#!/usr/bin/perl -w
use strict;
use CGI qw(:standard);
use CGI qw(param);

#   GENECENSUS TREEDISPLAY 2000
#  -----------------------------
# Yale Gerstein Bioinformatics : Jimmy Lin
#
# A program to display different trees
# and information associated with organisms
# on the nodes of the trees

# USER SPECIFICATIONS
#my $treename='ribosome';          # name of order
#my @treeorder=qw(Mgen Hinf);      # specification of order

my $input= param("type");     # types of trees: e.g. trad20, ribo_ssu, fold_a
my $viewnum= param("view");   # which tab is being pressed 1-6
my $big= param("bigview");

my $tabnum;                 # which tab is being pressed 1,2,3...
my $found=0;                # label whether name is found in datafile
my $treename;               # tree name, picture file - tree-$treename.gif
my $treedescrip;            # name description of tree
my @treeorder;              # specification of order in tree
my @otherorder;             # specification of order not in tree
my $treenode;               # number of nodes in tree
my $othernode;              # number of nodes not in tree
my $i;                      # counter
my $j;                      # counter 2

my @treeorder2;             # second tree order
my $markfortree=-1;         # shows a second tree

if (!param("type")){
    $input="20-ribo-ssu";
    }

if (!param("view")){
    $viewnum=1;
}

# DEFINITIONS
# species number assignment from TIGR
my %treenum=( 
 'Hinf'=>1,	'Mgen'=>2,	'Mjan'=>3,	'Syne'=>4,	'Mpne'=>5,
 'Scer'=>6,	'Hpyl'=>7,	'Ecol'=>8,	'Mthe'=>9,	'Bsub'=>10,
 'Aful'=>11,	'Bbur'=>12,	'Aaeo'=>13,	'Phor'=>14,	'Mtub'=>15,
 'Tpal'=>16,	'Ctra'=>17,	'Pfa2'=>18,	'Rpro'=>19,	'Hpy2'=>20,
 'Lei1'=>21,	'Cpne'=>22,	'Aper'=>23,	'Tmar'=>24,	'Pfa3'=>25,
 'Drad'=>26,	'Cjej'=>27,	'Nmen'=>28,	'Nme2'=>29,	'Ctr2'=>30,
 'Cpn2'=>31,    'Cele'=>32,     'Dmel'=>33,     'Hsap'=>34);

# print "treenum:$treenum{'Mpne'}\n";
# exit;


#names of datafiles
my %dataname=('treearray'=>1, 'treebasicdata'=>2, 'treeoverall'=>3, 'treesfamdata'=>4, 'tree-cog-21'=>5);

my @treedata;

#$treedata[$dataname{'treesfamdata'}]


my @treepresence;
for ($i=0; $i<35; $i++){
    $treepresence[$i]=0;
}


# array designating functions for different organisms

read_matrix("tree-cog-21"); #name, info, cell, meta, poor, JKLDOMNPTCGEFHIRS
read_matrix("treesfamdata");  #name, number, total, a,b,a+b,a/b,multi,sfam
read_matrix("treearray");# NAME, NUMBER,RESOURCE, size, FOLD TOTAL /1/2/3/4/5   COG TOTAL I/C/M
read_matrix("treebasicdata");  #Name, Number, Size (kbp), Proteins
read_matrix("treeoverall");   # name, #%AT, %At{nc},[code], (g-c)/g+c-0.50%, [nc]%,[code]%,size,#genes,%transcribed,longestnc,x=,datepublished


# print "Mgen-num2:$treedata[$dataname{'treearray'}][2][1]\n";

# READ TREEDATA.TXT
open (DATA, "./datafiles/treedata2.txt") or die "cannot open treedata2.txt";
my $line;
while (defined ($line = <DATA>)&&!$found) {
    chomp $line;
    if ($line =~ $input) {
	$found=1;                           # When type found in datafile
	$treename=$line;
	chomp ($line = <DATA>);
	$treedescrip=$line;
	chomp ($line=<DATA>);
	my $i;
	for ($i=0; $line !~ "END"; $i++){   # Read array order of tree
	    $treeorder[$i]=$line;
	    $treepresence[$treenum{$line}]=1;
	    chomp ($line=<DATA>);
	}
	chomp ($line=<DATA>);
	$j=0;
	for ($i=1; $i<35; $i++){   # Read array order not in tree
	    if ($treepresence[$i]==1){}
	    else {
		$otherorder[$j]=$treedata[$dataname{'treebasicdata'}][$i][0];
		$j++;
	    }
	}
    }
}

close DATA;

if (!$found){;}

#$treedescrip="Phylogenetic Tree Based on 16S Ribosomal Subunit";
#$treename='trad20';             # tree name, picture file - tree-$treename.gif
#@treeorder=qw(Cele Scer);       # specification of order in tree
#@otherorder=qw(Mgen Mgen);      # specification of order not in tree

