#Randomly generate a population of plants, and breeds and dies. is the purpose of this mess...
use Data::Dumper;
use warnings;
$popCt=1;
$seed = 20;
$germrate = .5;
$removal = 15;
$iteration = 20;

for (1 .. $popCt) 
{
	my ($refToArrA, $refToArrB, $refToArrC, $refToArrD) = makeArrays(); #creates a list of individuals, and chormosomes
		
	$counter++;
	&gener( $refToArrA, $refToArrB, $refToArrC, $refToArrD ); #creates the storage hash
	
#	print Data::Dumper->Dumpxs([\%HoH], [q{*HoH}]);
}

for (1 .. $iteration) {
&births();
&death();
}

print Data::Dumper->Dumpxs([\%HoH], [q{*HoH}]);

#no work is needed here, this works like I want
sub makeArrays
{


	$lower = 10;

	$upper = 20;
	
	
	my @chroma;
	my @chromb;
	my $ranpop;
	
	$ranpop = int rand($upper - $lower + 1) + $lower;
    my @arrA = ( 1 .. $ranpop );
	my @arrD = (1 .. $ranpop );

	my $limiter = 50;
	my @holda;
	my @holdb;
	while ($ranpop) 
	{
		my $genea = int rand ($limiter);
		push(@holda, $genea);	
		my $geneb = int rand ($limiter);
		push(@holdb, $geneb);
		$ranpop--;
	}
    my @arrB = ( @holda );
    my @arrC = ( @holdb );
    return \@arrA, \@arrB, \@arrC, \@arrD;
}
#this is also working
sub gener
{
	my ( $refToArrA, $refToArrB, $refToArrC, $refToArrD ) = @_;
	my @newind = @$refToArrA;
	my @newchroma = @$refToArrB;
	my @newchromb = @$refToArrC;
	my @newholder = @$refToArrD;
    for my $pop ( 1 .. $popCt )
    {
        $HoH{$counter} =
	{
		holder => [@newholder],
		individual  => [ @newind ],
		chromasome1 => [ @newchroma ],
		chromasome2 => [ @newchromb ],
	};
    }
}

sub births {
	my @holder =  @{$HoH{$counter}{'holder'}};
	my @ind = @{$HoH{$counter}{'individual'}};
	my @chroma = @{$HoH{$counter}{'chromasome1'}};
	my @chromb = @{$HoH{$counter}{'chromasome2'}};


	my $random = int rand $seed;	#randomly generate a number of seed that will be made in 1 generation			
	my $birth = int $random * $germrate; #only some of those seeds will germinate (survive)
	for (1 .. $birth) {
	
		srand;
		my $ender = $holder[$#holder];
		
		my $ranmom = (int rand $ender);
               #Picking the chroma and b from mom and dad to later recombine to make a seedling (offspring/new plant)
		my $moma = $chroma[$ranmom];
		my $momb = $chromb[$ranmom];

		my $randad = (int rand $ender);
		my $dada = $chroma[$randad];
		my $dadb = $chromb[$randad];
			
		$ender++;
		push @ind, $ender; #add new seedling to list
		push @holder, $ender; #this is explained below
		
#this creates a new seedling, with genetic material from mother and father plants

		my $selector = int(rand(2)) + 1;
		if ($selector == 1) {	
	             push @chroma, $dada;
                     push @chromb, $momb;
		} else {
		     push @chroma, $moma;
                     push @chromb, $dadb;
		}
	}
		
              #here I update the hash to keep everything straight.
                $HoH{$counter}{'holder'} = [@holder];
		$HoH{$counter}{'chromasome1'} = [@chroma];
		$HoH{$counter}{'chromasome2'} = [@chromb];
		$HoH{$counter}{'individual'} = [@ind];
}




sub death {
	my @holder = @{$HoH{$counter}{'holder'}};
	my @ind = @{$HoH{$counter}{'individual'}};
	my @chroma = @{$HoH{$counter}{'chromasome1'}};
	my @chromb = @{$HoH{$counter}{'chromasome2'}};

       #Randomly select a number of individuals to be removed from the population
	my $bottle = int rand $removal;
	

#select a list of individuals from the holder list...
#I added this list b/c the ind list tends to get out of order...
#and later in the code I needed a list in order...so I guess not sure.
	for ( 1 .. $bottle ) {
		($ranpop = splice(@holder, int rand(@holder), 1));
		push @killed, $ranpop;
#I now have a list of killed plants
	}
#This is picking the last value in the holder 
#to then create a new holder list 
#with the correct number of elements as plants that survive
	my $lastval = $holder[$#holder];
	@holder = (1 .. $lastval);
	

#Here I need to remove the killed plants from the chroma
#and chromb lists otherwise they are in the list and do not
#have a corresponding individual which was already removed above.
#ie. (the list shifts out of place).
#I need to maintain IND1-chroma1-chromb1, orentation in the  lists that I have.
#There maybe a better way to do this...but this is how I tried to attack the problem 

	while (@killed) {
		my $lastkill = $killed[$#killed];
		my $removed = $lastkill - 1;

		splice (@chroma, $removed, 1);
		splice (@chromb, $removed, 1);
		splice (@ind, $removed, 1);
#This is where the problem is
#the lists somehow get out of sync, and I am splicing in the 
#wrong place...

		pop @killed;
	}
	$HoH{$counter}{'holder'} = [@holder];
	$HoH{$counter}{'chromasome1'} = [@chroma];
	$HoH{$counter}{'chromasome2'} = [@chromb];
	$HoH{$counter}{'individual'} = [@ind];
}