#!/usr/bin/perl -T

###################################################
$program_name = "pbrow.cgi";
# Pair BROWser
#$program_path = "/web/genome/tmstat/";
#$program_path = "/csb/dme/granule/web/tmstat/cgi-bin/";
$program_path = "/data/web/tmstat/cgi-bin/";
$program_ver = "v.2.01";
$program_date = "000630";
$program_author = "Alessandro Senes";
$program_description .= 
"Enhanced version of the pair browser. New features:
 - inproved interface
 - it allow browsing of the complete list
 - it returns the data for all pairs in a input TM sequence
 - support all swiss-prot and genome databases

For the syntax call the cgi with ?opt=syntax

Versions:
2.00 First complete version
2.01 Corrected bug in sub ExponentRoundNumber, when the
     significance is 0 it returns <1E-40
";
      
###################################################

###################################################
# VARIABLES
###################################################

############################
# Convertion hash AA to number
############################
%aa = (
	"A" => 0,
	"C" => 1,
	"D" => 2,
	"E" => 3,
	"F" => 4,
	"G" => 5,
	"H" => 6,
	"I" => 7,
	"K" => 8,
	"L" => 9,
	"M" => 10,
	"N" => 11,
	"P" => 12,
	"Q" => 13,
	"R" => 14,
	"S" => 15,
	"T" => 16,
	"V" => 17,
	"W" => 18,
	"Y" => 19
	);

############################
# Convertion array number to AA 
############################
@aa = (
	"A",
	"C",
	"D",
	"E",
	"F",
	"G",
	"H",
	"I",
	"K",
	"L",
	"M",
	"N",
	"P",
	"Q",
	"R",
	"S",
	"T",
	"V",
	"W",
	"Y"
	);

############################
# 4 letter codes of genomes 
############################
@genomeCodes = (
	aaeo,
	aful,
	bbur,
	bsub,
	cele,
	cpne,
	ctra,
	ecol,
	hinf,
	hpyl,
	mgen,
	mjan,
	mpne,
	mthe,
	mtub,
	phor,
	rpro,
	scer,
	syne,
	tpal
	);

############################
# codes of the 3 Sprot databases
# all, single-span and multi-span
############################
@sprotCodes = (
	sprot,
	sprotsingle,
	sprotmulti
	);


############################
# Info string on databases
############################
$database_info{aaeo} = "All TMs in A.aeolicus genome (1227 TMs)";
$database_info{aful} = "All TMs in A.fulgidus genome (2122 TMs)";
$database_info{bbur} = "All TMs in B.burgdorferi genome (864 TMs)";
$database_info{bsub} = "All TMs in B.subtilis genome (5044 TMs)";
$database_info{cele} = "All TMs in C.elegans genome (21197 TMs)";
$database_info{cpne} = "All TMs in C.pneumoniae genome (1000 TMs)";
$database_info{ctra} = "All TMs in C.trachomatis genome (840 TMs)";
$database_info{ecol} = "All TMs in E.coli genome (5525 TMs)";
$database_info{hinf} = "All TMs in H.influenzae genome (1747 TMs)";
$database_info{hpyl} = "All TMs in H.pylori genome (1268 TMs)";
$database_info{mgen} = "All TMs in M.genitalium genome (490 TMs)";
$database_info{mjan} = "All TMs in M.jannaschii genome (1089 TMs)";
$database_info{mpne} = "All TMs in M.pneumoniae genome (616 TMs)";
$database_info{mthe} = "All TMs in M.thermoautotrophicum genome (1398 TMs) ";
$database_info{mtub} = "All TMs in M.tuberculosis genome (3114 TMs)";
$database_info{phor} = "All TMs in P.horikoshii genome (1703 TMs)                ";
$database_info{rpro} = "All TMs in R.prowazekii genome (972 TMs)";
$database_info{scer} = "All TMs in S.cerevisiae genome (4520 TMs)";
$database_info{syne} = "All TMs in Synechocystis sp. genome (2891 TMs)";
$database_info{tpal} = "All TMs in T.pallidum genome (749 TMs)";
$database_info{sprot} = "All TMs in Swiss-Prot rel.37 after homology removal";
$database_info{sprotsingle} = "Single-span TMs in Swiss-Prot rel.37 after homology removal";
$database_info{sprotmulti} = "Multi-span TMs in Swiss-Prot rel.37 after homology removal";
#$database_info{null} = "<FONT COLOR=\"#FF0000\"><B>Select a database</B></FONT>";
$database_info{null} = "Select a database";

############################
# Name of database
############################
$database_string{aaeo} = "A.aeolicus (1227 TMs)";
$database_string{aful} = "A.fulgidus (2122 TMs)";
$database_string{bbur} = "B.burgdorferi (864 TMs)";
$database_string{bsub} = "B.subtilis (5044 TMs)";
$database_string{cele} = "C.elegans (21197 TMs)";
$database_string{cpne} = "C.pneumoniae (1000 TMs)";
$database_string{ctra} = "C.trachomatis (840 TMs)";
$database_string{ecol} = "E.coli (5525 TMs)";
$database_string{hinf} = "H.influenzae (1747 TMs)";
$database_string{hpyl} = "H.pylori (1268 TMs)";
$database_string{mgen} = "M.genitalium (490 TMs)";
$database_string{mjan} = "M.jannaschii (1089 TMs)";
$database_string{mpne} = "M.pneumoniae (616 TMs)";
$database_string{mthe} = "M.thermoautotrophicum (1398 TMs)";
$database_string{mtub} = "M.tuberculosis (3114 TMs)";
$database_string{phor} = "P.horikoshii (1703 TMs)";
$database_string{rpro} = "R.prowazekii (972 TMs)";
$database_string{scer} = "S.cerevisiae (4520 TMs)";
$database_string{syne} = "Synechocystis sp. (2891 TMs)";
$database_string{tpal} = "T.pallidum (749 TMs)";
$database_string{sprot} = "Swiss-Prot database (13,606 TMs)";
$database_string{sprotsingle} = "Single-span Swiss-Prot database (1,410 TMs)";
$database_string{sprotmulti} = "Multi-span Swiss-Prot database (12,743 TMs)";

############################
# Links to genome pages
############################
$database_url{aaeo} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Aaeo/\" ONMOUSEOVER=\'infoBox(\"Click here for the Aaeo genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Aaeo</A>]";
$database_url{aful} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Aful/\" ONMOUSEOVER=\'infoBox(\"Click here for the Aful genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Aful</A>]";
$database_url{bbur} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Bbur/\" ONMOUSEOVER=\'infoBox(\"Click here for the Bbur genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Bbur</A>]";
$database_url{bsub} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Bsub/\" ONMOUSEOVER=\'infoBox(\"Click here for the Bsub genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Bsub</A>]";
$database_url{cele} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Cele/\" ONMOUSEOVER=\'infoBox(\"Click here for the Cele genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Cele</A>]";
$database_url{cpne} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Cpne/\" ONMOUSEOVER=\'infoBox(\"Click here for the Cpne genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Cpne</A>]";
$database_url{ctra} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Ctra/\" ONMOUSEOVER=\'infoBox(\"Click here for the Ctra genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Ctra</A>]";
$database_url{ecol} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Ecol/\" ONMOUSEOVER=\'infoBox(\"Click here for the Ecol genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Ecol</A>]";
$database_url{hinf} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Hinf/\" ONMOUSEOVER=\'infoBox(\"Click here for the Hinf genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Hinf</A>]";
$database_url{hpyl} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Hpyl/\" ONMOUSEOVER=\'infoBox(\"Click here for the Hpyl genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Hpyl</A>]";
$database_url{mgen} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Mgen/\" ONMOUSEOVER=\'infoBox(\"Click here for the Mgen genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Mgen</A>]";
$database_url{mjan} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Mjan/\" ONMOUSEOVER=\'infoBox(\"Click here for the Mjan genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Mjan</A>]";
$database_url{mpne} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Mpne/\" ONMOUSEOVER=\'infoBox(\"Click here for the Mpne genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Mpne</A>]";
$database_url{mthe} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Mthe/\" ONMOUSEOVER=\'infoBox(\"Click here for the Mthe genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Mthe</A>]";
$database_url{mtub} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Mtub/\" ONMOUSEOVER=\'infoBox(\"Click here for the Mtub genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Mtub</A>]";
$database_url{phor} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Phor/\" ONMOUSEOVER=\'infoBox(\"Click here for the Phor genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Phor</A>]";
$database_url{rpro} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Rpro/\" ONMOUSEOVER=\'infoBox(\"Click here for the Rpro genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Rpro</A>]";
$database_url{scer} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Scer/\" ONMOUSEOVER=\'infoBox(\"Click here for the Scer genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Scer</A>]";
$database_url{syne} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Syne/\" ONMOUSEOVER=\'infoBox(\"Click here for the Syne genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Syne</A>]";
$database_url{tpal} = " [<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/Tpal/\" ONMOUSEOVER=\'infoBox(\"Click here for the Tpal genome page\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Tpal</A>]";
$database_url{sprot} = "";
$database_url{sprotsingle} = "";
$database_url{sprotmulti} = "";

