#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 see
+d that will be made in 1 generation            
    my $birth = int $random * $germrate; #only some of those seeds wil
+l 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 rec
+ombine 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 fa
+ther 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 tha
+t I have.
#There maybe a better way to do this...but this is how I tried to atta
+ck 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];
}
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