$treenode=scalar(@treeorder);   # number of nodes in tree
$othernode=scalar(@otherorder); # number of nodes not in tree
my $pictreenode=$treenode+1;

#names of tabs
my %tabnames=(1=>'blank', 2=>'ribo', 3=>'fold', 4=>'sfam', 5=>'cog', 6=>'comp', 7=>'orf');

# links to Yale Resources
# when adding new resource, make sure to change resource in genome matrix to 1
my %yalelink=(
	      'Cele'=>"http://bioinfo.mbb.yale.edu/genome/worm_yeast/",
	      'Mgen'=>"http://bioinfo.mbb.yale.edu/genome/MG/"
	     );

#$treedata[$dataname{'treesfamdata'}]

# START

print <<EndOfStart;
Content-Type: text/html\n\n
<HTML><HEAD><TITLE>GeneCensus TreeServer</TITLE>
<META name=\"KEYWORDS\" content=\"Phylogenetics, Trees, GeneCensus, Gerstein, Bioinformatics\">
<META name=\"DESCRIPTION\" content=\"GeneCensus TreeServer\">
<SCRIPT LANGUAGE="javascript">
<!--
function PopUp(filename, winheight, winwidth, scrx, scry){
window.open(filename,"popDialog","height="+winheight+",width="+winwidth+",top="+scry+",left="+scrx+",toolbar=no,status=no,scrollbars=no,location=no,menubar=no,directories=no,resizable=no")
}
//-->
</SCRIPT>

</HEAD>
EndOfStart

my $hvar = `perl /web/genecensus/header/header.cgi tree`; print "$hvar";

print <<EndOfStart2;
<IMG SRC="./tab/genecensus-title.jpg"><BR>
  <CENTER><TABLE WIDTH="600" BORDERCOLOR="#000000" BORDER="0" CELLPADDING="0" CELLSPACING="0">
      <TR VALIGN="TOP">
        <TD VALIGN="TOP" COLSPAN="2">
          <CENTER>
            <TABLE BORDERCOLOR="#000000" BORDER="0" CELLPADDING="1" CELLSPACING="0">

EndOfStart2

#READ TREENAME AND ASSIGN TAB NUMBER

    if ($treename =~ /ribo/){$tabnum=2;}
elsif ($treename =~ /fold/){$tabnum=3;}
elsif ($treename =~ /sfam/){$tabnum=4;}
elsif ($treename =~ /cog/){$tabnum=5;}
elsif ($treename =~ /comp/){$tabnum=6;}
elsif ($treename =~ /dint/){$tabnum=6;}
elsif ($treename =~ /aa/){$tabnum=6;}
elsif ($treename =~ /orf/){$tabnum=7;}


print "<TR><TD COLSPAN=\" 13\" BGCOLOR=\"\#FFFFFF\" ALIGN=\"CENTER\">";
for ($i=1; $i<8; $i++){
    if ($i == $tabnum) {
	print "<IMG BORDER=\"0\" SRC=\"./tab/tab-$tabnames{$tabnum}-on.gif\">";
    }
    else {
	print "<A HREF=\"tree.cgi\?view=$viewnum";
	print "\&type=";
	if    ($i == 2){print "8-ribo-lsu";}
	elsif ($i == 3){print "20-fold-dist";}
	elsif ($i == 4){print "20-sfam-dist";}
	elsif ($i == 5){print "8-cog-all";}
	elsif ($i == 6){print "comp-dint-per";}
	elsif ($i == 7){print "8-orf-0030";}
	print "\"><IMG BORDER=\"0\" SRC=\"./tab/tab-$tabnames{$i}.gif\"></A>";
    }
}
print "</TD></TR>";

print "<TR><TD></TD></TR>";