############################
# Links to genome pages
############################
$database_location{aaeo} = $program_path."data/pairs.aaeo.dat";
$database_location{aful} = $program_path."data/pairs.aful.dat";
$database_location{bbur} = $program_path."data/pairs.bbur.dat";
$database_location{bsub} = $program_path."data/pairs.bsub.dat";
$database_location{cele} = $program_path."data/pairs.cele.dat";
$database_location{cpne} = $program_path."data/pairs.cpne.dat";
$database_location{ctra} = $program_path."data/pairs.ctra.dat";
$database_location{ecol} = $program_path."data/pairs.ecol.dat";
$database_location{hinf} = $program_path."data/pairs.hinf.dat";
$database_location{hpyl} = $program_path."data/pairs.hpyl.dat";
$database_location{mgen} = $program_path."data/pairs.mgen.dat";
$database_location{mjan} = $program_path."data/pairs.mjan.dat";
$database_location{mpne} = $program_path."data/pairs.mpne.dat";
$database_location{mthe} = $program_path."data/pairs.mthe.dat";
$database_location{mtub} = $program_path."data/pairs.mtub.dat";
$database_location{phor} = $program_path."data/pairs.phor.dat";
$database_location{rpro} = $program_path."data/pairs.rpro.dat";
$database_location{scer} = $program_path."data/pairs.scer.dat";
$database_location{syne} = $program_path."data/pairs.syne.dat";
$database_location{tpal} = $program_path."data/pairs.tpal.dat";
$database_location{sprot} = $program_path."data/pairs.dat";
$database_location{sprotsingle} = $program_path."data/pairs.single.dat";
$database_location{sprotmulti} = $program_path."data/pairs.multi.dat";


###################################################
# Done with variables
###################################################


$time = localtime();


###################################################
# Call the subroutine that parses the web input
###################################################
$errorCode = &ReadParse;

if ($errorCode) {
	&Error($errorCode);
	exit;
}

if ($field{opt} eq "syntax") {
	print "Content-type: text/html\n\n";
	print "<TABLE WIDTH=500 BORDER=1>\n";
	print "<TR><TD><B>Argument</B></TD><TD><B>Description</B></TD><TD><B>Values</B></TD></TR>\n";
	print "<TR><TD>seq</TD><TD>Amino acid sequence</TD><TD>Amino acid one letter code<BR>Any combination of <I>ACDEFGHIKLMNPQRSTVWY</I><BR>Other characters OK<BR>Up to 50 characters<BR>Case insensitive</TD></TR>\n";
	print "<TR><TD>db</TD><TD>database data</TD><TD><I>sprot</I>: Swiss-prot database<BR><I>sprotsingle</I>: Swiss-prot single span<BR><I>sprotmulti</I>: Swiss-prot multi span<BR><I>aaeo</I>: Aaeo genome<BR><I>aful</I>: Aful genome<BR><I>bbur</I>: Bbur genome<BR><I>bsub</I>: Bsub genome<BR><I>cele</I>: Cele genome<BR><I>cpne</I>: Cele genome<BR><I>ctra</I>: Ctra genome<BR><I>ecol</I>: Ecol genome<BR><I>hinf</I>: Hinf genome<BR><I>hypl</I>: Hypl genome<BR><I>mgen</I>: Mgen genome<BR><I>mjan</I>: Mjan genome<BR><I>mpne</I>: Mpne genome<BR><I>mthe</I>: Mthe genome<BR><I>mtub</I>: Mtub genome<BR><I>phor</I>: Phor genome<BR><I>rpro</I>: Rpro genome<BR><I>scer</I>: Scer genome<BR><I>syne</I>: Syne genome<BR><I>tpal</I>: Tpal genome<BR>Case insensitive</TD></TR>\n";
	print "<TR><TD>dbtype</TD><TD>database type for select box</TD><TD><I>sprot</I>: displays Swiss-prot databases<BR><I>genome</I>: display genome databases<BR>Optional, default <I>sprot</I><BR>Case insensitive<BR>Overridden by <I>db</I> argument<BR>Case insensitive</TD></TR>\n";
	print "<TR><TD>sort</TD><TD>sorting options</TD><TD><I>PAIR</I> & <I>PAIRDOWN</I>: by pair in alphabetical order<BR><I>PAIRUP</I>: by pair in reverse order<BR><I>COUNT</I> & <I>COUNTUP</I>: by number in segment, larger to smaller<BR><I>COUNTDOWN</I>: by number in segment, smaller to larger<BR><I>OBS</I> & <I>OBSUP</I>: by number observed in database, larger to smaller<BR><I>OBSDOWN</I>: by number observed in database, smaller to larger<BR><I>EXP</I> & <I>EXPUP</I>: by number expected in database, larger to smaller<BR><I>EXPDOWN</I>: by number expected in database, smaller to larger<BR><I>SIGN</I> & <I>SIGNUP</I>: by significance, smaller to larger p value<BR><I>SIGNDOWN</I>: by significance, larger to smaller p value<BR><I>ODD</I> & <I>ODDUP</I>: by odds ratio, larger to smaller<BR><I>ODDDOWN</I>: by odds ratio, larger to smaller<BR>Optional, default <I>SIGN</I><BR>Case insensitive</TD></TR>\n";
	print "<TR><TD>opt</TD><TD>options</TD><TD><I>syntax</I>: returns this page<BR>Case insensitive</TD></TR>\n";
	print "</TABLE>";
	exit;
} elsif ($field{opt} eq "help") {
	print "Content-type: text/html\n\n";
	print "Help here soon<BR>\n";
	print "<FORM><INPUT TYPE=\"button\" NAME=\"\" VALUE=\"Close window\" OnClick=\"javascript: window.close()\">";
	exit;
} elsif ($field{opt} ne "sequence" && $field{opt} ne "residues" && $field{opt} ne "sorted") {
	if ($field{seq}) {
		$field{opt} = "sequence";
	} elsif ($field{res1} && $field{res2} &&$field{reg}) {
		$field{opt} = "residues";
	} else {
		$field{opt} = "sorted";
	}
}



$field{dbtype} =~ tr/A-Z/a-z/;
if ($field{dbtype} eq "genome") {
	$select_menu = "genome";
} else {
	$select_menu = "sprot";
}

$field{db} =~ tr/A-Z/a-z/;

if ($field{db} eq "sprot") {
	$open_db = $database_location{sprot};
	$selected_option{sprot} = "SELECTED";
	$select_menu = "sprot";
} elsif ($field{db} eq "sprotsingle") {
	$open_db = $database_location{sprotsingle};
	$selected_option{sprotsingle} = "SELECTED";
	$select_menu = "sprot";
} elsif ($field{db} eq "sprotmulti") {
	$open_db = $database_location{sprotmulti};
	$selected_option{sprotmulti} = "SELECTED";
	$select_menu = "sprot";
} elsif ($field{db} eq "aaeo") {
	$open_db = $database_location{aaeo};
	$selected_option{aaeo}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "aful") {
	$open_db = $database_location{aful};
	$selected_option{aful}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "bbur") {
	$open_db = $database_location{bbur};
	$selected_option{bbur}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "bsub") {
	$open_db = $database_location{bsub};
	$selected_option{bsub}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "cele") {
	$open_db = $database_location{cele};
	$selected_option{cele}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "cpne") {
	$open_db = $database_location{cpne};
	$selected_option{cpne}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "ctra") {
	$open_db = $database_location{ctra};
	$selected_option{ctra}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "ecol") {
	$open_db = $database_location{ecol};
	$selected_option{ecol}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "hinf") {
	$open_db = $database_location{hinf};
	$selected_option{hinf}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "hpyl") {
	$open_db = $database_location{hpyl};
	$selected_option{hpyl}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "mgen") {
	$open_db = $database_location{mgen};
	$selected_option{mgen}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "mjan") {
	$open_db = $database_location{mjan};
	$selected_option{mjan}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "mpne") {
	$open_db = $database_location{mpne};
	$selected_option{mpne}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "mthe") {
	$open_db = $database_location{mthe};
	$selected_option{mthe}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "mtub") {
	$open_db = $database_location{mtub};
	$selected_option{mtub}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "phor") {
	$open_db = $database_location{phor};
	$selected_option{phor}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "rpro") {
	$open_db = $database_location{rpro};
	$selected_option{rpro}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "scer") {
	$open_db = $database_location{scer};
	$selected_option{scer}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "syne") {
	$open_db = $database_location{syne};
	$selected_option{syne}  = "SELECTED";
	$select_menu = "genome";
} elsif ($field{db} eq "tpal") {
	$open_db = $database_location{tpal};
	$selected_option{tpal}  = "SELECTED";
	$select_menu = "genome";
} else {
	$field{db} = "null";
	$selected_option{null} = "SELECTED";
}

