use strict;
use warnings;

# Set this to either 'ms2' or 'ms3'
my $includeFilter = 'ms3';

#Edit this to create a different named outputfile
my $outfile = "SN.txt";


## parse FT2 file
my @masses = (126.127725,127.124760,127.131079,128.128114,128.134433,129.131468,129.137787,130.134822,130.141141,131.138176); #TMT 10-plex
my @errortolerances;
for my $i (0..9) {
	$errortolerances[$i] = $masses[$i]*4e-6;#8ppm or +/- 4ppm
}
my $lowerbound = $masses[0] - $errortolerances[0];
my $upperbound = $masses[9] + $errortolerances[0];
#my $dirloc = $ARGV[0];
#my $outfile = $ARGV[1];
my $dirloc = '';

my @filelist = glob($dirloc . '*.FT2');
open OUT,">$outfile" or die "could not create file $outfile\n";
print "Found these files:\n File >>" . (join "<<\n File >>",@filelist) . "<<\n";

my @out;
foreach my $filename (@filelist) {
print "opening $filename\n";
open IN, "$filename";
my $shortfilename = $filename;
$shortfilename =~ s/\.FT2$//;
my $currentscan;
my @sn;
my $ignoreflag = 1;
while (my $line = <IN>) {
	if ($line =~ m/^S	(\d+)/) {
		if (defined($currentscan) && $#sn > 0 && $ignoreflag == 0) {
			my $sns = join "\t",@sn;
			push @out, "$shortfilename\t$currentscan\t$sns\n";
		}
		@sn = ('','','','','','','','','','');
		$currentscan = $1;
	} elsif ($line =~ m/^I	ScanFilter/) {
		if ($line =~ m/$includeFilter/i) {
			$ignoreflag = 0;
		} else {
			$ignoreflag = 1;
		}
	} elsif ($line =~ m/^\d/) {
		my @splitline = split(/\t/,$line);
		if ($#splitline >= 4) {
			my ($mzval,$intval,$noiseval) = @splitline[0,1,4];
			if ($mzval <= $upperbound && $mzval >= $lowerbound) {
				foreach my $i (0..9) {
					if (abs($mzval - $masses[$i]) < $errortolerances[$i]) {
						if ($sn[$i] eq '') {
							$sn[$i] = $intval/$noiseval;
						} else {
							my $newsn = $intval/$noiseval;
							if ($sn[$i] < $newsn) {
								$sn[$i] = $newsn;
							}
						}
					}
				}
			}
		}
	}
}
close IN;
}
print "writing output\n";
print OUT @out;
close OUT;