# SUBTABS

my $stabref="<A HREF=\"tree.cgi?view=$viewnum";
my $stabfont="<FONT FACE=\"verdana, helvetica, arial\" COLOR=\"Yellow\" SIZE=\"1\"";
print "<TR><TD COLSPAN=\"13\" HEIGHT=\"10\" BGCOLOR=\"#000077\" ALIGN=\"CENTER\"><FONT COLOR=\"FFFFAA\" SIZE=\"-1\">";
if ($tabnum == 1){
    print " ";
}
elsif ($tabnum ==2){
    print "$stabref\&type=8-ribo-lsu\">$stabfont>LSU rRNA</A></FONT> _ ";
    print "$stabref\&type=8-ribo-ssu\">$stabfont>8 SSU rRNA</A></FONT>  _";
    print "$stabref\&type=20-ribo-ssu\">$stabfont>20 SSU rRNA</A></FONT> _ ";
}
elsif ($tabnum ==3){
    print "$stabref\&type=8-fold-all\">$stabfont>All Folds</A></FONT> _ ";
    print "$stabref\&type=8-fold-a\">  $stabfont>All Alpha</A></FONT> _ ";
    print "$stabref\&type=8-fold-b\">  $stabfont>All Beta</A></FONT> _ ";
    print "$stabref\&type=8-fold-apb\">$stabfont>A+B</A></FONT>  _";
    print "$stabref\&type=8-fold-ab\"> $stabfont>A/B</A></FONT>  _";   
    print "</TD></TR><TR><TD COLSPAN=\"13\" HEIGHT=\"10\" BGCOLOR=\"#000077\" ALIGN=\"CENTER\">";
    print "$stabref\&type=20-fold-pars\">$stabfont>All Folds 20 Parsimony</A></FONT>  _";
    print "$stabref\&type=20-fold-dist\"> $stabfont>All Folds 20 Distance</A></FONT>  _";
}
elsif ($tabnum ==4){
    print "$stabref\&type=20-sfam-dist\">$stabfont>20 Distance</A></FONT> _ ";  
    print "$stabref\&type=20-sfam-pars\">$stabfont>20 Parsimony</A></FONT> _ ";
    print "$stabref\&type=8-sfam-dist\">$stabfont>8 Distance</A></FONT> _ ";  
    print "$stabref\&type=8-sfam-pars\">$stabfont>8 Parsimony</A></FONT> _ ";
}
elsif ($tabnum ==5){    
    print "$stabref\&type=8-cog-all\">  $stabfont>All Cogs</A></FONT> _ ";
    print "$stabref\&type=8-cog-meta\"> $stabfont>Metabolism</A></FONT> _ ";
    print "$stabref\&type=8-cog-cell\"> $stabfont>Cellular Proc.</A></FONT> _ ";
    print "$stabref\&type=8-cog-info\"> $stabfont>Info S & P</A></FONT> _ ";  
    print "</TD></TR><TR><TD COLSPAN=\"13\" HEIGHT=\"10\" BGCOLOR=\"#000077\" ALIGN=\"CENTER\">";
    print "$stabref\&type=8-cog-c\">  $stabfont>C</A></FONT> _";
    print "$stabref\&type=8-cog-e\">  $stabfont>E</A></FONT> _";
    print "$stabref\&type=8-cog-f\">  $stabfont>F</A></FONT> _";
    print "$stabref\&type=8-cog-g\">  $stabfont>G</A></FONT> _";
    print "$stabref\&type=8-cog-h\">  $stabfont>H</A></FONT> _";
    print "$stabref\&type=8-cog-i\">  $stabfont>I</A></FONT> _";
    print "$stabref\&type=8-cog-j\">  $stabfont>J</A></FONT> _";
    print "$stabref\&type=8-cog-k\">  $stabfont>K</A></FONT> _";
    print "$stabref\&type=8-cog-l\">  $stabfont>L</A></FONT> _";
    print "$stabref\&type=8-cog-m\">  $stabfont>M</A></FONT> _";   
    print "$stabref\&type=8-cog-n\">  $stabfont>N</A></FONT> _";
    print "$stabref\&type=8-cog-o\">  $stabfont>O</A></FONT> _";
    print "$stabref\&type=8-cog-p\">  $stabfont>P</A></FONT> _";
    print "$stabref\&type=8-cog-r\">  $stabfont>R</A></FONT> _";
}
elsif ($tabnum ==6){    
    print "$stabref\&type=comp-dint-per\">$stabfont>Dinucleotide 20A</A></FONT>  _";
    print "$stabref\&type=comp-aa-per\">  $stabfont>Amino Acid 20A</A></FONT>  _";
    print "$stabref\&type=20-dint-per\">$stabfont>Dinucleotide 20</A></FONT>  _";
    print "$stabref\&type=20-aa-per\">  $stabfont>Amino Acid 20</A></FONT>";
    print "</TD></TR><TR><TD COLSPAN=\"13\" HEIGHT=\"10\" BGCOLOR=\"#000077\" ALIGN=\"CENTER\">";
    print "$stabref\&type=20-dint-freq\">$stabfont>20 Dint raw</A></FONT>  _";
    print "$stabref\&type=20-aa-freq\">  $stabfont>20 AA 20 raw</A></FONT>  _";
    print "$stabref\&type=8-aa-freq\">  $stabfont>8 AA raw</A></FONT>  _";
    print "$stabref\&type=8-aa-per\">  $stabfont>8 AA per</A></FONT>  _";   
    print "$stabref\&type=8-dint-freq\">  $stabfont>8 dint raw</A></FONT>  _";
    print "$stabref\&type=8-dint-per\">  $stabfont>8 dint</A></FONT>  _";
}
elsif ($tabnum ==7){
    print "$stabref\&type=8-orf-0030\">$stabfont>Orf 30</A></FONT>  _";
    print "$stabref\&type=8-orf-0072\">$stabfont>Orf 72</A></FONT>  _";
    print "$stabref\&type=8-orf-0089\">$stabfont>Orf 89</A></FONT>  _";
    print "$stabref\&type=8-orf-0092\">$stabfont>Orf 92</A></FONT>  _";
    print "$stabref\&type=8-orf-0125\">$stabfont>Orf 125</A></FONT>  _";   
    print "$stabref\&type=8-orf-0126\">$stabfont>Orf 126</A></FONT>  _";   
    print "$stabref\&type=8-orf-0149\">$stabfont>Orf 149</A></FONT>  _";    
    print "</TD></TR><TR><TD COLSPAN=\"13\" HEIGHT=\"10\" BGCOLOR=\"#000077\" ALIGN=\"CENTER\">";
    print "$stabref\&type=8-orf-0166\">$stabfont>Orf 166</A></FONT>  _";    
    print "$stabref\&type=8-orf-0200\">$stabfont>Orf 200</A></FONT>  _";
    print "$stabref\&type=8-orf-0250\">$stabfont>Orf 250</A></FONT>  _";
    print "$stabref\&type=8-orf-0256\">$stabfont>Orf 256</A></FONT>  _";
    print "$stabref\&type=8-orf-0525\">$stabfont>Orf 525</A></FONT>  _";
    print "$stabref\&type=8-orf-0552\">$stabfont>Orf 552</A></FONT>  _";
}

