#!/usr/bin/perl

# Randal R. Ketchem, Ph.D.                619.784.9879 (voice1)
# Department of Molecular Biology, MB-9   619.784.8754 (voice2)
# The Scripps Research Institute          619.784.9985 (FAX)
# 10550 N. Torrey Pines Road              ketchemr@scripps.edu (email)
# La Jolla, CA 92037-1027                 http://www.scripps.edu/~ketchemr

# noevio file:
##  ATOM A          ATOM B        BOUND  MT   AVE  +-  RMS  : per structure
# 19 TYR CZ       13 ILE MD        0.01  1D  14.11 +-  1.94 :   15.23  12.39 13.02  11.91  15.81  10.93  17.79  14.76  14.58  14.66  # ar_ambig:1
# The peak number is in the comment field as "peak file name:peak number".

require "ctime.pl";
require "getopt.pl";

if($#ARGV != 5)
{
   $prgName = `basename $0`;
   chop($prgName);
   die <<EOHELP;

Grabs the peaks in an ambiguity noevio output file that are of a designated
number. For example, grab all peaks that have an ambiguity of three. Will
read a quoted number group to place astericks next to peaks <= number.

Usage: $prgName -b ["bins"] -n [number of peaks] -p [peak file] [> out]
EOHELP
}

&Getopt('bnp');
@bins = reverse sort bynumber split(' ', $opt_b);
$numPeaks = $opt_n;
$numPeaks = 1 if(!$numPeaks);
$noevioFile = $opt_p;
$commentPeakFile = $noevioFile;
$commentPeakFile =~ s/.*\///;

open(NOEVIOFILE, $noevioFile) || die("Cannot open $noevioFile: $!\n");
while(<NOEVIOFILE>)
{
   next if(/^\s*#/);
   next if(/^\s*$/);
   chop;

   $peakNum = $_;
   $peakNum =~ s/.*://;
   $peakNum =~ s/ .*//;
   $count{$peakNum}++;
}
close(NOEVIOFILE);

$countPeaks = 0;
foreach (sort bynumber keys %count)
{ ++$countPeaks if($count{$_} == $numPeaks); }

sub bynumber { $a <=> $b; }

$date = &ctime(time);
print "# Date: $date";
print "# Peak File: $commentPeakFile\n";
print "# bins:"; foreach $bin (@bins) { print " $bin"; } print "\n";
print "# Number to match: $numPeaks\n";
print "# Number of matches: $countPeaks\n";
#print "#   ATOM 1        ATOM 2      distance # peak file:peak #\n";
print "# ATOM A          ATOM B         BOUND  MTD    AVE +- RMS";
print "  : each : input comment\n";

open(NOEVIOFILE, $noevioFile) || die("Cannot open $noevioFile: $!\n");
while(<NOEVIOFILE>)
{
   next if(/^\s*#/);
   next if(/^\s*$/);
   chop;
# 19 TYR CZ       13 ILE MD        0.01  1D  14.11 +-  1.94 :   15.23  12.39 13.02  11.91  15.81  10.93  17.79  14.76  14.58  14.66  # ar_ambig:1
   $peakNum = $_;
   $peakNum =~ s/.*://;
   $peakNum =~ s/ .*//;
   @words = split;
   $mark = "";
   if($count{$peakNum} == $numPeaks)
   {
      $avg = $words[8];
      foreach $bin (@bins) { $mark .= "*" if($avg <= $bin); }
#      while(length($mark) < scalar(@bins)) { $mark .= " "; }
      print "\n" if($peakNum != $oldPeakNum);
      $oldPeakNum = $peakNum;
      print "$_";
      print " $mark" if($mark);
      print "\n";
   }
}
close(NOEVIOFILE);