package Jpred;

=head1 NAME

jpred.pm -- Jpred module to define all necessary global and environment variables

=cut

use warnings;
use strict;

BEGIN {
  use Exporter;
  our @ISA = ('Exporter');
  our @EXPORT = qw(
  $WEBSERVER
  $WEBSERVERCGI
  $SERVERROOT
  $SRSSERVER
  $CHKLOG
  $RESULTS
  $PDBLNK
  $CSS
  $IMAGES
  $JNET
  $TIMEOUT
  $BATCHLIM
  $DUNDEE
  $JPREDUSER
  $JPREDEMAIL
  $MAILHOST
  $JPREDROOT
  $BINDIR
  $LIBDIR
  $JOBDIR
  $PREFIX
  $RESOURCE
  $BLASTDB
  $SWALL
  $SWALLFILT
  $PDB
  $PDB_DAT
  $JPREDHEAD
  $JPREDFOOT
  xsystem
  setup_jpred_env
  );
  our @EXPORT_OK = @EXPORT;
}

# library path for Mail::CheckUser dependency for jpred_form.
# for some reason doesn't work if in PERL5LIB
use lib '/sw/lib/perl5.10.1/lib/perl5';

# URIs
#our $WEBSERVER    = 'http://www.compbio.dundee.ac.uk/www-jpred';
our $WEBSERVER    = 'http://webserv1.cluster.lifesci.dundee.ac.uk:3209';
our $WEBSERVERCGI = "$WEBSERVER/cgi-bin";

#$SERVERROOT = "$WEBSERVER/~www-jpred";
our $SERVERROOT = "$WEBSERVER";
our $SRSSERVER  = 'http://srs.ebi.ac.uk/srs6bin/cgi-bin';
our $CHKLOG     = "$WEBSERVERCGI/chklog?";
our $RESULTS    = "$SERVERROOT/results";
our $PDBLNK     = "http://www.ebi.ac.uk/pdbsum/";
our $CSS        = "$SERVERROOT/jpred.css";
our $IMAGES     = "$SERVERROOT/images";
our $JNET       = "$SERVERROOT/about.html#jnet";

# This is the time (in seconds) the job is allowed to take
our $TIMEOUT  = 60 * 60;    # now is 60mins
our $BATCHLIM = 200;

our $DUNDEE = "http://www.dundee.ac.uk";

# e-mail details
our $JPREDUSER  = 'www-jpred';
our $JPREDEMAIL = 'www-jpred@compbio.dundee.ac.uk';
our $MAILHOST   = 'smtp.lifesci.dundee.ac.uk';        # CC 19/05/06 - updated to current smtp host from weevil

# Server paths
#our $JPREDROOT = '/homes/www-jpred/live';
#our $JPREDROOT = '/homes/www-jpred/devel';
our $JPREDROOT = '/home/asherstnev/Projects/Jpred.project/jpred/branches/portable';

# Directory for binaries either on the cluster or on the www server
our $BINDIR = "$JPREDROOT/bin";

# path to perl modules
our $LIBDIR = "$JPREDROOT/lib";

# Cluster paths
our $JOBDIR = "$JPREDROOT/public_html/results";       # directory for output

# Cluster names
our $PREFIX   = "jp_";                                # Prefix for job submissions (qstat will only display 10 chars of job name)
our $RESOURCE = "www_service2";                       # Resource for the submission to use

# Variables for external programs
# psiblast
$ENV{BLASTMAT} = "$JPREDROOT/data/blast";
our $BLASTDB = $JPREDROOT . "/databases";
$ENV{BLASTDB} = $BLASTDB;
our $SWALL     = "$BLASTDB/uniref90";
our $SWALLFILT = "$SWALL.filt";
our $PDB       = '/db/blastdb/pdb';
our $PDB_DAT   = '/db/blastdb/DB.dat';

# ncoils matrix location
$ENV{COILSDIR} = "$JPREDROOT/data/coils";

sub setup_jpred_env {
  my $newJPREDROOT = shift;

  $JPREDROOT = $newJPREDROOT if (defined $newJPREDROOT);

  $BINDIR = "$JPREDROOT/bin";
  $LIBDIR = "$JPREDROOT/lib";
  $JOBDIR = "$JPREDROOT/public_html/results";

  $ENV{BLASTMAT} = "$JPREDROOT/data/blast";
  $BLASTDB = $JPREDROOT . "/databases";
  $ENV{BLASTDB} = $BLASTDB;
  $SWALL     = "$BLASTDB/uniref90";
  $SWALLFILT = "$SWALL.filt";
}

# Error checking system call
sub xsystem {
  my ($command) = @_;
  my $rc = 0xffff & system $command;
  if ( $rc == 0 ) {
    return;
  } elsif ( $rc == 0xff00 ) {
    print "'$command' failed!\n";
    die "Jpred failed\n";
  } elsif ( ( $rc & 0xff ) == 0 ) {
    $rc >>= 8;
    die "'$command' did something else! (exited $rc)\n";
  } else {
    if ( $rc & 0x80 ) {
      $rc &= ~0x80;
      print "'$command' dumped core!\n";
      die "Jpred failed\n";
    }
  }
}

# The header and footer for any HTML produced dynamically
our $JPREDHEAD = "      <div id=\"header\">

         <a href=\"$DUNDEE\">
         <img class=\"uod\" src=\"$IMAGES/logo_white_small.gif\" height=\"100\" width=\"108\" title=\"University of Dundee\" alt=\"University of Dundee Logo\" />
         </a>
        <a href=\"$SERVERROOT/index.html\"> 
	<img src=\"$IMAGES/jpred3.png\" border=\"0\" height=\"102\" width=\"520\" title=\"Jpred Logo\" alt=\"Jpred Logo\" />
	</a>
         <a href=\"http://www.compbio.dundee.ac.uk\">
            <img src=\"$IMAGES/group.png\" border=\"0\" height=\"102\" width=\"70\" title=\"Group Link\" alt=\"The Barton Group\" />
         </a>

         <div id=\"navigation\">
            <table border=\"0\" cellpadding=\"0\" width=\"100%\">
               <tr>
                  <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/index.html\">Home</a></td>

                  <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/about.html\">About</a></td>
                  <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/new.html\">News</a></td>
                  <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/faq.html\">FAQ</a></td>
                  <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/help.html\">Help</a></td>
                  <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/contact.html\">Contact</a></td>
               </tr>

             </table>
         </div> <!-- End #navigation -->
      </div> <!-- End #header -->
";

our $JPREDFOOT = '
      <script type="text/javascript">
         var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
         document.write(unescape("%3Cscript src=\'" + gaJsHost + "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
      </script>
      <script type="text/javascript">
         try{
            var pageTracker = _gat._getTracker("UA-5356328-1");
            pageTracker._trackPageview();
         } catch(err) {}
      </script>
';
1;

=head1 DESCRIPTION

This module defines all the global and envirnmental variables required by the Jpred server scripts and binaries.

=head1 AUTHOR

I'm not sure who originally wrote this module, but I guess all of the following contributed:

James Cuff
Jon Barber
Chris Cole <christian@cole.name> (current maintainer)

=cut