) {
($in_id, $in_strangenum, $let, $num) = split (' ', $_, 4);
if($in_id eq $in_idclass) {
$prejfound = 1;
last;
} #
} # while
if($prejfound) {
print "This is classified as $let-$num.
" .
"This initial assignment was made based on an identity of $in_strangenum %.
In words, this classification is:\n", p;
@nnum = split(/[^0-9\.]+/,$num);
for $inum (@nnum) {
next if ($inum eq "");
# print "$inum\n\r";
if($inum =~ /\.$/) {
chop $inum;
}
# print "$inum\n\r";
if($inum =~ /^\./) {
$inum = substr ($inum, 1);
}
# print "$inum\n\r";
push @nnum_out, $inum;
} # for
if($#nnum_out == -1) {
# print 'Level II SCOP database search failed:',"\n";
# print 'Unknown foreign key is found:', $num, "\n";
print "$num (a complete classification is not available ".
"at the present time).";
}
else
{
$"="\n"; #"
# print "@nnum_out\n";
# call julloopkup on each of @nnum_out
print p;
# print scalar(@nnum_out), p;
for $nnum_count (0 .. length(@nnum_out)-1) {
# GOTO: jullookup.txt and get the DESCRIPTION
$jfound = 0;
open F3, "<$file3";
while () {
($in_let, $in_num, $in_stuff) = split (' ', $_, 3);
if($in_let eq $let && $in_num eq $nnum_out[$nnum_count]) {
$jfound = 1;
last;
}
} # while ()
close F3;
if($jfound) {
@aaa = split /\s*\|\s*/, $in_stuff;
# print $#aaa;
$" = "\n"; # print "@aaa\n"; # "
for $i (0 .. $#aaa) {
print $aaa[$i] , p ;
}
} # if $jfound
else
{
print "similar to the functions of the other $num ".
"domains
(a more detailed description is not available ".
"at the present time)",p;
} # else $jfound
} # for $nnum_count
}
}
else {
print "\n Sorry, Level I of SCOP database failed to locate your entry",p;
print "$in_id, $in_strangenum, $let, $num",p;
}
} #foreach
} # if $found
else
{
print "Sorry, your entry is not found in our SCOP database" , p;
}
print "\n\n
\n";
###################### Riley classification: ######################
print ("GenProtEC ".
"Classification
");
$rfound = 0;
my %riley_pid;
open(F1, ") {
($in_id100, $in_idclass, $in_pid) = split (' ', $_, 3);
if($in_id100 =~ m/^d?$id100/) {
$rfound = 1;
$riley_pid{$in_idclass} = $in_pid;
# print "$in_id100, $in_idclass, $in_pid", p;
}
} # while
print p;
close F1;
if($rfound){
foreach $riley_idclass (sort keys %riley_pid){
$in_idclass = $riley_idclass;
$in_pid = $riley_pid{$riley_idclass};
print "
\n";
print "The representative RILEY ID is ".
"$in_idclass " .
"with an identity of $in_pid %." , p;
if($in_pid > 85) {
$riley_num = get_mmmming_riley_number($in_idclass, "riley_scop_relate.txt");
if($riley_num eq "") {
print "Level II Riley database search failed: no functional description " .
"is available. Please, try again later after we augment our database.",p;
}
else
{
print "This is classified as $riley_num." .
"(No extra fields at the moment.) In words, this classification is:\n", p;
@riley_str = get_mmmming_riley_strings($riley_num, "riley_cat_decode.txt");
$" = "
\n";
print "@riley_str
\n";
} #if($riley_num eq "")
} else {
print "Function can not be reliably assigned ".
"due to the low identity value.
",p;
}
} # foreach
} else {
print "Sorry, your entry is not found in our Riley database.", p;
} #rfound
print "
\n";
######################### MIPS classification: #################################
print ("MIPS ".
"Classification
");
$mfound = 0;
my %mips_pid;
open(F1, ") {
($in_id100, $in_idclass, $in_pid) = split (' ', $_, 3);
if($in_id100 =~ m/^d?$id100/) {
$mfound = 1;
$mips_pid{$in_idclass} = $in_pid;
}
} # while
close F1;
if($mfound) {
foreach $mips_idclass (sort keys %mips_pid){
$in_idclass = $mips_idclass;
$in_pid = $mips_pid{$mips_idclass};
print "
\n";
print "The representative MIPS ID is ".
