#!/usr/bin/perl

#
# Generates a blc file from the concise file, reads in the sequence
# alignments those records in @data
#

#
#  CC 22/06/07 - bug fix in 'conversion' of coil-coiled predictions
#  CC 22/05/06 - bug fix in final foreach loop
#

use strict;
use warnings;

if ($ARGV[0]) { open(IN, "<$ARGV[0]") or die($!); }
else { open(IN, "<-") or die($!); }

# The names of the records from the concise file that we want
my @data = ("JNETALIGN", "JNETHMM", "jnetpred", "JNETPSSM", "JNETCONF", "JNETSOL25", "JNETSOL5", "JNETSOL0", "Lupas_21", "Lupas_14", "Lupas_28");

my %convert = ("JNETALIGN" => "jalign",
	"JNETHMM" => "jhmm",
	"jnetpred" => "jnet",
	"JNETPSSM" => "jpssm",
	"JNETCONF" => "conf",
	"JNETSOL25" => "sol25",
	"JNETSOL5" => "sol5",
	"JNETSOL0" => "sol0",
	"Lupas_21" => "lupas_21",
	"Lupas_14" => "lupas_14",
	"Lupas_28" => "lupas_28",
	);

my (@seq, %seq, @pred, %pred);   # CC - these could be replaced with a tied hash, for future edits.

#
# Read in the concise file and extract the data
#

while (<IN>) {
	if (/^\n/) { next; }
	my ($id, $seq) = split(":", $_);
	if (!$id || !$seq) { next; }		# Check we have proper values
	chomp($seq);
	$seq =~ s/,//g;
	if ($id =~ /align\d*;/) {
		@_ = split(";", $id);		# Then its an alignment
		push @seq, $_[1];
		$seq{$_[1]} = $seq;
		}
	foreach (@data) {
		if ($id eq $_) {
			push @pred, $_;
			$pred{$_} = $seq;
			}
		}
	}
close(IN);

my @blc;
my $gap;
my $seq_len = length($seq{$seq[0]}) - 1; 
foreach (0..$seq_len) { $gap .= " "; }

push @blc, $gap;

foreach (@seq) {
	$seq{$_} =~ s/\.|-/ /g;
	push @blc, $seq{$_};
	}
push @blc, $gap;
push @blc, $gap;
push @blc, $gap;
foreach (@pred) {
	## CC 22/06/07 - Convert 8-state secondary structure types to 3-state types unless
	## it's a coil-coil prediction where 'C' is a valid prediction.
	## I think this is a throw-back from when Jpred was a consensus server?
   if ($_ =~ /Lupas/i) {
      $pred{$_} =~ s/-/ /g;
   } else {
      $pred{$_} =~ s/[TCYWXZ_SI\?-]/ /g;
      $pred{$_} =~ s/G/H/g;
   }
   push @blc, $pred{$_};
}

foreach (@seq) {
	print ">$_\n";
	}
print ">\n>\n>\n";
foreach (@pred) {
	print ">$convert{$_}\n";
	}
print " * iteration 1\n";
#print " $seq_len\n";

foreach my $i (0..$seq_len) {
	foreach (@blc) {
      ### CC 22/05/06 - below has been changed due to bug where if
      # statement return false when $b == 0. This should actually
      # be true when parsing the JNETCONF string of integers.
      #
      # Now we test whether the variable is defined rather than true.
      # NB: not sure what do if the variable is not defined?
      
		#if (my $b = substr($_, $i, 1)) { print $b; }
      
      my $value = substr($_, $i, 1);
      print $value if defined($value);
		}
	print "\n";
	}
print " *";