if ($select_menu eq "genome") {
	$database_option_code = "<SELECT NAME=\"db\"><OPTION VALUE=\"\" $selected_option{null}>Select a genome database<OPTION VALUE=\"aaeo\" $selected_option{aaeo}>$database_string{aaeo}<OPTION VALUE=\"aful\" $selected_option{aful}>$database_string{aful}<OPTION VALUE=\"bbur\" $selected_option{bbur}>$database_string{bbur}<OPTION VALUE=\"bsub\" $selected_option{bsub}>$database_string{bsub}<OPTION VALUE=\"cele\" $selected_option{cele}>$database_string{cele}<OPTION VALUE=\"cpne\" $selected_option{cpne}>$database_string{cpne}<OPTION VALUE=\"ctra\" $selected_option{ctra}>$database_string{ctra}<OPTION VALUE=\"ecol\" $selected_option{ecol}>$database_string{ecol}<OPTION VALUE=\"hinf\" $selected_option{hinf}>$database_string{hinf}<OPTION VALUE=\"hpyl\" $selected_option{hpyl}>$database_string{hpyl}<OPTION VALUE=\"mgen\" $selected_option{mgen}>$database_string{mgen}<OPTION VALUE=\"mjan\" $selected_option{mjan}>$database_string{mjan}<OPTION VALUE=\"mpne\" $selected_option{mpne}>$database_string{mpne}<OPTION VALUE=\"mthe\" $selected_option{mthe}>$database_string{mthe}<OPTION VALUE=\"mtub\" $selected_option{mtub}>$database_string{mtub}<OPTION VALUE=\"phor\" $selected_option{phor}>$database_string{phor}<OPTION VALUE=\"rpro\" $selected_option{rpro}>$database_string{rpro}<OPTION VALUE=\"scer\" $selected_option{scer}>$database_string{scer}<OPTION VALUE=\"syne\" $selected_option{syne}>$database_string{syne}<OPTION VALUE=\"tpal\" $selected_option{tpal}>$database_string{tpal}</SELECT>";
	$radio_dbtype_genome = "CHECKED";
} else {
	$database_option_code = "<SELECT NAME=\"db\"><OPTION VALUE=\"\" $selected_option{null}>Select a Swiss-Prot database<OPTION VALUE=\"sprot\" $selected_option{sprot}>$database_string{sprot}<OPTION VALUE=\"sprotsingle\" $selected_option{sprotsingle}>$database_string{sprotsingle}<OPTION VALUE=\"sprotmulti\" $selected_option{sprotmulti}>$database_string{sprotmulti}</SELECT>";
	$radio_dbtype_sprot = "CHECKED";
}


if ($field{opt} eq "sequence") {
	
	$javaScript = "submitSequence.js";
	$boxColor = "#DDDDFF";

	###################################################
	# Start counting the pairs found in the sequence
	###################################################

	$totalPairs = 0;
	$totalUniquePairs = 0;

	if ($field{seq}) {

		###################################################
		# Change the sequence to all UPPERCASE
		###################################################
		$field{seq} =~ tr/a-z/A-Z/;

		###################################################
		# Trim the sequence if to long 
		###################################################
		if (length($field{seq}) > 40) {
			$oversizedString = 1;
			$field{seq} = substr($field{seq}, 0, 40);
		} elsif (length($field{seq}) == 0) {
			$nullString = 1;
		}

		###################################################
		# For each letter of the sequence...
		###################################################
		for ($skip=0;$skip<length($field{seq});$skip++) {

			$res1 = substr($field{seq},$skip,1);

			###################################################
			# ...if the first residue is one of the 20 AA
			# cound all pairs it forms at registries 1 to 10...
			###################################################
			if ($res1 =~ /[ACDEFGHIKLMNPQRSTVWY]/) {
				for ($reg=1;$reg<11;$reg++) {
					$res2 = substr($field{seq},$skip + $reg,1);
					###################################################
					# ...if the second residue is OK, convert $res1 and 
					# $res2 to numbers (%aa) and add one to the count of 
					# $res1/$res2/$reg pairs in the array @paircount.
					# Increment $totalPairs and if it is the first time
					# the pair is found increment also $totalUniquePairs.
					###################################################
					if ($res2 =~ /[ACDEFGHIKLMNPQRSTVWY]/) {
						$paircount[$aa{$res1}][$aa{$res2}][$reg]++;

						$totalPairs++;
						if ($paircount[$aa{$res1}][$aa{$res2}][$reg] == 1) {
							$totalUniquePairs++;
							$pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg] = $field{seq};
							$pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg] =~ tr/A-Z/-/;
						}
	#					$pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg] = substr($pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg],0,$skip).$res1.substr($pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg],$skip+1,$reg-1).$res2.substr($pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg],$skip + $reg + 1,length($pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg])-$skip-$reg-1);
	#					print "$pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg]<BR>\n";
						substr($pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg],$skip,1) = substr($field{seq},$skip,1);
						substr($pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg],$skip + $reg,1) = substr($field{seq},$skip + $reg,1);
					}
				}
			}
		}

	}

	if ($totalPairs) {


		for ($res1=0;$res1<20;$res1++) {
			for ($res2=0;$res2<20;$res2++) {
				for ($reg=1;$reg<11;$reg++) {
					if ($paircount[$res1][$res2][$reg]>0) {
						if ($matchString) {
							$matchString .= "|";
						}
						$matchString .= "^$aa[$res1]$aa[$res2]$reg\$";
					}
				}
			}
		}


		open (PAIRS, $open_db);
		@pairdata = <PAIRS>;
		close PAIRS;
		for ($i=0;$i<@pairdata;$i++) {

			$pairdata[$i] =~ s/\n//g;
			@split = split("\t", $pairdata[$i]);
			if ($split[0] =~ /$matchString/) {
				push @pair, $split[0];
				$res1 = substr($split[0],0,1);
				$res2 = substr($split[0],1,1);
				$reg = substr($split[0],2,length($split[0])-2);
				push @indexedPair, "<A HREF=\"javascript: fakeLink()\" ONMOUSEOVER=\'infoBox(\"$pairHighlightedSeq[$aa{$res1}][$aa{$res2}][$reg]\");return true\' ONMOUSEOUT=\'resetBox()\'>$split[0]</A> ($paircount[$aa{$res1}][$aa{$res2}][$reg])";
				push @max, $split[1];
				if (!$split[2]) {
					$split[2] = 0;
				}
				push @obs, $split[2];
				push @exp, $split[3];
				push @roundExp, &RoundNumber($split[3],1);
				push @sd, $split[4];
				push @roundSd, &RoundNumber($split[4],2);
				push @sign, $split[5];
				push @roundSign, &ExponentRoundNumber($split[5],2);
				push @od, $split[6];
				push @roundOd, &RoundNumber($split[6],2);
			}
		}
	}
	
} elsif ($field{opt} eq "residues") {

	$javaScript = "submitResidues.js";
	$boxColor = "#DDFFDD";
	$res1 = $field{res1};
	$res1 =~ s/[\n ]//g;
	$res1 =~ s/X/ACDEFGHIKLMNPQRSTVWY/g;
	$res1 =~ tr/[a-z]/[A-Z]/;

	if ($res1 && !($res1 =~ /^[ACDEFGHIKLMNPQRSTVWY,]+$/)) {
		&Error(1);
		exit;
	}

	@split = split(",", $res1);

	for ($i=0;$i<@split;$i++) {
		for ($j=0;$j<@aa;$j++) {

			if ($split[$i] eq $aa[$j]) {
				$res1[$aa{$aa[$j]}] = 1;
			}
		}
	}

	for ($i=0;$i<@aa;$i++) {
		if ($res1[$i]) {
			$res1_total++;
			$res1_sel .= "$aa[$i],";
			$res1_search_string .= $aa[$i];
			$res1_checked[$i] = "CHECKED";
		}
	}
	$res1_sel =~ s/,$//g;
	if (!$res1_sel) {
		$res1_sel = "<FONT COLOR=\"#FF0000\">?</FONT>";
	}


	$res2 = $field{res2};
	$res2 =~ s/[\n ]//g;
	$res2 =~ s/X/ACDEFGHIKLMNPQRSTVWY/g;
	$res2 =~ tr/[a-z]/[A-Z]/;

	if ($res2 && !($res2 =~ /^[ACDEFGHIKLMNPQRSTVWY,]+$/)) {
		&Error(2);
		exit;
	}

	@split = split(",", $res2);

	for ($i=0;$i<@split;$i++) {
		for ($j=0;$j<@aa;$j++) {

			if ($split[$i] eq $aa[$j]) {
				$res2[$aa{$aa[$j]}] = 1;
			}
		}
	}

	for ($i=0;$i<@aa;$i++) {
		if ($res2[$i]) {
			$res2_total++;
			$res2_sel .= "$aa[$i],";
			$res2_search_string .= $aa[$i];
			$res2_checked[$i] = "CHECKED";
		}
	}
	$res2_sel =~ s/,$//g;
	if (!$res2_sel) {
		$res2_sel = "<FONT COLOR=\"#FF0000\">?</FONT>";
	}




