'#9900ff',
             -MARGINHEIGHT=>0,
             -MARGINWIDTH=>0,
             -TOPMARGIN=>5,
             -LEFTMARGIN=>5);

# create local variables for receiving the data

my $name;
my $description;
my $accession;
my $version;
my $sth;








print "<TABLE BORDER=0><TR>";
print " <TD ALIGN='left' VALIGN='top'><A HREF='http://www.stellabase.org/'><IMG
        SRC='http://www.stellabase.org/html/images/stella.png' BORDER=0></TD>";

print "<TD ALIGN='left' VALIGN='middle'>";

print "<A HREF='http://www.stellabase.org/'><IMG SRC='http://www.stellabase.org/html/images/stellabase_title.png' HEIGHT=58 WIDTH=353 BORDER=0 ALT='Cnidbase: Comparative Evolutionary Genomics Database'></A></TD>";
print "</TABLE>";


print "<p align=CENTER><font size='2'>";
print $cgi->a({-href=>'http://www.stellabase.org/index.html'},"Home");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/about.html'},"About");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/gene_search.html'},"Gene Search");
print " - ";
print $cgi->a({-href=>'http://cnidbase.bu.edu/?show_expression_search=1&org=3'},"Gene Expresssion Search");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/primer_lib_search.html'},"Primer Library Search");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/gen_stock.html'},"Genetic Stock Search");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/htdig/search.html'},"Literature Search");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/blast/blast_cs.html'},"Blast");
print "<BR>";
print $cgi->a({-href=>'http://www.stellabase.org/html/dump_primers.html'},"Add Primers");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/dump_stock.html'},"Add Stock");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/dump_notes.html'},"Add Notes About a Gene");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/cnidbase_proteomes.html'},"Compare Genomes");
print " - ";
print $cgi->a({-href=>'http://www.stellabase.org/html/cnidpfam_search.html'},"Search Genomes");
print "</font></p>";



print "<H3 align=CENTER>";


print $cgi->p("Browse the following Pfam families.  Click on a family name to search the <I>Nematostella</I> genome for that family.  Click on description to be redirected to the Pfam database at the Sanger Institute to retieve additional information about this family.");
print "</H3>";


print $cgi->hr;

print "<BLOCKQUOTE>";
print "<FORM name='search_pfam' action='cnidbase_search_pfam.cgi' method='post'>";

print "<p align='left'><input type='text' name='keyword' value='Keyword Search'><input type='submit' value='Go'><a href='http://www.stellabase.org/html/help.html#keyword_search'>Help</p></form>";
print "</BLOCKQUOTE>";

print $cgi->hr;



print "<BLOCKQUOTE>";

      $q = qq{SELECT name, description, accession, version from pfam;};


my $sth = $dbh->prepare($q) or die "Can't prepare statement: $DBI::errstr";

my $rc = $sth->execute;

#headings to table
print "<TABLE BORDER=1 BORDERCOLR=Red>";
print "<TR><TH>Pfam Name</TH>";
print "<TH>Description</TH>";
print "<TH>Pfam Accession/Version</TH></TR>";

# loop through rows of data and print them
          while (($name, $description, $accession, $version) = $sth->fetchrow_array)
           {
              my $pfam=$accession;
              my $url1= 'http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?'.$pfam.'';
              my $url2= 'cnidbase_pfam_search.cgi?name='. $name.'';
           
            { 
      		print "<TR><TD align=center><a href=\"$url2\">$name</a></TD>";
              print "<TD align=center>$description</TD>";
              print "<TD align=center><a href=\"$url1\" target=PFAM>$accession/$version</TD>";
	}
	}

        
              print "</TABLE>";
             
die $sth->errstr if $sth->err;

print $cgi->br;
print $cgi->hr;
print "Questions, comments, suggestions:   ";
print $cgi->a({-href=>'mailto:busully@bu.edu'},'busully@bu.edu   ');


$dbh->disconnect;
print $cgi->end_html;