# Yee-Shiuan Chen 

$pop_size = @ARGV[0];					#takes in population size
$max_gen = @ARGV[1];					#takes in number of generations
$fitness_value = @ARGV[2];				#takes in fitness value 

$answer = 0;						#this variable carries the percentage fixation

for ($t = 0; $t < 100; $t++) {				#for 100 trails

	$individual[2] = 0;				#individual 2 is the number of homozygous mutant(bio5488)
	$individual[1] = 1;				#individual 1 is the number of heterozygotes(start as one)
	$individual[0] = $pop_size - 1;			#individual 0 is the number of homozygous wild-types(- the het)

	for ($j = 0; $j < $max_gen; $j++) {		#counts the number of generations
		distribute();				#call "distribute" function to calculate the probabilities
		make_next_G();				#call "make_next_G" to assign the next generation

		if ($individual[2] == $pop_size) {	#if homozygous mutants dominate the population			
			$answer++;			#add one to answer
			last;				#leave the loop 'cause there is no point
		}
		if (($individual[1]+$individual[2]) == 0 ) {		#if hets and homozygous mutants disappear from population
			last;				#leave the loop 'cause there is no point
		}
	}
}
print "$answer%\n";					#print the answer


sub distribute {							#defines the subfunction
	$density[0] = $individual[0] * 1;				#this defines the number range for homo wt
	$density[1] = $individual[1] * $fitness_value + $density[0]; 	#number range for het if dominant	
	#$density[1] = $individual[1] + $density[0]; 			#number range for het if recessive
	$density[2] = $individual[2] * $fitness_value + $density[1];	#number range for homo mutant
}

sub make_next_G {						#defines sub function
	for ($i = 0; $i < 3; $i++) {				#for each types of individual
		$individual[$i] = 0;				#make everything zero for the new generation
	}
	for ($i = 0; $i < $pop_size; $i++) {			#for the entire population
		$individual[(sample() + sample())]++;		#for each individual call "sample" twice for each allele
	}							#if both allele is wt, then 0+0=0 and add 1 to $indivi[0]
}								#if het, then 0+1 or 1+0 = 1 and add 1 to $indivi[1]
								#if homo mutant then 1+1=2 and add 1 to $indivi[2]
	
sub sample {								#defines sub function
	$random_number = int rand ($density[2]);			#piack a random integer any where from 1 to max
	for ($a = 0; $a < 3; $a++) {					#for three types of genotypes
		if ($random_number < $density[$a]) {			#if number less than a particular type (0,1 or 2)
			$output = int ($a / 2);				#if 0 then 0/2=0 and output 0 
									#if 2 then 2/2=1 and output 1
			if ($a == 1) {					#if 1 then it's a het and have to pick between
				$output = int rand (2);			#0 and 1 again to see if mutant or wt
			}
			return ($output);				#return the output
			last;						#leave the loop
		}
	}
}