	$reg = $field{reg};
	$reg =~ s/[\n ]//g;

	if ($reg && !($reg =~ /^[0-9,]+$/)) {
		&Error(3);
		exit;
	}

	@split = split(",", $reg);

	for ($i=0;$i<@split;$i++) {
		if ($split[$i] >= 1 && $split[$i] <= 10) {
			$reg[$split[$i]] = 1;
		}
	}

	for ($i=1;$i<=10;$i++) {
		if ($reg[$i]) {
			$reg_total++;
			$reg_sel .= "$i,";
			push @reg_search, $i;
			$reg_checked[$i] = "CHECKED";
		}
	}
	$reg_sel =~ s/,$//g;
	if (!$reg_sel) {
		$reg_sel = "<FONT COLOR=\"#FF0000\">?</FONT>";
	}


	if ($field{rev} eq "FR") {
		for ($i=0;$i<@aa;$i++) {
			if ($res1[$i] && $res2[$i]) {
				$res1_res2_overlap++;
			}
		}
		$total_combinations = ((2 * $res1_total * $res2_total) - $res1_res2_overlap) * $reg_total;
		$revFR_checked = "CHECKED";
		$search_type_string = "forward & reversed";
	} elsif ($field{rev} eq "R") {
		$total_combinations = $res1_total * $res2_total * $reg_total;
		$revR_checked = "CHECKED";
		$search_type_string = "reversed";
	} else {
		$total_combinations = $res1_total * $res2_total * $reg_total;
		$revF_checked = "CHECKED";
		$search_type_string = "";
	}

	open (PAIRS, $open_db);
	@pairdata = <PAIRS>;
	close PAIRS;


	if ($field{rev} eq "FR") {
		for ($i=0;$i<@pairdata;$i++) {

			for ($j=0;$j<@reg_search;$j++) {
				$pairdata[$i] =~ s/\n//g;
				@split = split("\t", $pairdata[$i]);
				if ($split[0] =~ /^[$res1_search_string][$res2_search_string]$reg_search[$j]$/ || $split[0] =~ /^[$res2_search_string][$res1_search_string]$reg_search[$j]$/) {
					push @pair, $split[0];
					push @indexedPair, $split[0];
					push @max, $split[1];
					if (!$split[2]) {
						$split[2] = 0;
					}
					push @obs, $split[2];
					push @exp, $split[3];
					push @roundExp, &RoundNumber($split[3],1);
					push @sd, $split[4];
					push @roundSd, &RoundNumber($split[4],2);
					push @sign, $split[5];
					push @roundSign, &ExponentRoundNumber($split[5],2);
					push @od, $split[6];
					push @roundOd, &RoundNumber($split[6],2);
				}
			}
		}
	} elsif($field{rev} eq "R") {
		for ($i=0;$i<@pairdata;$i++) {

			for ($j=0;$j<@reg_search;$j++) {
				$pairdata[$i] =~ s/\n//g;
				@split = split("\t", $pairdata[$i]);
				if ($split[0] =~ /^[$res2_search_string][$res1_search_string]$reg_search[$j]$/) {
					push @pair, $split[0];
					push @indexedPair, $split[0];
					push @max, $split[1];
					if (!$split[2]) {
						$split[2] = 0;
					}
					push @obs, $split[2];
					push @exp, $split[3];
					push @roundExp, &RoundNumber($split[3],1);
					push @sd, $split[4];
					push @roundSd, &RoundNumber($split[4],2);
					push @sign, $split[5];
					push @roundSign, &ExponentRoundNumber($split[5],2);
					push @od, $split[6];
					push @roundOd, &RoundNumber($split[6],2);
				}
			}
		}
	} else {
		for ($i=0;$i<@pairdata;$i++) {

			for ($j=0;$j<@reg_search;$j++) {
				$pairdata[$i] =~ s/\n//g;
				@split = split("\t", $pairdata[$i]);
				if ($split[0] =~ /^[$res1_search_string][$res2_search_string]$reg_search[$j]$/) {
					push @pair, $split[0];
					push @indexedPair, $split[0];
					push @max, $split[1];
					if (!$split[2]) {
						$split[2] = 0;
					}
					push @obs, $split[2];
					push @exp, $split[3];
					push @roundExp, &RoundNumber($split[3],1);
					push @sd, $split[4];
					push @roundSd, &RoundNumber($split[4],2);
					push @sign, $split[5];
					push @roundSign, &ExponentRoundNumber($split[5],2);
					push @od, $split[6];
					push @roundOd, &RoundNumber($split[6],2);
				}
			}
		}
	}

	
} elsif ($field{opt} eq "sorted") {
	$boxColor = "#FFDDDD";
	$javaScript = "submitSorted.js";
}


print "Content-type: text/html\n\n";
print "<HTML>\n";
print "<HEAD>\n";
print "<SCRIPT SRC=\"$javaScript\" Language = \"JavaScript\">\n"; 
print "</SCRIPT>\n";
print "<TITLE>TMSTAT - Pair Browser</TITLE>\n";
print "<META NAME=\"GENERATOR\" CONTENT=\"$program_name $program_ver $time\">\n";
print "</HEAD>\n";
print "\n";
print "<BODY BGCOLOR=\"#FFFFFF\" TEXT=\"#00006A\" LINK=\"#A14030\" VLINK=\"#A14030\">\n";


$field{sort} =~ tr/a-z/A-Z/;

$pairImgUp = "arrowupgrayed.gif";
$pairImgDown = "arrowdowngrayed.gif";
$countImgUp = "arrowupgrayed.gif";
$countImgDown = "arrowdowngrayed.gif";
$signImgUp = "arrowupgrayed.gif";
$signImgDown = "arrowdowngrayed.gif";
$obsImgUp = "arrowupgrayed.gif";
$obsImgDown = "arrowdowngrayed.gif";
$expImgUp = "arrowupgrayed.gif";
$expImgDown = "arrowdowngrayed.gif";
$oddImgUp = "arrowupgrayed.gif";
$oddImgDown = "arrowdowngrayed.gif";


if ($field{sort} eq "PAIR" || $field{sort} eq "PAIRUP" || $field{sort} eq "PAIRDOWN") {
	$sort_string = "pair";
	if ($field{sort} eq "PAIRUP") {
		$pairImgUp = "arrowup.gif";
	} else {
		$pairImgDown = "arrowdown.gif";
		$field{sort} = "PAIRDOWN";
	}
} elsif ($field{sort} eq "COUNT" || $field{sort} eq "COUNTUP" || $field{sort} eq "COUNTDOWN") {
	$sort_string = "number in query sequence";
	if ($field{sort} eq "COUNTDOWN") {
		$countImgUp = "arrowup.gif";
	} else {
		$countImgDown = "arrowdown.gif";
		$field{sort} = "COUNTUP";
	}
} elsif ($field{sort} eq "OBS" || $field{sort} eq "OBSUP" || $field{sort} eq "OBSDOWN") {
	$sort_string = "number observed";
	if ($field{sort} eq "OBSDOWN") {
		$obsImgUp = "arrowup.gif";
	} else {
		$obsImgDown = "arrowdown.gif";
		$field{sort} = "OBSUP";
	}
} elsif ($field{sort} eq "EXP" || $field{sort} eq "EXPUP" || $field{sort} eq "EXPDOWN") {
	$sort_string = "number expected";
	if ($field{sort} eq "EXPDOWN") {
		$expImgUp = "arrowup.gif";
	} else {
		$expImgDown = "arrowdown.gif";
		$field{sort} = "EXPUP";
	}
} elsif ($field{sort} eq "SIGN" || $field{sort} eq "SIGNUP" || $field{sort} eq "SIGNDOWN") {
	$sort_string = "significance";
	if ($field{sort} eq "SIGNDOWN") {
		$signImgUp = "arrowup.gif";
	} else {
		$signImgDown = "arrowdown.gif";
		$field{sort} = "SIGNUP";
	}
} elsif ($field{sort} eq "ODD" || $field{sort} eq "ODDUP" || $field{sort} eq "ODDDOWN") {
	$sort_string = "odds ratio";
	if ($field{sort} eq "ODDDOWN") {
		$oddImgUp = "arrowup.gif";
	} else {
		$oddImgDown = "arrowdown.gif";
		$field{sort} =	 "ODDUP";
	}
} else {
	$field{sort} = "SIGNUP";
	$sort_string = "significance";
	$signImgDown = "arrowdown.gif";
}



if ($field{opt} eq "sequence") {
	if (!$field{seq} || $field{db} eq "null") {
		if (!$field{seq}) {
			$resultString .= "<FONT COLOR=\"#FF0000\">Input the sequence of a TM segment</FONT><BR>\n";
		}
		if ($field{db} eq "null") {
			$resultString .= "<FONT COLOR=\"#FF0000\">Select a database</FONT><BR>\n";
		}
	} elsif ($totalUniquePairs == 0) {
		$resultString .= "No pairs found in the sequence<BR>\n";
	} else {
		$displayPairs = 1;
		$resultString = "$totalUniquePairs pairs found, sorted by $sort_string";
		if ($oversizedString) {
			$resultString = "$totalUniquePairs pairs found, sorted by $sort_string (<FONT COLOR=\"#FF0000\">Sequence truncated to 40 residues</FONT>)";
		}
	}
} elsif  ($field{opt} eq "residues") {
	if (!$field{res1} || !$field{res2} || !$field{reg} || $field{db} eq "null") {
		if (!$field{res1}) {
			$resultString .= "<FONT COLOR=\"#FF0000\">Select one or more amino acids for residue 1</FONT><BR>\n";
		}
		if (!$field{res2}) {
			$resultString .= "<FONT COLOR=\"#FF0000\">Select one or more amino acids for residue 2</FONT><BR>\n";
		}
		if (!$field{reg}) {
			$resultString .= "<FONT COLOR=\"#FF0000\">Select one or more separation registers</FONT><BR>\n";
		}
		if ($field{db} eq "null") {
			$resultString .= "<FONT COLOR=\"#FF0000\">Select a database</FONT><BR>\n";
		}
	} elsif ($total_combinations > 400) {
		$resultString .= "<FONT COLOR=\"#FF0000\">Too many combinations: $total_combinations (max. 400)</FONT><BR>\n";
	} else {
		$displayPairs = 1;
		$resultString = "$total_combinations combinations, sorted by $sort_string";
	}
} elsif  ($field{opt} eq "sorted") {

