$arxeio_structures = $ARGV[0];
$arxeio_seqs = $ARGV[1];
$arxeio_align = $arxeio_seqs.'.align.final_align';

$/="//\n";							#apo to arxeio domwn apothikeuw AC, akolouthia kai consensus tis topologias
open DOMES, $arxeio_structures;
while(<DOMES>)
{
	if($_=~/^>(\w{6})\|.*?\t([\w\d\_]+)/m)
	{
		$structure_prot=$_;
		$tm_ac=$1;
		$tm_pfam=$2;
	
		if($structure_prot=~/^SEQ:(.*)/m)
		{
			$tm_seq=$1;
		}

		if($structure_prot=~/^CON:(.*)/m)
		{
			$tm_cons=$1;
		}
	}
	
	$hash_structure{$tm_ac} = $tm_seq;
	$hash_cons{$tm_ac} = $tm_cons;

	#$HoA_3D{$tm_ac} = [$tm_pfam, $tm_seq, $tm_cons];	#    Ektypwsi:  print "$ac: @{ $HoA_3D{$ac} }\n";
	$tm_ac=$tm_seq=$tm_cons=$tm_pfam='';
}
close DOMES;
$/="\n";

open ALIGN, $arxeio_align;					#apo to arxeio alignment apothikeuw kathe AC, tin antistoixi
while(<ALIGN>)							#stoixismeni seq kai apo pou ksekinaei i seq tis stoixisis
{								#(giati exoume steilei mono to kommati pou xtypaei sto Pfam gia stoixisi)
	if($_=~/^(.*?)\|(\d+)-\d+\t(.*)/)
	{
		$ac_align=$1;		
		$arxi_align=$2;
		$seq_align = $3;
		
		$hash_align{$ac_align}=$seq_align;
		$hash_start_align{$ac_align}=$arxi_align-1;
	}
}
close ALIGN;

foreach $a(keys %hash_align)
{
	if(exists($hash_structure{$a}))				#an i akolouthia exei 3-D domi, ftiaxnw neo LBL seq me vasi tis allages pou exei epiferei i stoixisi (- kai .)
	{
		$seq_structure = $hash_structure{$a};		#print $seq_structure."\n";
		$lbl_structure = $hash_cons{$a};		#print $lbl_structure."\n";
		$seq_apo_alignment = $hash_align{$a};
		$thesi_arxis_alignment = $hash_start_align{$a};

		@split_structure_lbl = split(//,$lbl_structure);
		@split_seq_apo_alignment = split(//,$seq_apo_alignment);

		$count_trash=0;
		for ($i=0; $i<=$#split_seq_apo_alignment; $i++)
		{
			
			if($split_seq_apo_alignment[$i] ne '-' && $split_seq_apo_alignment[$i] ne '.')
			{
				$thesi_wanted=$thesi_arxis_alignment + ($i-$count_trash);
				#print $i."\t".$split_seq_apo_alignment[$i]."\t".$count_trash."\t".$thesi_wanted."\t".$split_structure_lbl[$thesi_wanted]."\n";
				$lbl_structure_new.=$split_structure_lbl[$thesi_wanted];
			}
	
			else
			{
				$count_trash++;
				#print $i."\t".$split_seq_apo_alignment[$i]."\t".$count_trash."\t".$thesi_wanted."\t".$split_seq_apo_alignment[$i]."\n";
				$lbl_structure_new.=$split_seq_apo_alignment[$i];
			}
		}
		print $lbl_structure_new."\n";
		
   		while ($lbl_structure_new=~/[.-]*([^.-])(?:\1|[.-])*/g)
		{
			$arxi  = $-[0];
			$telos = $+[0]-1;
			$eidos = $1;
	
			push @AoA, [$eidos, $arxi, $telos];
		}
	}
	else						#ean i akolouthia den anikei se 3D domi, apla tin apothikeuw kai tin epeksergazomai parakatw
	{
		$not_3D{$a}=$hash_align{$a};
	}
}

	#for $i ( 0 .. $#AoA ) 
	#{
    	#	print "row $i is: @{$AoA[$i]}\n";
	#}

foreach $k(keys %not_3D)					#pairnw twra tis akolouthies pou den exoun domi
{
	$seq_no_3D=$not_3D{$k};

	$copy_seq_no_3D=$seq_no_3D;				#ftiaxnw antigrafo tis akolouthias no3d kai diwxnw - kai .
	$copy_seq_no_3D =~ s/[-.]+//g;
	@split_copy_seq_no_3D=split(//, $copy_seq_no_3D);	#split i akolouthia align alla xwris - kai .
	@split_seq_no3D = split(//, $seq_no_3D);		#split i original akolouthia align
	print '>'.$k."\n";
	print $seq_no_3D."\n\n";