"$in_idclass " .
"with an identity of $in_pid %." , p;
if($in_pid > 85) {
@aa = get_mmmming_mips_numbers($in_idclass,'mips_scop_relate.txt');
for(@aa) {
print "This is classified as $_." .
"(Multiple Classifications possible in MIPS.) In words,
this classification is:\n", p;
$_string = get_mmmming_mips_string($_, 'mips_cat_decode.txt');
if ( ($s=get_superclass ($_)) ne "") {
$s_string = get_mmmming_mips_string($s,'mips_cat_decode.txt');
if ( ($ss=get_superclass ($s)) ne "") {
$ss_string = get_mmmming_mips_string($ss,'mips_cat_decode.txt');
}
}
print "$ss_string
\n";
print "$s_string
\n";
print "$_string
\n";
print "
\n";
} # for
} else { # if($in_pid > 85)
print "Function can not be reliably assigned ".
"due to the low identity value.
";
}
} #foreach
} else {
print "Sorry, your entry is not found in our MIPS database";
} #if(mfound)
print "\n\n
\n";
#-----------
} # if param
else
{
print "Parameters were not passed properly to search.cgi", p;
}
print '';
#+++++ Subrutines: +++++++++++++++++++++++++++++++++++++++++++++++
sub get_mmmming_riley_number {
my $key = shift;
my $file1 = shift;
my $found = 0;
my $in_key, $number, $rest;
local *F1;
open F1, "<".$file1;
while() {
# print $_;
($in_key, $number, $rest) = split(' ',$_,3);
if($key eq $in_key) {
$found = 1; $in_pid *= 1.00 ;
last;
}
}
if ( not $found ) {
print "riley number not found. Alas!\n";
return my $xyi = "";
}
# print "$number\n";
return $number;
}
#----------------------------------------------------
sub get_mmmming_riley_strings {
my $key = shift;
my $file = shift;
my $found = 0;
my $in_key, $rest;
local *F1;
open F1, "<".$file;
# print $key, " : ", length($key), "\n";
while() {
($in_key, $rest)= split(' ',$_,2);
# print length($in_key),"\n";
if($key eq $in_key) {
$found = 1; $in_pid *= 1.00 ;
last;
}
}
if ( not $found ) {
print "riley string not found. Alas!\n";
return my $xyi = ();
}
# print "$in_key\n";
# print "$rest\n";
my @a;
($a[0],$a[1],$a[2])= split(/\s*[0-9\.]+\s*/,$rest,3);
return @a;
}
#----------------------------------------------------
sub get_mmmming_mips_numbers {
my $key = shift;
my $file = shift;
my $found = 0;
my $in_key, $rest;
local *F1;
open F1, "<".$file;
# print $key, " : ", length($key), "\n";
while() {
($in_key, $rest)= split(' ',$_,2);
# print length($in_key),"\n";
if($key eq $in_key) {
$found = 1; $in_pid *= 1.00 ;
last;
}
}
if ( not $found ) {
print "MIPS Supercategory was not found.",p;
return my $xyi = ();
}
# print "$in_key\n";
# print "$rest\n";
my @a, @b;
@a = split(' ',$rest);
@b = split(';',$a[9]);
return @b;
}
#----------------------------------------------------
sub get_mmmming_mips_string {
my $key = shift;
my $file = shift;
my $found = 0;
my $in_key, $rest;
local *F1;
open F1, "<".$file;
# print $key, " : ", length($key), "\n";
while() {
chomp;
next unless /^[0-9]/ ;
($in_key, $rest)= split(' ',$_,2);
# print length($in_key),"\n";
if($key eq $in_key) {
$found = 1; $in_pid *= 1.00 ;
last;
}
}
if ( not $found ) {
print "MIPS category was not found.",p;
return my $xyi = "";
}
return $rest;
}
#----------------------------------------
sub get_superclass {
my $a = shift;
if ( /(.*)\.[0-9][0-9]/ ) {
return $1;
}
return "";
}
';
#
# print '