	if ($field{db} ne "null") {
		$displayPairs = 1;
		
		if ($field{sort} eq "PAIR" || $field{sort} eq "PAIRUP" || $field{sort} eq "PAIRDOWN") {
			$open_db =~ s/\.dat$/\.pair.0.dat/;
		} elsif ($field{sort} eq "OBS" || $field{sort} eq "OBSUP" || $field{sort} eq "OBSDOWN") {
			$open_db =~ s/\.dat$/\.obs.0.dat/;
		} elsif ($field{sort} eq "EXP" || $field{sort} eq "EXPUP" || $field{sort} eq "EXPDOWN") {
			$open_db =~ s/\.dat$/\.exp.0.dat/;
		} elsif ($field{sort} eq "SIGN" || $field{sort} eq "SIGNUP" || $field{sort} eq "SIGNDOWN") {
			$open_db =~ s/\.dat$/\.sign.0.dat/;
		} elsif ($field{sort} eq "ODD" || $field{sort} eq "ODDUP" || $field{sort} eq "ODDDOWN") {
			$open_db =~ s/\.dat$/\.od.0.dat/;
		}

		open (PAIRS, $open_db);
		@pairdata = <PAIRS>;
		close PAIRS;
#000
#		exit;
###		
#		print "AAAA\n";;
		for ($i=0;$i<@pairdata;$i++) {
#			print "$i<BR>\n";
			$pairdata[$i] =~ s/\n//g;
			@split = split("\t", $pairdata[$i]);
			push @pair, $split[0];
			push @indexedPair, $split[0];
			push @max, $split[1];
			if (!$split[2]) {
				$split[2] = 0;
			}
			push @obs, $split[2];
			push @exp, $split[3];
			push @roundExp, &RoundNumber($split[3],1);
			push @sd, $split[4];
			push @roundSd, &RoundNumber($split[4],2);
			push @sign, $split[5];
			push @roundSign, &ExponentRoundNumber($split[5],2);
#			push @roundSign, $split[5],2;
			push @od, $split[6];
			push @roundOd, &RoundNumber($split[6],2);
		}

		$field{num_sorted} = int($field{num_sorted});
		if ($field{num_sorted} < 1) {
			$field{num_sorted} = 40;
		} elsif ($field{num_sorted} > 200) {
			$field{num_sorted} = 200;
		}
		if ($tot_pages > int($tot_pages)) {
			$tot_pages = int($tot_pages) + 1;
		}

		$field{start_sorted} = int($field{start_sorted});
		if ($field{start_sorted} < 1) {
			$field{start_sorted} = 1;
		} elsif ($field{start_sorted} > 4000) {
			$field{start_sorted} = 4000;
		}


		$after_pages = (4000 - $field{start_sorted} + 1) / $field{num_sorted};
		if ($after_pages > int($after_pages)) {
			$after_pages = int($after_pages) + 1;
		}
		$before_pages = ($field{start_sorted} - 1) / $field{num_sorted};
		if ($before_pages > int($before_pages)) {
			$before_pages = int($before_pages) + 1;
		}
		$tot_pages = $after_pages + $before_pages;
		$curr_page = $before_pages + 1;
		$prev_start_sorted = $field{start_sorted} - $field{num_sorted};
		if ($prev_start_sorted < 1) {
			$prev_start_sorted = 1;
		}
		$next_start_sorted = $field{start_sorted} + $field{num_sorted};
		if ($next_start_sorted > 4000) {
			$next_start_sorted = 4000;
		}

		$firstPair = &Ordinal($field{start_sorted});
		$lastPair = $field{start_sorted} + $field{num_sorted} - 1;
		$lastPair = &Ordinal($lastPair);
		$resultString = "Pair list sorted by $sort_string, from $firstPair to $lastPair";
	} else {
		$resultString = "<FONT COLOR=\"#FF0000\"><B>Please select a database</B></FONT>";
		$field{start_sorted} = 1;
		$field{num_sorted} = 40;
		$tot_pages = 0;
		$curr_page = 0;
	}
	
