#!/usr/bin/perl
#####going from diploid individuals to half-sib families#####

#######returns hash containing individuals
sub Mate(){
##### each individual needs to be mated with x other individuals
# loop as many times as pollen parents needed per mother plant
%eachPPUnique = ();
%gen2 = ();
@halfSibId = ();
foreach $id (keys %population){
      print "id: $id\n";
      # to hold hash of array of individuals
      %halfSibFamily = ();
      # count how many times loop is gone through
      $countNoPP = 0; #starting at 1 means counts always 1 more than expected
      # start a hash to make sure each pollen donor drawn is not self, and has not already pollinated this mother plant
      %eachPPUnique = ();
      # put the id of the mother plant in hash
      # hash {$key} = [value];   
      $eachPPUnique{$id}=1;
      while($countNoPP < $noCrosses){
            # Grab random $value = $genOne{idGI}
            $rangePP = $noIndividuals;
            $randomNoPP = int(rand($rangePP)); 
            ### check if already in %eachPollenUnique
            # if (exists($hash{$key}))
            if (exists ($eachPPUnique{$randomNoPP})) {
            }
            ### if new
            else {
                  # keep track of how many pollen parents (PP) for this mother plant (MP)
                  $countNoPP++;
                  # keep track of how many new individuals are made of from this mating
                  # re-initialize because new mating pair
                  $countNoCrossesPerPP = 0;
                  while ($countNoCrossesPerPP < $noIndividualsPerCross){
                        # empty arrays for creation of new individual
                        @gameteReturned = ();
                        @gameteMP = ();
                        @gametePP = ();
                        @individualGen2 = ();
                        # add to hash (add $randomNoPP to %eachPPUnique)
                        $eachPPUnique{$randomNoPP} = 1;
                        # send mother plant (MP) to be crossed over, and gamete selected
                        $MP = $id; #mother plant
                        require "./switchgrass CrossOverMP.pl";
                        CrossOverMP (\%population);
                        @gameteMP = @gameteReturned;                                                 
                        # call up pollen parent (PP)
                        $PP = $randomNoPP; #pollen parent
                        # send PP to be crossed	
                        require "./switchgrass CrossOverPP.pl";
                        CrossOverPP (\%population);
                        # return array holding gamete from mother plant
                        @gametePP = @gameteReturned;
                        # create new individual from 2 gametes
                        foreach $locusGameteMP (@gameteMP){
                              $locusGametePP = shift(@gametePP);
                              $locusGen2 = $locusGameteMP._.$locusGametePP;
                              push(@individualGen2, $locusGen2);
                        }
                        # note that have done another instance of this mating
                        $countNoCrossesPerPP++;
                        ### add arrays (individuals)to hash (families)
                        # hash key is MP id concatenated to PP id
                        $indId = MP.$MP._.PP.$PP._.$countNoCrossesPerPP;
                        # create hash of arrays to give individuals ids (keys in hash)
                        # hash {$key} = [value];
                        $halfSibFamily{$indId}=[@individualGen2];                                  
                 }#while       
            }#else
                   
       }#while
$gen2{$MP} = \%halfSibFamily;
}

# sub end
}
1;