print "</FONT></TD></TR>";

print "<TR><TD></TD></TR>";
print "<TR><TD><BR></TD></TR>";

# ----------
# TREE TITLE
# ----------

print "<TR><TD COLSPAN=\" 13\" BGCOLOR=\"\#330044\" ALIGN=\"CENTER\"><FONT SIZE=\"5\" FACE=\"helvetica, arial\" COLOR=\"\#FFFFF\">Tree Based On $treedescrip</FONT></TD></TR>";

# -----------
# VIEW SELECT
# -----------

my %viewname=('1'=>'taxonomy', '2'=>'composition','3'=>'fold','4'=>'superfamily','5'=>'oldCOG','7'=>'rRNAtree','6'=>'newCOG');

print "<TR><TD BGCOLOR=\"#99AAFF\" COLSPAN=\"1\" ALIGN=\"left\"><FONT COLOR=\"#99AAFF\">.</FONT></TD>";
print "<TD BGCOLOR=\"#99AAFF\" COLSPAN=\"9 \" BGCOLOR=\"\#FFFFFF\" ALIGN=\"CENTER\">";
print "<TABLE BGCOLOR=\"#8899EE\">";
print "<TR><TD BGCOLOR=\"\#8899EE\"><FONT FACE=\"arial\" SIZE=\"1\"><A HREF=\"tree.cgi?view=$viewnum&type=$input&bigview=1\" ALT=\"test\">[B] </A><B>SelectView:</B></FONT></TD>";
for ($i=1; $i<8; $i++){
    if ($i == $viewnum) {
#	print "<IMG BORDER=\"0\" SRC=\"./tab/tab-$tabnames{$tabnum}-on.gif\">";
	print "<TD BGCOLOR=\"\#EEEE44\">";
	print "<FONT FACE=\"arial\" SIZE=\"2\">";
	print "$viewname{$i}";
	print "</FONT>";
	print "</TD>";
    }
    else {
	print "<TD BGCOLOR=\"\#8899EE\">";
	print "<A HREF=\"tree.cgi\?view=$i";
	print "\&type=";
	print "$treename";
#	print "\"><IMG BORDER=\"0\" SRC=\"./tab/tab-$tabnames{$i}.gif\"></A>";
	print "\">";
	print "<FONT FACE=\"arial\" SIZE=\"2\">";
	print "$viewname{$i}";
	print "</FONT>";
	print "</A></TD>";
    }
}
print "</TR></TABLE>";