}


############################
# Open table
############################
print "<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 WIDTH=500>\n";
############################
# Print header band with title and help button
############################
print "<TR><TD COLSPAN=5 BGCOLOR=\"#00006A\"><FONT  COLOR=\"#FFFFFF\" FACE=\"arial, helvetica\" SIZE=2><B>Amino acid pair analysis in transmembrane (TM) domains</FONT></TD><FORM NAME=\"help\"><TD BGCOLOR=\"#00006A\" ALIGN=\"right\"><INPUT TYPE=\"button\" NAME=\"help\" VALUE=\"&nbsp;?&nbsp;\" OnClick=\"javascript: openHelp(\'$program_name?opt=help\')\"></TD></FORM></TR>\n";
############################
# Open selection form and display current database
############################
print "<TR><TD COLSPAN=6><FORM NAME=\"select\" METHOD=\"GET\" ACTION=\"$program_name\"><FONT FACE=\"arial, helvetica\" SIZE=2><BR>\n<B>Database: <A HREF=\"javascript: fakeLink()\" ONMOUSEOVER=\'infoBox(\"$database_info{$field{db}}\");return true\' ONMOUSEOUT=\'resetBox();return true\'>$database_info{$field{db}}</A>$database_url{$field{db}}</B><BR>\n";
############################
# Display database radio and selection fields
############################
print "<INPUT TYPE=\"radio\" NAME=\"dbtype\" VALUE=\"sprot\" $radio_dbtype_sprot onClick=\"dbSelection(\'sprot\')\"><A HREF=\"javascript: dbSelection(\'sprot\')\" ONMOUSEOVER=\'infoBox(\"All TM domains in Swiss-Prot rel.37 after homology removal\");return true\' ONMOUSEOUT=\'resetBox()\'>Swiss-Prot</A><INPUT TYPE=\"radio\" NAME=\"dbtype\" VALUE=\"genome\" $radio_dbtype_genome onClick=\"dbSelection(\'genome\')\"><A HREF=\"javascript: dbSelection(\'genome\')\" ONMOUSEOVER=\'infoBox(\"All TM domains in genome databases\");return true\' ONMOUSEOUT=\'resetBox()\'>Genomes</A> $database_option_code</FONT></TD></TR>\n";
############################
# Separation line
############################
print "<TR><TD COLSPAN=6><HR SIZE=1 WIDTH=100% NOSHADE></TD></TR>\n";
############################
# Tabs
############################
print "<TR><TD COLSPAN=6 ALIGN=\"left\"><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0><TR><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: changeTab(\'sequence\')\" ONMOUSEOVER=\'infoBox(\"Significance of all pairs in the TM sequence of your choiche\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/lefttabblue.gif\" BORDER=0 WIDTH=20 HEIGHT=21><B>Input TM sequence</B><IMG SRC=\"img/righttabblue.gif\" BORDER=0 WIDTH=20 HEIGHT=21></A></FONT></TD><TD BGCOLOR=\"#DDFFDD\" ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: changeTab(\'residues\')\" ONMOUSEOVER=\'infoBox(\"Browse pair data selecting residue and register combinations\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/lefttabgreen.gif\" BORDER=0 WIDTH=20 HEIGHT=21><B>Selected patterns</B><IMG SRC=\"img/righttabgreen.gif\" BORDER=0 WIDTH=20 HEIGHT=21></A></FONT></TD><TD BGCOLOR=\"#FFDDDD\" ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: changeTab(\'sorted\')\" ONMOUSEOVER=\'infoBox(\"See complete pair analysis result list with sorting options\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/lefttabpink.gif\" BORDER=0 WIDTH=20 HEIGHT=21><B>All data, sorted</B><IMG SRC=\"img/righttabpink.gif\" BORDER=0 WIDTH=20 HEIGHT=21></A></FONT></TD></TR></TABLE></TD></TR>\n";
############################
# Print message line
############################
print "<TR><TD BGCOLOR=\"$boxColor\" COLSPAN=6><FONT FACE=\"arial, helvetica\" SIZE=2><BR>\n<CENTER><B>$resultString</B></CENTER><BR>\n</FONT></TD></TR>\n";
############################
# Input sequence field and send buttons
############################
if ($field{opt} eq "sequence") {
	print "<TR BGCOLOR=\"$boxColor\"><TD COLSPAN=6><FONT FACE=\"courier, courier new\" SIZE=2><INPUT NAME=\"seq\" VALUE=\"$field{seq}\" SIZE=40 MAXLENGTH=40></FONT>&nbsp;<FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"button\" VALUE=\"Send TM domain\" OnClick=\"javascript: submitSort(\'\')\"><INPUT TYPE=\"hidden\" NAME=\"sort\" VALUE=\"$field{sort}\"><INPUT TYPE=\"hidden\" NAME=\"opt\" VALUE=\"sequence\"></FONT></FORM></TD></TR>\n";
} elsif ($field{opt} eq "residues") {
	print "<TR><TD BGCOLOR=\"$boxColor\" COLSPAN=6><CENTER><TABLE BGCOLOR=\"$boxColor\" BORDER=0 CELLSPACING=0 CELLPADDING=0 WIDTH=500>";
	print "<TR>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><BR><A HREF=\"javascript: fakeLink(\'\')\" ONMOUSEOVER=\'infoBox(\"Select one or more residues for position 1 in the pair\");return true\' ONMOUSEOUT=\'resetBox()\'>Res.1</A></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>A<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[0]  VALUE=\"A,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>C<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[1]  VALUE=\"C,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>D<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[2]  VALUE=\"D,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>E<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[3]  VALUE=\"E,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>F<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[4]  VALUE=\"F,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>G<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[5]  VALUE=\"G,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>H<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[6]  VALUE=\"H,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>I<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[7]  VALUE=\"I,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>K<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[8]  VALUE=\"K,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>L<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[9]  VALUE=\"L,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>M<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[10] VALUE=\"M,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>N<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[11] VALUE=\"N,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>P<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[12] VALUE=\"P,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>Q<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[13] VALUE=\"Q,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>R<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[14] VALUE=\"R,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>S<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[15] VALUE=\"S,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>T<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[16] VALUE=\"T,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>V<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[17] VALUE=\"V,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>W<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[18] VALUE=\"W,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>Y<BR><INPUT TYPE=\"checkbox\" NAME=\"res1\" $res1_checked[19] VALUE=\"Y,\"></FONT></TD>\n";
	print "<TD ALIGN=\"left\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=1><BR><INPUT TYPE=\"button\" NAME=\"all\" VALUE=\"All\" onClick = \'res1all()\'><INPUT TYPE=\"button\" NAME=\"all\" VALUE=\"Clear\" onClick = \'res1clear()\'></FONT></TD>\n";
	print "</TR>\n";
	print "<TR>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: fakeLink(\'\')\" ONMOUSEOVER=\'infoBox(\"Select one or more residues for position 2 in the pair\");return true\' ONMOUSEOUT=\'resetBox()\'>Res.2</A></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[0]  VALUE=\"A,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[1]  VALUE=\"C,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[2]  VALUE=\"D,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[3]  VALUE=\"E,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[4]  VALUE=\"F,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[5]  VALUE=\"G,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[6]  VALUE=\"H,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[7]  VALUE=\"I,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[8]  VALUE=\"K,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[9]  VALUE=\"L,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[10] VALUE=\"M,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[11] VALUE=\"N,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[12] VALUE=\"P,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[13] VALUE=\"Q,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[14] VALUE=\"R,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[15] VALUE=\"S,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[16] VALUE=\"T,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[17] VALUE=\"V,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[18] VALUE=\"W,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"checkbox\" NAME=\"res2\" $res2_checked[19] VALUE=\"Y,\"></FONT></TD>\n";
	print "<TD ALIGN=\"left\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=1><INPUT TYPE=\"button\" NAME=\"all\" VALUE=\"All\" onClick = \'res2all()\'><INPUT TYPE=\"button\" NAME=\"all\" VALUE=\"Clear\" onClick = \'res2clear()\'></FONT></TD>\n";
	print "</TR>\n";
	print "<TR>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2><BR><A HREF=\"javascript: fakeLink(\'\')\" ONMOUSEOVER=\'infoBox(\"Select one or more separation registers (example: 3 = i,i+3)\");return true\' ONMOUSEOUT=\'resetBox()\'>Reg.</A></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>1<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[1]  VALUE=\"1,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>2<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[2]  VALUE=\"2,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>3<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[3]  VALUE=\"3,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>4<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[4]  VALUE=\"4,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>5<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[5]  VALUE=\"5,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>6<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[6]  VALUE=\"6,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>7<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[7]  VALUE=\"7,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>8<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[8]  VALUE=\"8,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>9<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[9]  VALUE=\"9,\"></FONT></TD>\n";
	print "<TD ALIGN=\"center\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=2>10<BR><INPUT TYPE=\"checkbox\" NAME=\"reg\" $reg_checked[10]  VALUE=\"10,\"></FONT></TD>\n";
	print "<TD COLSPAN=4 ALIGN=\"left\" VALIGN=\"top\"><FONT FACE=\"arial, helvetica\" SIZE=1><BR><INPUT TYPE=\"button\" NAME=\"all\" VALUE=\"All\" onClick = \'regall()\'><INPUT TYPE=\"button\" NAME=\"all\" VALUE=\"Clear\" onClick = \'regclear()\'></FONT></TD>\n";
	print "<TD COLSPAN=7 ALIGN=\"right\" VALIGN=\"middle\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"button\" VALUE=\"Send combinations\" OnClick=\"javascript: submitSort(\'\')\"><INPUT TYPE=\"hidden\" NAME=\"sort\" VALUE=\"$field{sort}\"></FONT></TD>\n";
	print "</TR>\n";
	print "</TABLE>\n";
	print "<INPUT TYPE=\"hidden\" NAME=\"opt\" VALUE=\"residues\"><FONT FACE=\"arial, helvetica\" SIZE=2>Query: <INPUT TYPE=\"radio\" NAME=\"rev\" $revF_checked VALUE=\"F\"><A HREF=\"javascript: fakeLink(\'\')\" ONMOUSEOVER=\'infoBox(\"Example: Res1=A, Res2=L, Reg=3: returns AL3\");return true\' ONMOUSEOUT=\'resetBox()\'>Forward</A> <INPUT TYPE=\"radio\" NAME=\"rev\" $revR_checked VALUE=\"R\"><A HREF=\"javascript: fakeLink(\'\')\" ONMOUSEOVER=\'infoBox(\"Example: Res1=A, Res2=L, Reg=3: returns LA3\");return true\' ONMOUSEOUT=\'resetBox()\'>Reversed</A> <INPUT TYPE=\"radio\" NAME=\"rev\" $revFR_checked VALUE=\"FR\"><A HREF=\"javascript: fakeLink(\'\')\" ONMOUSEOVER=\'infoBox(\"Example: Res1=A, Res2=L, Reg=3: returns AL3+LA3\");return true\' ONMOUSEOUT=\'resetBox()\'>Forward & reversed</A></FONT>";
	print "</TD></TR></FORM>\n";

} elsif ($field{opt} eq "sorted") {
	print "<TR BGCOLOR=\"$boxColor\"><TD COLSPAN=6 ALIGN=\"center\"><INPUT TYPE=\"hidden\" NAME=\"opt\" VALUE=\"sorted\"><FONT FACE=\"arial, helvetica\" SIZE=2>Display <INPUT NAME=\"num_sorted\" VALUE=\"$field{num_sorted}\" SIZE=4 MAXLENGTH=4> pairs, starting from <INPUT NAME=\"start_sorted\" VALUE=\"$field{start_sorted}\" SIZE=4 MAXLENGTH=4><INPUT TYPE=\"hidden\" NAME=\"sort\" VALUE=\"$field{sort}\"> <INPUT TYPE=\"button\" VALUE=\"Send\" OnClick=\"javascript: submitSort(\'\')\"></FONT></TD></TR>\n";
	print "<TR BGCOLOR=\"$boxColor\"><TD COLSPAN=6 ALIGN=\"center\"><FONT FACE=\"arial, helvetica\" SIZE=2><INPUT TYPE=\"button\" VALUE=\"&lt;&lt;\" OnClick=\"javascript: changePage(\'$prev_start_sorted\')\"> Page $curr_page of $tot_pages <INPUT TYPE=\"button\" VALUE=\"&gt;&gt;\" OnClick=\"javascript: changePage(\'$next_start_sorted\')\"></FORM></TD></TR>\n";
}
############################
# Info display textbox
############################
print "<TR><TD BGCOLOR=\"$boxColor\" COLSPAN=6><FORM NAME=\"infotext\"><FONT FACE=\"courier, courier new\" SIZE=2><FONT FACE=courier, courier new><INPUT NAME=\"defline\" SIZE=60 VALUE=\"Mouse-over to show more information (also on status bar).\"></FONT></CENTER></FORM></TD></TR>\n";
############################
# Close table
############################
print "</TABLE>\n";

