#!/usr/bin/perl

use strict;
use ProbeSearch;
use constant SUCCESS => 0;
use constant ERROR => -1;
require XML::Simple;
use subs ;
use Data::Dumper;


sub get_targets
{  
   my $targets;
   while ( $targets eq "" )
   {
	print "Which Target(s), All, or Quit  (ex: 1  1,2  all) : ";
        chop($targets = <STDIN>);

        exit if ($targets =~ m/^ *[Qq]uit *$/);
        # Convert "All" to list of targets
	$targets = "1,2,3,4,5" if ($targets =~ m/^ *[Aa]ll *$/);

        if (!($targets =~ m/^ *[0-9](,\d)* *$/))
        {
	     print "$targets: Not a valid target list\n ";
             $targets="";
        }
   }
   return $targets;
}


sub get_location
{  
   my $start;
   
   while ( $start eq "" )
   {
	print "Starting Basepair : ";
        chop($start= <STDIN>);

        exit if ($start =~ m/^ *[Qq]uit *$/);
        # Convert "All" to list of targets
	$start= "all" if ($start=~ m/^ *[Aa]ll *$/);

        if (!($start =~ m/^ *[0-9]+ *$/))
        {
	     print "$start : Not a valid target list\n ";
             $start ="";
        }
   }
   return $start;
}


sub get_species
{  
   my $species;
   while ( $species eq "" )
   {
        print "Species List\n";
        print "============\n";
        print " 1.  Mouse\n";
        print " 2.  Baboon\n";
        print " 3.  Cat\n";
        print " 4.  Chicken\n";
        print " 5.  Chimp\n";
        print " 6.  Cow\n";
        print " 7.  Dog\n";
        print " 8.  Fugu\n";
        print " 9.  Pig\n";
        print " 10. Rat\n";
        print " 11. Tetra\n";
        print " 12. Zebra Fish\n\n";
	print "Which Species(s), All, or Quit  (ex: 1  1,2  all) : ";
        chop($species= <STDIN>);

        exit if ($species=~ m/^ *[Qq]uit *$/);
        # Convert "All" to list of targets
	$species = "1,2,3,4,5,6,7,8,9,10,11,12" if ($species =~ m/^ *[Aa]ll *$/);

        if (!($species =~ m/^ *[0-9](,\d)* *$/))
        {
	     print "Sspecies : Not a valid target list\n ";
             $species = "";
        }
   }
   return $species;
}

sub select_probes
{
   my $species;
   my $target;
   my $start;
   my $end;
   my $file;

   ($species, $target, $start, $end) = (@_);
   $file = "/home/bcarlson/data/";
   $file .= "Target$target/";
   $file .= "human_".$species."_T".$target.".verbose.probes.xml";

   my $xs = new XML::Simple();
   my $probe_analysis= $xs->XMLin($file);
   for (my $i=0; $i<@{$probe_analysis->{parent_alignment}}; $i++)
   {
      if (($start <= $probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{start}) &&
          ($end >= $probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{end}))
      { print "SELECT : "; 
        print "[$species] ";
        print "[".$probe_analysis->{parent_alignment}->[$i]->{probe}->{sequence}."]  ";
        print "[".$probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{start}."]  ";
        print "[".$probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{end}."]\n";
        print "\n";
      }
      #else
      #{ print "IGNORE : "; }

      #print "Probe End [".$probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{end}."]\n";
      #print "[$species] ";
      #print "[".$probe_analysis->{parent_alignment}->[$i]->{probe}->{sequence}."]  ";
      #print "[".$probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{start}."]  ";
      #print "[".$probe_analysis->{parent_alignment}->[$i]->{species}->{species1}->{end}."]\n";
      #print "\n";
   }
   
   
}

sub getParams {
    my %opts;
    my $errstr = "";
    use Getopt::Long;
    GetOptions(\%opts, 'help');

    if (defined($opts{help}))
    {
      $errstr = "\n";
    }

    if ($errstr) {
        print <<"END_USAGE";

Description: 

This script will take a species, target and bp range and return all the
probes in that range. Currently everything is hard coded.

Usage: select_probes.pl 


END_USAGE
        print "\n$errstr" if ($errstr);
        die("\n");
    }
}

#my $species = get_species();
#my $targets = get_targets();
print "PROCESSING TARGET 3\n";
select_probes "cat",3,1850000,2850000;
select_probes "chicken",3,1850000,2850000;
select_probes "cow",3,1850000,2850000;
select_probes "dog",3,1850000,2850000;
select_probes "fugu",3,1850000,2850000;
select_probes "mouse",3,1850000,2850000;
select_probes "pig",3,1850000,2850000;
select_probes "rat",3,1850000,2850000;
select_probes "tetraodon",3,1850000,2850000;
select_probes "zfish",3,1850000,2850000;
print "PROCESSING TARGET 5\n";
select_probes "cat",5,2000000,27500000;
select_probes "cow",5,2000000,27500000;
select_probes "dog",5,2000000,27500000;
select_probes "mouse",5,2000000,27500000;
select_probes "pig",5,2000000,27500000;
select_probes "rat",5,2000000,27500000;
select_probes "zfish",5,2000000,27500000;

#print "Processing species [$species]\n";
#print "For Targets [$targets]\n";