# --------------------
# TREE COLUMN HEADINGS
# --------------------

my $TA="<TD ALIGN=\"CENTER\" BGCOLOR=\"#99AAFF\" WIDTH=\"80\"><CENTER><A HREF=\"http://bioinfo.mbb.yale.edu/genecensus/help/#view-$viewname{$viewnum}\"><FONT FACE=\"verdana, helvetica, arial\" SIZE=\"2\"";

print "<TR>";
print "<TD ALIGN=\"CENTER\" BGCOLOR=\"#99AAFF\"><FONT FACE=\"verdana, helvetica, arial\" SIZE=\"2\">Tree  <A HREF=\"./treefiles/$treename.tre\">[download]</A></FONT></TD>";
print "<TD ALIGN=\"LEFT\" WIDTH=\"130\" BGCOLOR=\"#99AAFF\"><FONT FACE=\"verdana, helvetica, arial\" SIZE=\"2\">Organism</FONT></TD>";


if ($viewnum == 1){  
    print "$TA>Yale Resources</A></CENTER></FONT></TD>";
    print "$TA>Superkingdom </A></CENTER></FONT></TD>";
    print "$TA>Kingdom</A></CENTER></FONT></TD>";
    print "$TA>Phylum</A></CENTER></FONT></TD>";
    print "$TA>Class</A></CENTER></FONT></TD>";
}
if ($viewnum == 2){  
    print "$TA>Yale Resources</A>";
    print "$TA>Genome Size Mb</A></FONT></TD>";
    print "$TA>Size</A></FONT></TD>";
    print "$TA>Number Genes</A></FONT></TD>";
    print "$TA>AT Content %</A></FONT></TD>";   
    print "$TA>(G-C)/(G+C) %</A></FONT></TD>";   
#   print "$TA>Transcription %</A></FONT></TD>";   
}
elsif ($viewnum == 3){
    print "$TA>Yale Resources</A></FONT></TD>";
    print "$TA>All Folds</A></FONT></TD>";
    print "$TA>All A Folds</A></FONT></TD>";
    print "$TA>All B Folds</A></FONT></TD>";
    print "$TA>A+B Folds</A></FONT></TD>";
    print "$TA>A/B Folds</A></FONT></TD>";
    print "$TA>Multi Folds</A></FONT></TD>";
}
elsif ($viewnum == 4){
    print "$TA>Yale Resources</A></FONT></TD>";
    print "$TA>All Sfams</A></FONT></TD>";
    print "$TA>All A Sfams</A></FONT></TD>";
    print "$TA>All B Sfams</A></FONT></TD>";
    print "$TA>A+B Sfams</A></FONT></TD>";
    print "$TA>A/B Sfams</A></FONT></TD>";
    print "$TA>Multi Sfams</A></FONT></TD>";
    print "$TA>Small Sfams</A></FONT></TD>";
}

if ($viewnum == 5){    
    print "$TA>Yale Resources</A></FONT></TD>";
    print "$TA>All COGs</A></FONT></TD>";    
    print "$TA>Metabolism [CGEFHI]</A></FONT></TD>";
    print "$TA>Cellular [OMNP]</A></FONT></TD>";
    print "$TA>Information [JKL]</A></FONT></TD>";
}
if ($viewnum == 7){
    print "<TD ALIGN=\"CENTER\" BGCOLOR=\"#99AAFF\" WIDTH=\"120\"><CENTER><A HREF=\"http://bioinfo.mbb.yale.edu/genecensus/help/#tree\"><FONT FACE=\"verdana, helvetica, arial\" SIZE=\"2\">Traditional Tree</A></FONT></TD>";
    print "$TA>Organisms</A></FONT></TD>";
}