if ($displayPairs) {
	############################
	# Open table
	############################
	print "<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=2 WIDTH=500>";
	############################
	# Print header of columns
	############################
	print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'PAIR\')\" ONMOUSEOVER=\'infoBox(\"Pair (example AL3 = Ala & Leu at i, i+3, AxxL)\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Pair</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'OBS\')\" ONMOUSEOVER=\'infoBox(\"Occurrence of the pair in the database of TM domains\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Observed</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'EXP\')\" ONMOUSEOVER=\'infoBox(\"Random expectation of the pair in the database of TM domains\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Expected</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: fakeLink()\" ONMOUSEOVER=\'infoBox(\"Standard deviation of the random expectation distribution\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>St.Dev.</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'SIGN\')\" ONMOUSEOVER=\'infoBox(\"P value of the difference between observed and expected\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Significance</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'ODD\')\" ONMOUSEOVER=\'infoBox(\"Ratio observed/expected (if >1 pair is over-represented)\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Odds ratio</B></A></FONT></TD></TR>\n";
	#print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'PAIR\')\" ONMOUSEOVER=\'infoBox(\"Pair (example AL3 = Ala & Leu at i, i+3, AxxL)\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Pair</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'COUNT\')\" ONMOUSEOVER=\'infoBox(\"Number of times the pair is present in the TM segment\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>(#)</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'OBS\')\" ONMOUSEOVER=\'infoBox(\"Occurrence of the pair in the database of TM domains\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Observed</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'EXP\')\" ONMOUSEOVER=\'infoBox(\"Random expectation of the pair in the database of TM domains\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Expected</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: fakeLink()\" ONMOUSEOVER=\'infoBox(\"Standard deviation of the random expectation distribution\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>St.Dev.</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'SIGN\')\" ONMOUSEOVER=\'infoBox(\"P value of the difference between observed and expected\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Significance</B></A></FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: submitSort(\'ODD\')\" ONMOUSEOVER=\'infoBox(\"Ratio observed/expected (if >1 pair is over-represented)\");return true\' ONMOUSEOUT=\'resetBox();return true\'><B>Odds ratio</B></A></FONT></TD></TR>\n";
	############################
	# Print sortin arrow images
	############################
	print "<TR><TD VALIGN=\"top\" ALIGN=\"left\"><A HREF=\"javascript: submitSort(\'PAIRUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by pair in reversed alphabetical order\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$pairImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'PAIRDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by pair in alphabetical order\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$pairImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'OBSDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$obsImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'OBSUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$obsImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'EXPDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$expImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'EXPUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$expImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\"><CENTER><FONT FACE=\"arial, helvetica\" SIZE=1>&nbsp;</FONT></CENTER></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'SIGNDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by p value, lower to higher significance\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$signImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'SIGNUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by p value, higher to lower significance\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$signImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'ODDDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by odds ratio, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$oddImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'ODDUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by odds ratio, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$oddImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD></TR>\n";
	#print "<TR><TD VALIGN=\"top\" ALIGN=\"left\"><A HREF=\"javascript: submitSort(\'PAIRUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by pair in reversed alphabetical order\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$pairImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'PAIRDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by pair in alphabetical order\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$pairImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'COUNTDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by number in segment, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$countImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'COUNTUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by number in segment, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$countImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'OBSDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$obsImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'OBSUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$obsImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'EXPDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$expImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'EXPUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by occurrence in TM database, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$expImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\"><CENTER><FONT FACE=\"arial, helvetica\" SIZE=1>&nbsp;</FONT></CENTER></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'SIGNDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by p value, lower to higher significance\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$signImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'SIGNUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by p value, higher to lower significance\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$signImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD><TD VALIGN=\"top\" ALIGN=\"right\"><A HREF=\"javascript: submitSort(\'ODDDOWN\')\" ONMOUSEOVER=\'infoBox(\"Sort by odds ratio, smaller to larger number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$oddImgUp\" BORDER=0 WIDTH=26 HEIGHT=9></A><BR><A HREF=\"javascript: submitSort(\'ODDUP\')\" ONMOUSEOVER=\'infoBox(\"Sort by odds ratio, larger to smaller number\");return true\' ONMOUSEOUT=\'resetBox();return true\'><IMG SRC=\"img/$oddImgDown\" BORDER=0 WIDTH=26 HEIGHT=9></A></TD></TR>\n";
	############################
	# Separation line
	############################
	print "<TR><TD COLSPAN=6><HR SIZE=1 WIDTH=100% NOSHADE></TD></TR>\n";
	
	if ($field{opt} eq "sorted") {
		if ($field{sort} eq "PAIR" || $field{sort} eq "PAIRUP" || $field{sort} eq "PAIRDOWN") {
			if ($field{sort} eq "PAIRUP") {
				for ($i=$#pair-$field{start_sorted}+1;$i>=$#pair-$field{num_sorted}-$field{start_sorted}+2 && $i>=0;$i--) {
					print "<TR><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			} else {
				for ($i=$field{start_sorted}-1;$i<=$field{num_sorted}+$field{start_sorted}-2 && $i<=$#pair;$i++) {
					print "<TR><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			}
		} elsif ($field{sort} eq "OBS" || $field{sort} eq "OBSUP" || $field{sort} eq "OBSDOWN") {
			if ($field{sort} eq "OBSDOWN") {
				for ($i=$field{start_sorted}-1;$i<=$field{num_sorted}+$field{start_sorted}-2 && $i<=$#pair;$i++) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			} else {
				for ($i=$#pair-$field{start_sorted}+1;$i>=$#pair-$field{num_sorted}-$field{start_sorted}+2 && $i>=0;$i--) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			}
		} elsif ($field{sort} eq "EXP" || $field{sort} eq "EXPUP" || $field{sort} eq "EXPDOWN") {
			if ($field{sort} eq "EXPDOWN") {
				for ($i=$field{start_sorted}-1;$i<=$field{num_sorted}+$field{start_sorted}-2 && $i<=$#pair;$i++) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			} else {
				for ($i=$#pair-$field{start_sorted}+1;$i>=$#pair-$field{num_sorted}-$field{start_sorted}+2 && $i>=0;$i--) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			}
		} elsif ($field{sort} eq "SIGN" || $field{sort} eq "SIGNUP" || $field{sort} eq "SIGNDOWN") {
			if ($field{sort} eq "SIGNUP") {
				for ($i=$field{start_sorted}-1;$i<=$field{num_sorted}+$field{start_sorted}-2 && $i<=$#pair;$i++) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			} else {
				for ($i=$#pair-$field{start_sorted}+1;$i>=$#pair-$field{num_sorted}-$field{start_sorted}+2 && $i>=0;$i--) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			}
		} elsif ($field{sort} eq "ODD" || $field{sort} eq "ODDUP" || $field{sort} eq "ODDDOWN") {
			if ($field{sort} eq "ODDDOWN") {
				for ($i=$field{start_sorted}-1;$i<=$field{num_sorted}+$field{start_sorted}-2 && $i<=$#pair;$i++) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			} else {
				for ($i=$#pair-$field{start_sorted}+1;$i>=$#pair-$field{num_sorted}-$field{start_sorted}+2 && $i>=0;$i--) {
					print "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				}
			}
		}
	} else {

		############################
		# If pairs were found and a database 
		# given print results
		############################
	#	} elsif ($field{sort} eq "COUNT" || $field{sort} eq "COUNTUP" || $field{sort} eq "COUNTDOWN") {
	#		for ($i=0;$i<@pair;$i++) {
	#			$record[$i] = "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
	##			$record[$i] = "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>($count[$i])</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
	#		}
	#		if ($field{sort} eq "COUNTDOWN") {
	#			&SortArrays(0, \@count, \@record);
	#		} else {
	#			&SortArrays(1, \@count, \@record);
	#		}
	#		for ($i=0;$i<@pair;$i++) {
	#			print $record[$i];
	#		}
		if ($field{sort} eq "PAIR" || $field{sort} eq "PAIRUP" || $field{sort} eq "PAIRDOWN") {
			for ($i=0;$i<@pair;$i++) {
				$PAIRrecord[$i] = $aa{substr($pair[$i], 0, 1)} * 2000 + $aa{substr($pair[$i], 1, 1)} * 100 + substr($pair[$i], 2, length($pair[$i]) - 2);
				$record[$i] = "<TR><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
			}
			if ($field{sort} eq "PAIRUP") {
				&SortArrays(1, \@PAIRrecord, \@record);
			} else {
				&SortArrays(0, \@PAIRrecord, \@record);
			}
			for ($i=0;$i<@pair;$i++) {
				print $record[$i];
			}
		} elsif ($field{sort} eq "OBS" || $field{sort} eq "OBSUP" || $field{sort} eq "OBSDOWN") {
			for ($i=0;$i<@pair;$i++) {
				$OBSrecord[$i] = $obs[$i];
				$record[$i] = "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
			}
			if ($field{sort} eq "OBSDOWN") {
				&SortArrays(0, \@OBSrecord, \@record);
			} else {
				&SortArrays(1, \@OBSrecord, \@record);
			}
			for ($i=0;$i<@pair;$i++) {
				print $record[$i];
			}
		} elsif ($field{sort} eq "EXP" || $field{sort} eq "EXPUP" || $field{sort} eq "EXPDOWN") {
			for ($i=0;$i<@pair;$i++) {
				$EXPrecord[$i] = $exp[$i];
				$record[$i] = "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
			}
			if ($field{sort} eq "EXPDOWN") {
				&SortArrays(0, \@EXPrecord, \@record);
			} else {
				&SortArrays(1, \@EXPrecord, \@record);
			}
			for ($i=0;$i<@pair;$i++) {
				print $record[$i];
			}
		} elsif ($field{sort} eq "SIGN" || $field{sort} eq "SIGNUP" || $field{sort} eq "SIGNDOWN") {
			for ($i=0;$i<@pair;$i++) {
				$record[$i] = "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\" ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
				if ($obs[$i] >= $exp[$i]) {
					$Orecord[$o] = $record[$i];
					$OSIGNrecord[$o] = $sign[$i];
					$o++;
				} else {
					$Urecord[$u] = $record[$i];
					$USIGNrecord[$u] = $sign[$i];
					$u++;
				}