	$count_axrista=0;
	
	for $i ( 0 .. $#AoA ) 			
	{
		if($AoA[$i]->[0] eq 'I')
		{
			$arxi_I = $AoA[$i]->[1];
			$telos_I = $AoA[$i]->[2];
			$mikos_I = ($telos_I-$arxi_I)+1;
			
			$substring_I=substr($seq_no_3D,$arxi_I,$mikos_I);
			$axrista_I  = ($substring_I =~ tr/-.//);
			$count_axrista=$axrista_I+$count_axrista;
			
		}

		elsif($AoA[$i]->[0] eq 'O')
		{
			$arxi_O = $AoA[$i]->[1];
			$telos_O = $AoA[$i]->[2];
			$mikos_O = ($telos_O-$arxi_O)+1;
			
			$substring_O=substr($seq_no_3D,$arxi_O,$mikos_O);
			$axrista_O  = ($substring_O =~ tr/-.//);
			$count_axrista=$axrista_O+$count_axrista;
			
		}
		
    		elsif($AoA[$i]->[0] eq 'M')				#vriskw ola ta TM kommatia tou AoA tis structure
		{	
			$count_axrista_entering=$count_axrista;
			#print "row $i is: @{$AoA[$i]}\n";
			$arxi_tm = $AoA[$i]->[1];			#arxi kai telos twn TMs stis seq twn ypoloipwn proteins tou align
			$telos_tm = $AoA[$i]->[2];
			$mikos_tm = ($telos_tm-$arxi_tm)+1;

			$substring_M=substr($seq_no_3D,$arxi_tm,$mikos_tm);
			#print $substring_M."\t".length($substring_M)."\t".$arxi_tm."\t".$telos_tm."\n";
			$axrista_M = ($substring_M =~ tr/-.//);				#ypologizw - kai . se kathe TM kommati 
			$count_axrista_exiting=$axrista_M+$count_axrista;
			if($axrista_M>0) {$count_axrista=$count_axrista_exiting};
			$substring_M=~ s/[-.]+//g;					#diwnxnw ta - kai . kai elegxw....
						
			if(length($substring_M)>=7)			#...an to TM pou apomenei exei mikos >=7, eimaste OK kai to kratame, alliws...
			{
				$thesi_telikis_arxis  = $hash_start_align{$k}+$arxi_tm-$count_axrista_entering;
				$thesi_telikou_telous = $hash_start_align{$k}+$telos_tm-$count_axrista_exiting;
				
				#print 'MIKOS_MIN_7'."\t".$substring_M."\t".length($substring_M)."\t".$thesi_telikis_arxis."\t".$thesi_telikou_telous."\t".'BIKA ME: '."\t".$count_axrista_entering."\t".'VGIKA ME: '."\t".$count_axrista_exiting."\t".'AXRISTA MESA: '."\t".$axrista_M."\n";
				push @AoA, [$k, ($thesi_M_se_arxiki_seq+$arxi_tm), ($thesi_M_se_arxiki_seq+$mikos_tm)];
				
			}
			else						#stis parakatw periptwseis prepei na prostethoun AA sto Tm ,wste na ginei toulaxiston mikos 7
			{
				$extra_length=7-length($substring_M);
				$arxi_epomeno_kommati=$AoA[$i+1]->[1];
				$telos_epomeno_kommati=$AoA[$i+1]->[2];
				$mikos_epomeno_kommati=$telos_epomeno_kommati-$arxi_epomeno_kommati+1;

				$arxi_proigoumeno_kommati=$AoA[$i-1]->[1];
				$telos_proigoumeno_kommati=$AoA[$i-1]->[2];
				$mikos_proigoumeno_kommati=$telos_proigoumeno_kommati-$arxi_proigoumeno_kommati+1;
				
				$substring_proigoumeno = substr($seq_no_3D,$arxi_proigoumeno_kommati,$mikos_proigoumeno_kommati);	#ayto to kanw giati mporei to epomeno/proigoumeno kommati na exei 10AA
				$substring_epomeno = substr($seq_no_3D,$arxi_epomeno_kommati,$mikos_epomeno_kommati);			#alla ta 7 na einai - i .
				$substring_proigoumeno=~ s/[-.]+//g;
				$substring_epomeno=~ s/[-.]+//g;			
				$actual_length_proigoumeno = length($substring_proigoumeno);
				$actual_length_epomeno = length($substring_epomeno);
				
				if($split_seq_no3D[$telos_tm] ne '-' && $split_seq_no3D[$telos_tm] ne '.' && ($split_seq_no3D[$arxi_tm]  eq '.' or $split_seq_no3D[$arxi_tm]  eq '-')) #edw prepei na proekteinw pros ta aristera [typos: ---...XX]
				{
				print $substring_M."\t".length($substring_M)."\t".$arxi_tm."\t".$telos_tm."\t".'PROIGOUMENO:'."\t".$substring_proigoumeno."\t".'EPOMENO:'."\t".$substring_epomeno."\n";