if ($viewnum == 6){
    print "$TA>Yale Resources</A></FONT></TD>";    
    print "$TA>All COGs</A></FONT></TD>";    
    print "$TA>Metabolism [CGEFHI]</A></FONT></TD>";
    print "$TA>Cellular [OMNP]</A></FONT></TD>";
    print "$TA>Information [JKL]</A></FONT></TD>";
    print "$TA>Poor</A></FONT></TD>";
}


print "</TR>";
print "<TR>";
print "<TD VALIGN=\"TOP\" ALIGN=\"RIGHT\" ROWSPAN=$pictreenode><IMG BORDER=\"0\"";
if($big == 1){
    if ($treenode == 8)
    {print " HEIGHT=240 WIDTH=100% ";}
    if ($treenode == 20)
    {print " HEIGHT=632 WIDTH=100% ";}
}
print "SRC=\"./treepics/";
print "$treename.gif\"></TD>";
print "<TD HEIGHT=\"1\" COLSPAN=\"12\"></TD>";
print "</TR>";

# ------------
# TREE PROGRAM
# ------------
my $nodes;

foreach $nodes (@treeorder) {
    print "<TR>";
    displayline($nodes);
}


# NOT IN PHYLOGENETIC TREE

my $nontreenode;

print "<TR><TD COLSPAN=\"13\" ALIGN=\"CENTER\" BGCOLOR=\"\#401c76\"><FONT SIZE=\"3\" FACE=\"helvetica, arial\" COLOR=\"\#FFFFFF\"><B>";
print "Organisms that are not in the Tree</B></TD></TR>";

foreach $nontreenode (@otherorder) {
    print "<TR><TD></TD>";
    displayline($nontreenode);
}

print "</TABLE></CENTER></TD></TR>";
print "<TR><TD><HR>";
print "<CENTER><A HREF=\"mailto:jimmy.lin\@yale.edu\">Click here to mail questions</A></CENTER>";
for ($i=1; $i<8; $i++){
	print "<IMG HEIGHT=\"1\" WIDTH=\"1\" BORDER=\"0\" SRC=\"./tab/tab-$tabnames{$tabnum}-on.gif\">";
    }
print "</TD></TR>";
print "</TABLE></CENTER></BODY></HTML>";

# -----------------
# DISPLAY LINE TOOL
# -----------------

sub displayline {
    my ($node)=@_;


    print "<TD BGCOLOR=\"\#EEFFFF\">";
#   print "<A HREF=\"http://bioinfo.mbb.yale.edu/genome/db99/$node\">$node</A>";
    print "<B><A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/$node/\"><FONT SIZE=\"3\" COLOR=\"#000000\" FACE=\"helvetica, arial\">$node</FONT></A></B>";
    print "</TD>";

#names of tabs
    my %superkingdomcolor=('Bacteria'=>'#FF0000', 'Eukaryota'=>'#339933', 'Archaea'=>'#0000FF');
    my %superkingdomlink=('Bacteria'=>'2', 'Eukaryota'=>'2759', 'Archaea'=>'2157');
    my %taxonomycolor=('Euryarchaeota'=>'#0000FF', 
'Methanococcales'=>'#00CCCC', 'Methanococcaceae'=>'#00CCCC',
'Thermococcales'=>'#0000CC', 'Thermococcaceae'=>'#0000CC',
'MethanoBacteriales'=>'#0055FF','MethanoBacteriaceae'=>'#0055FF',
'Archaeoglobales'=>'#000055', 'Archaeoglobaceae'=>'#000055',
'Metazoa'=>'#007766','Nematoda'=>'#007766','Chromadorea'=>'#007766',
'Fungi'=>'#00CC00','Ascomycota'=>'#00CC00','Hemiascomycetes'=>'#00CC00',
'Aquificales'=>'#CC00CC','Aquificaceae'=>'#CC00CC','Aquifex'=>'#CC00CC',
'Firmicutes'=>'#990000',
'Bacillus/Clostridium_group'=>'#770022',
'Bacillus/Staphylococcus_group'=>'#770022',
'Mollicutes'=>'#440022',
'ActinoBacteria'=>'#881111', 'Actinobacteridae'=>'#881111', 
'ProteoBacteria'=>'#FF0000',
'gamma_subdivision'=>'#BB0044',
'epsilon_subdivision'=>'#FF00CC','Helicobacter_group'=>'#FF00CC',
'alpha_subdivision'=>'#FF00FF','Rickettsiales'=>'#FF00FF',
'Spirochaetales'=>'#CC0000', 'Spirochaetaceae'=>'#CC0000',
'Borrelia'=>'#DD1188',
'Treponema'=>'#CC1177',
'EnteroBacteriaceae'=>'#BB0022',
'Pasteurellaceae'=>'#BB0077',
'CyanoBacteria'=>'#550022', 'Chroococcales'=>'#550022', 'Synechocystis'=>'#550022',
'Chlamydiales'=>'#FF6666', 'Chlamydiaceae'=>'#FF6666', 
'Chlamydophila'=>'#DD77AA', 
'Chlamydia'=>'#DD88AA',
'Arthropoda'=> '#007733','Tracheata'=>'#007733',
'Alveolata'=>'#006611', 'Apicomplexa'=>'#006611', 'Haemosporida'=>'#006611',
'Euglenozoa'=>'#009900', 'Kinetoplastida'=>'#009900', 'Trypanosomatidae'=>'#009900',
'Crenarchaeota'=>'#000077','Desulfurococcales'=>'#000077', 
'Desulfurococcaceae'=>'#000077',
'Thermotogales'=>'#881111', 'Thermotoga'=>'#881111', 
'N/A'=>'#000000',
'Campylobacter_group'=>'#FF0088',
'beta_subdivision'=>'#EE0011', 'Neisseriaceae'=>'#EE0011',
'Chordata'=>'#22CC22','Craniata'=>'#22CC22' 
);