			}
			if ($field{sort} eq "SIGNDOWN") {
				&SortArrays(1, \@OSIGNrecord, \@Orecord);
				&SortArrays(1, \@USIGNrecord, \@Urecord);
			} else {
				&SortArrays(0, \@OSIGNrecord, \@Orecord);
				&SortArrays(0, \@USIGNrecord, \@Urecord);
			}
			print "<TR><TD COLSPAN=6><FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: fakeLink()\" ONMOUSEOVER=\'infoBox(\"Pairs found more frequently than random (over-represented)\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Observed > Expected (Odds ratio > 1)</FONT></TD></TR>\n";
			for ($i=0;$i<@OSIGNrecord;$i++) {
				print $Orecord[$i];
			}
			print "<TR><TD COLSPAN=6><HR SIZE=1 WIDTH=50% NOSHADE>\n<FONT FACE=\"arial, helvetica\" SIZE=2><A HREF=\"javascript: fakeLink()\" ONMOUSEOVER=\'infoBox(\"Pairs found less frequently than random (under-represented)\");return true\' ONMOUSEOUT=\'resetBox();return true\'>Observed < Expected (Odds ratio < 1)</FONT></TD></TR>\n";
			for ($i=0;$i<@USIGNrecord;$i++) {
				print $Urecord[$i];
			}
		} elsif ($field{sort} eq "ODD" || $field{sort} eq "ODDUP" || $field{sort} eq "ODDDOWN") {
			for ($i=0;$i<@pair;$i++) {
				$ODDrecord[$i] = $od[$i];
				$record[$i] = "<TR><TD ALIGN=\"left\"><FONT FACE=\"arial, helvetica\" SIZE=2>$indexedPair[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$obs[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundExp[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSd[$i]</FONT></TD><TD ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundSign[$i]</FONT></TD><TD BGCOLOR=\"#DDDDFF\"ALIGN=\"right\"><FONT FACE=\"arial, helvetica\" SIZE=2>$roundOd[$i]</FONT></TD></TR>\n";
			}
			if ($field{sort} eq "ODDDOWN") {
				&SortArrays(0, \@ODDrecord, \@record);
			} else {
				&SortArrays(1, \@ODDrecord, \@record);
			}
			for ($i=0;$i<@pair;$i++) {
				print $record[$i];
			}
		}
	}

	print "<TR><TD COLSPAN=7><HR SIZE=1 WIDTH=100% NOSHADE></TD></TR>\n";
	print "</TABLE>\n";
}	






sub ReadParse {
	
	my $buffer;
	my $pair;
	my @pairs;
	my $name;
	my $value;
	my $ErrorCode;

	if ($ENV{'REQUEST_METHOD'} eq 'POST') {
		if ($ENV{'CONTENT_LENGTH'} > 1000) {
			$ErrorCode = "24";
			return ($ErrorCode);
		}
		read(STDIN, $buffer, $ENV{'CONTENT_LENGTH'});

	} else {
		
		if (length($ENV{'QUERY_STRING'}) < 1000) {
			$buffer = $ENV{'QUERY_STRING'};
		} else {
			$ErrorCode = "25";
			return ($ErrorCode);
		}
	}
	
	@pairs = split (/&/, $buffer);
	foreach $pair (@pairs) {
		($name, $value) = split (/=/, $pair);
		$value =~ tr/+/ /;
		$value =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C", hex($1))/eg;
		$value =~ s/\r\n/\n/g;
		$field{$name} .= $value;
	}
	return (0);
}


sub RoundNumber {
	
	my $number = shift;
	my $decimals = shift;
	my $pos;

	
	$number *= (10 ** int($decimals));
	
	if ($number > 0) {
		$number += 0.5;
	} else {
		$number -= 0.5;
	}
	
	$number = int($number);
	
	$number /= (10 ** int($decimals));
	
	
	if ($number =~ /\./g) {
		$pos = pos($number);
		while (length($number) <  $pos + $decimals) {
			$number .= "0";
		}
	} else {
		$number .= ".";
		$number =~ /\./g;
		$pos = length($number);
		while (length($number) <  $pos + $decimals) {
			$number .= "0";
		}
	}
		
	
	return $number;
	
}


sub ExponentRoundNumber {
	
	my $number = shift;
	my $decimals = shift;
	my $exponent;
	my $sign_exp;
	
	if ($number == 0) {
		$number = "&lt;1x10<SUP>40</SUP>";
		return $number;
	}

	if ($number > 1 - 10 ** (-1 * $decimals) && $number < 1 + 10 ** (-1 * $decimals)) {
		$number = 1;
	}

	if ($number =~ /[0-9]e\-[0-9]/g) {
		$pos = pos($number);
		$exponent = substr($number, $pos-2, length($number) - $pos + 2);
		$number = substr($number, 0, $pos-3);
		$number /= (10 ** (0 - $decimals));
	} elsif ($number =~ /[0-9]e\+[0-9]/g) {
		$pos = pos($number);
		$exponent = substr($number, $pos-1, length($number) - $pos + 1);
		$number = substr($number, 0, $pos-3);
		$number /= (10 ** (0 - $decimals));
	} else {
		$exponent = log($number)/log(10);
		if ($exponent >= 0) {
			$exponent = int($exponent);
		} else {
			$exponent = int($exponent-1);
#			$exponent = int($exponent-1);
		}
		$number /= (10 ** ($exponent - $decimals));
	}
	
	
	if ($number > 0) {
		$number += 0.5;
	} else {
		$number -= 0.5;
	}
	
	$number = int($number);
	
	$number *= (10 ** int($0 - $decimals));
	
	if ($exponent < 0) {
		$exponent *= -1;
		$sign_exp = "-";
	} else {
		$sign_exp = "+";
	}
		
	while (length($exponent) < 2) {
		$exponent = "0".$exponent;
	}
	
	
#	$number .= "E".$sign_exp.$exponent;
	$number .= "x10<SUP>".$sign_exp.$exponent."</SUP>";
	
	return $number;
	
}


sub SortArrays {

	###################################
	#v.1.01
	#This sub sorts up to 4 arrays ascending
	#on the first of the two.
	#Arguments passes as references:
	#    &SortArrays(order, \@array1,\@array2);
	# order = 0 -> ascending
	# order = 1 -> descending
	###################################

	my $order = shift;
	my $masterArray = shift;
	my $slaveArray0 = shift;
	my $slaveArray1 = shift;
	my $slaveArray2 = shift;
	my $doneSorting;
	my $size;
	my $skip;
	my $i;
	my $tmpMaster;
	my $tmpSlave0;
	my $tmpSlave1;
	my $tmpSlave2;
	my @newMaster;
	my @newSlave0;
	my @newSlave1;
	my @newSlave2;
	

	if ($order) {
		while (!$doneSorting) {

			$size = @$masterArray;

			if ($size > 0 ) {

				$tmpMaster = shift(@$masterArray);
				$tmpSlave0 = shift(@$slaveArray0);
				$tmpSlave1 = shift(@$slaveArray1);
				$tmpSlave2 = shift(@$slaveArray2);

				$skip = 0;
				for ($i=0;$i<@newMaster;$i++) {
					if ($newMaster[$i] > $tmpMaster) {
						$skip++;
					} else {
						$i = @newMaster;
					}
				}

				splice(@newMaster, $skip, 0, $tmpMaster);		
				splice(@newSlave0, $skip, 0, $tmpSlave0);		
				splice(@newSlave1, $skip, 0, $tmpSlave1);		
				splice(@newSlave2, $skip, 0, $tmpSlave2);		

			} else {

				$doneSorting = 1;
				@$masterArray = @newMaster;
				@$slaveArray0 = @newSlave0;
				@$slaveArray1 = @newSlave1;
				@$slaveArray2 = @newSlave2;

			}


		}
	} else {
		while (!$doneSorting) {

			$size = @$masterArray;

			if ($size > 0 ) {

				$tmpMaster = shift(@$masterArray);
				$tmpSlave0 = shift(@$slaveArray0);
				$tmpSlave1 = shift(@$slaveArray1);
				$tmpSlave2 = shift(@$slaveArray2);

				$skip = 0;
				for ($i=0;$i<@newMaster;$i++) {
					if ($newMaster[$i] < $tmpMaster) {
						$skip++;
					} else {
						$i = @newMaster;
					}
				}

				splice(@newMaster, $skip, 0, $tmpMaster);		
				splice(@newSlave0, $skip, 0, $tmpSlave0);		
				splice(@newSlave1, $skip, 0, $tmpSlave1);		
				splice(@newSlave2, $skip, 0, $tmpSlave2);		

			} else {

				$doneSorting = 1;
				@$masterArray = @newMaster;
				@$slaveArray0 = @newSlave0;
				@$slaveArray1 = @newSlave1;
				@$slaveArray2 = @newSlave2;

			}


		}
	}
		

}

sub Error() {
	
	my $code = shift;
	
	print "Error $code<BR>\n";
	
}

sub Ordinal() {
	my $input = shift;
	my $output;
	
	if (substr($input, length($input)-1,1) eq "1") {
		$output = $input."st";
	} elsif (substr($input, length($input)-1,1) eq "2") {
		$output = $input."nd";
	} elsif (substr($input, length($input)-1,1) eq "3") {
		$output = $input."rd";
	} else {
		$output = $input."th";
	}
	
	return $output;
		
	
}