##</code><code>##

#!/usr/bin/perl

$fileName   = $ARGV[0];
$windowSize = $ARGV[1];
$windowIncrement = $ARGV[2];

open(CPF, $fileName) or die ("Can't open file ", $fileName);
@lines = <CPF>;
close (CPF) or warn ("Unable to close ", $fileName);
$n = @lines;

$index = 0;
@allNames;
@allSeq;
$nbTaxa;
$nbGenes;
#$lastLine = "start";

$alternatingIter = sub {return $_[0]};
$followedIter = sub {return (($_[0] % 10) - 1) };
$iter;

chop $lines[0];
($nbTaxa,$nbGenes)=split / +/, $lines[0];	

&sorter ($lines[1]);


	if (((length $second) == 0) && ($first =~ /[AGTC]+/)){	
		$iter = $followedIter;
		chop ($first);
		$allSeq[$index]= $allSeq[$index].$first;

		print "TYPE: just sequence  -->  ";
		print "first:".$first.";  second:".$second.";\n";
	}


	elsif (((length $second) > 0) && ($first =~ /(\w)+/) &&  ($second =~ /[AGTC]+/) ){	
		$iter = $alternatingIter;
		$allNames [$index] = $first;
		chop ($second);
		$allSeq [$index] = $second;
		$index++;

		print "TYPE: name + sequence -->  ";
		print "first:".$first.";  second:".$second.";\n";
	}

foreach $tmp (@lines[3..@lines]){
	&sorter ($tmp);
}


sub sorter {
	$tmp = $_[0];
	($first, $second)= split / +/, $tmp;

	if (((length $second) == 0) && ($first =~ /[AGTC]+/)){	
		chop ($first);
		$allSeq[$index]= $allSeq[$index].$first;

		print "TYPE: just sequence  -->  ";
		print "first:".$first.";  second:".$second.";\n";
	}


	elsif (((length $second) > 0) && ($first =~ /(\w)+/) &&  ($second =~ /[AGTC]+/) ){	
		$allNames [$index] = $first;
		chop ($second);
		$allSeq [$index] = $second;
		$index++;

		print "TYPE: name + sequence -->  ";
		print "first:".$first.";  second:".$second.";\n";
	}
	elsif($first eq "\n"){
		print "TYPE: do nothing -->  ";
		print "first:".$first.";  second:".$second.";\n";
	}
	else{
		print "TYPE: you have a problem with the format of file".$fileName." -->  ";
		print "first:".$first.";  second:".$second.";\n";
	}
	print "index: ".$index."\n";
}