    if ($viewnum==1){
	#SUPERKINGDOM
	displayresource($node);
	print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
	print "<A HREF=\"#\" onClick=\"PopUp(\'http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&id=";
	print "$superkingdomlink{$treedata[$dataname{'treebasicdata'}][$treenum{$node}][7]}\', 400, 500, 50, 50); return true\">";
	#print "<FONT SIZE=\"-1\" FACE=\"helvetica, arial\" ";
	#print "COLOR=\"$superkingdomcolor{$treedata[$dataname{'treebasicdata'}][$treenum{$node}][6]}\">";
	#print "<B>$treedata[$dataname{'treebasicdata'}][$treenum{$node}][6]</B></FONT>";
	##print "<IMG SRC=\"icons/bacteria.jpg\">";
	print "<IMG BORDER=\"0\" SRC=\"icons/";
	print "$treedata[$dataname{'treebasicdata'}][$treenum{$node}][7]";
	print "-i.jpg\">";
	print "</CENTER></TD>";

	for ($i=8;$i<11;$i++){ 
	    print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
#	    print "<A HREF=\"#\" onClick=\"PopUp(\'http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&id=";
#	    print "$taxonomylink{$treedata[$dataname{'treebasicdata'}][$treenum{$node}][$i]}\', 400, 500, 50, 50); return true\">";#	    
	    print "<A HREF=\"#\" onClick=\"PopUp(\'http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?name=";
	    print "$treedata[$dataname{'treebasicdata'}][$treenum{$node}][$i]\', 400, 500, 50, 50); return true\">";
	    print "<FONT FACE=\"helvetica, arial\" SIZE=\"-1\"";
	    print "COLOR=\"$taxonomycolor{$treedata[$dataname{'treebasicdata'}][$treenum{$node}][$i]}\">";
	    print "$treedata[$dataname{'treebasicdata'}][$treenum{$node}][$i]</FONT></CENTER></TD>";    
	    print "</A>";
	    }
    }
# DISPLAY LINE FOR RIBOSOME    
    elsif ($viewnum==2){
        displayresource($node);
	print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
	print "$treedata[$dataname{'treearray'}][$treenum{$node}][3]</CENTER></TD>";
	print "<TD><CENTER>$treedata[$dataname{'treeoverall'}][$treenum{$node}][8]</CENTER></TD>";
	print "<TD><CENTER>$treedata[$dataname{'treeoverall'}][$treenum{$node}][9]</CENTER></TD>";
	print "<TD><CENTER>$treedata[$dataname{'treeoverall'}][$treenum{$node}][2]</CENTER></TD>";
	print "<TD><CENTER>$treedata[$dataname{'treeoverall'}][$treenum{$node}][5]</CENTER></TD>";
#       print "$TA=cog-meta\">$F2 Transcription %</A></FONT></TD>";   
    }
# DISPLAY LINE FOR FOLD
    elsif ($viewnum==3){
        displayresource($node);
	for ($i=4;$i<10;$i++){
	    print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
	    print "$treedata[$dataname{'treearray'}][$treenum{$node}][$i]</CENTER></TD>";
	}
    }
   elsif ($viewnum==4){
       displayresource($node);
	for ($i=2;$i<9;$i++){
	    print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
	    print "$treedata[$dataname{'treesfamdata'}][$treenum{$node}][$i]</CENTER></TD>";
	}
    }
  elsif ($viewnum==6){
      displayresource($node);
      for ($i=1;$i<6;$i++){
	    print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
	    print "$treedata[$dataname{'tree-cog-21'}][$treenum{$node}][$i]</CENTER></TD>";
	}
    }

