Creating a genetics calculator in PHP, issues with wrong results - php

Question

I'm trying to make a genetic calculator. I have the following code:
<?php
$gene1 = 'BA';
$geneA = array();
$i = 0;
while ($i < strlen($gene1)) $geneA[] = substr($gene1,$i++,2);
$gene2 = 'MSBA';
$geneB = array();
$i = 0;
while ($i < strlen($gene2)) $geneB[] = substr($gene2,$i++,2);
$possabilities = array();
foreach ($geneA as $A) {
foreach ($geneB as $B) {
if ($A === strtoupper($A)) $possabilities[] = $A.$B;
else {
if ($B === strtoupper($B)) $possabilities[] = $B.$A;
else $possabilities[] = $A.$B;
}
}
}
print_r($possabilities);
?>
Which works to a degree, it pairs the genes in the array, however it isn't working properly. This pairing should just return BABA and MSBA. Instead it returns this:
Array ( [0] => BAMS [1] => BASB [2] => BABA [3] => BAA [4] => AMS [5] => ASB [6] => ABA [7] => AA )
Which isn't exactly ideal for my project. I thought a better idea would be to comma separate the genes like this $gene1 = 'BA'; and $gene2 = 'MS,BA'; and run a loop combining each gene that way, but i am unsure on how to do this properly. Can anyone shed some light on the idea at all?

Answer 1

I hope I'm right in assuming that
Genes are always made up of two pairs (MS, but not "M" and "S")
Each member of $geneA should be matched with each member of $geneB
Part 1: Resolving the error
In this case your algorithm for splitting has a serious flaw: It always progresses just for one step in the original string ($gene1 and $gene2)
function getGeneArray($geneString) {
// check the argument for fitting your needs!
if ( strlen($geneString) % 2 == 1 ) {
die('Supplied geneString is not made of pairs!'); // better not die - handle errors according to your application methodology
}
// add additional error-catching (there are only certain possible base-pairs, if something else is found you should reject the string
$genes = array();
$i = 0;
while ( $i < strlen($geneString) )
{
$genes[] = substr($geneString, $i, 2);
$i += 2; // Here is your mistake, you just $i++
}
return $genes;
}
With this little function you a) reduce duplicates in your code and b) get a determined outcome (no wrong genes)
Part 2: Making code document itself
Looking at your code it becomes clear, that uppercase-gene-pairs must come befor lowercase pairs, I try to communicate that with the code by using an extra function with a clear name.
function combinePairs($A, $B) {
// uppercase genes build the string first, which means B must be uppercase to come first and A cant be uppercase
if (strtoupper($A) !== $A && strotoupper($B) === $B) {
return $B.$A;
}
return $A.$B;
}
Part 3: Plugging it together
$geneA = getGeneArray($gene1);
$geneB = getGeneArray($gene2);
$possibilities = array();
foreach ($geneA as $A) {
foreach ($geneB as $B) {
$possibilities[] = combinePairs($A, $B);
}
}
print_r($possibilities);
Final Note
As a programmer you want to cater the needs of your client or input source, so of course you can split your genes with commas. Try to use the format most usable for your application and client input. In this case you could easily optain an array by using explode() (explode in the manual)