					if ($actual_length_epomeno-$extra_length<1 && $actual_length_proigoumeno-$extra_length<1)	#an de mporw na paw pouthena, to afinw ws exei
					{
					$final_tm=$substring_M;
					$thesi_telikis_arxis  = $hash_start_align{$k}+$arxi_tm-$count_axrista_entering;
					$thesi_telikou_telous = $hash_start_align{$k}+$telos_tm-$count_axrista_exiting;						
					print 'EXEI ALLAGI:'."\t".$substring_M."\t".length($substring_M)."\t".$thesi_telikis_arxis."\t".$thesi_telikou_telous."\t".'BIKA ME: '."\t".$count_axrista_entering."\t".'VGIKA ME: '."\t".$count_axrista_exiting."\t".'AXRISTA MESA: '."\t".$axrista_M.":: DE MPORW";
					print substr($copy_seq_no_3D,$thesi_telikis_arxis,($thesi_telikou_telous-$thesi_telikis_arxis+1));
					last;
					}

					elsif($actual_length_proigoumeno-$extra_length>=1)							#an to mikos tou proigoumeno kommatiou-extra_AA>1, kanw kanonika tin proektasi pros ta aristera
					{
					$thesi=index($copy_seq_no_3D,$substring_M); 
					$extra_AAs = substr($copy_seq_no_3D,$thesi-$extra_length,$extra_length);
					$final_tm=$extra_AAs.$substring_M;
					#$thesi_telikis_arxis  = $hash_start_align{$k}+$arxi_tm-$count_axrista_entering-$extra_length;
					#$thesi_telikou_telous = $hash_start_align{$k}+$telos_tm-$count_axrista_exiting;
					$thesi_telikis_arxis  = $arxi_tm-$count_axrista_entering-$extra_length;
					$thesi_telikou_telous = $telos_tm-$count_axrista_exiting;
					
					print 'EXEI ALLAGI:'."\t".$substring_M."\t".length($substring_M)."\t".'ARXIKA'.($hash_start_align{$k}+$arxi_tm-$count_axrista_entering)."-".($hash_start_align{$k}+$telos_tm-$count_axrista_exiting)."\t".'TELIKA: '.$thesi_telikis_arxis."-".$thesi_telikou_telous."\t".'BIKA ME: '."\t".$count_axrista_entering."\t".'VGIKA ME: '."\t".$count_axrista_exiting."\t".'AXRISTA MESA: '."\t".$axrista_M."::";
					print substr($copy_seq_no_3D,$thesi_telikis_arxis,($thesi_telikou_telous-$thesi_telikis_arxis+1));
					last;
					}

					else # to paw kai pros tis 2 kateuthinseis, arkei ta oria tou telikou TM na apexoun toulaxiston kata 1 AA apo to proigoumeno/epomeno kommati($actual_length_epomeno-$extra_length>=1 && $actual_length_proigoumeno-$extra_length<1)	#an exw provlima me to mikos tou proigoumeno kommatiou, alla to epomeno-extra_AA>1 paw pros ta deksia anagkastika
					{
=pod
my $str = "ABCDEFGHIJKLMNOP";
my $seed = "FGHI";
my $length = 7;

my $slen = length $seed;
my $ipos = index $str,$seed;

my $lexpand = $slen < $length ? ($length - $slen)/2 : 0;
$lexpand = $ipos < $lexpand ? $ipos : $lexpand;
print +(substr $str,($ipos - $lexpand),$length),"\n";
=cut

					$thesi=index($copy_seq_no_3D,$substring_M);
					 
					$orio_epomenou=$split_copy_seq_no_3D
					$extra_AAs = substr($copy_seq_no_3D,$thesi,$extra_length);
					$final_tm=$extra_AAs.$substring_M;
					$thesi_telikis_arxis  = $hash_start_align{$k}+$arxi_tm-$count_axrista_entering;
					$thesi_telikou_telous = $hash_start_align{$k}+$telos_tm-$count_axrista_exiting+$extra_length;
					print 'EXEI ALLAGI:'."\t".$substring_M."\t".length($substring_M)."\t".$thesi_telikis_arxis."\t".$thesi_telikou_telous."\t".'BIKA ME: '."\t".$count_axrista_entering."\t".'VGIKA ME: '."\t".$count_axrista_exiting."\t".'AXRISTA MESA: '."\t".$axrista_M."::";
					print substr($copy_seq_no_3D,$thesi_telikis_arxis,($thesi_telikou_telous-$thesi_telikis_arxis+1));
					last;	
					}

				}
				
			}
			
		}
		
	}
	print "\n";
}