    elsif ($viewnum==7){
	if ($markfortree==-1){
	    if ( $treenode==8 ){
		$treename="8-ribo-ssu";
		@treeorder2=qw(Scer Mjan Mpne Mgen Syne Hpyl Hinf Ecol);
		print "<TD ALIGN=\"RIGHT\" VALIGN=\"TOP\" WIDTH=\"270\" ALIGN=\"RIGHT\" ROWSPAN=$pictreenode>";
		# print "<IMG BORDER=\"3\" SRC=\"./treepics/blank.gif\">";
		print "<IMG BORDER=\"0\" SRC=\"./treepics/";
		print "$treename.gif\"></TD>";
		$markfortree=0;
	    }
	    if ( $treenode == 20){
		$treename="20-ribo-ssu";
		@treeorder2=qw(Cele Scer Mjan Phor Mthe Aful Aaeo Mtub Bsub Mpne Mgen Hpyl Rpro Ecol Hinf Bbur Tpal Syne Cpne Ctra);
		print "<TD VALIGN=\"TOP\" WIDTH=\"270\" ALIGN=\"RIGHT\" ROWSPAN=$pictreenode>";
		print "<IMG BORDER=\"0\" SRC=\"./treepics/";
		print "$treename.gif\"></TD>";
		$markfortree=0;
		}
	}
	else {
	    $markfortree++;
	}
	print "<TD BGCOLOR=\"\#EEFFFF\">";
	print "<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/$treeorder2[$markfortree]/\">";
	print "<FONT SIZE=\"3\" COLOR=\"#000000\" FACE=\"helvetica, arial\"><B>$treeorder2[$markfortree]</FONT></B></A>";
#	print "</TD></CENTER></TD>";
	print "</TD>";
    }
    elsif ($viewnum==5){
	displayresource($node);
	for ($i=10;$i<14;$i++){
	    print "<TD CELLPADDING=\"0\" CELLSPACING=\"0\"><CENTER>";
	    print "$treedata[$dataname{'treearray'}][$treenum{$node}][$i]</CENTER></TD>";
	}
	#this level is for fold view only
    }
    # this level is for all views
}

# DISPLAY WHETHER RESOURCES OR NOT
sub displayresource {
    my ($nodeA)=@_;
    print "<TD cellpadding=\"0\" cellspacing=\"0\"><CENTER>";
    print "<A HREF=\"http://bioinfo.mbb.yale.edu/genome/orgs/$nodeA\">";
    print "<IMG BORDER=\"0\" NAME=\"image1\" SRC=\"./pics/circleoff.jpg\"></A>";
	if ($treedata[$dataname{'treearray'}][$treenum{$nodeA}][2] == 0){ 
	    print "</CENTER></TD>";}                  #print space when no present 
	elsif ($treedata[$dataname{'treearray'}][$treenum{$nodeA}][2] == 1){
	    print "";
	    print "<A HREF=\"$yalelink{$nodeA}\">";
	    print "<IMG BORDER=0 SRC=\"pics/circleon.jpg\"></CENTER></TD>  ";}
	else{
	    print "matrix element not 0 or 1";}
}



sub read_matrix {
    my ($filename)=@_;
    open (DATA, "./datafiles/$filename.txt") or die "cannot open $filename.txt";
    my $tree_chunk;
    my @store_array;
    my $x=0;
    my $y=0;
    while (<DATA>) {    
	$y=0;
	for $tree_chunk (split()){
	    # print "$tree_chunk ";
	    $treedata[$dataname{$filename}][$x][$y]=$tree_chunk;
            #store_array[$x][$y]=$tree_chunk;
	    $y++;
	}
	# print "\n";
	$x++;
    }    
    close DATA;
}