Compare one by one characters from a mysql db with php - php

Question

I'm trying to compare in my DB a row with another character by character and give as a result the id which best fits the given data. For example I have on my DB the user David with a AAA sequence and I want to compare it with one I give in which is a ABA so I'd like to receive a percentage (66.6% in this case) of match,
I have done until here but don't know how to go on:
$uname = $_POST['sequence'];
$query = "SELECT name FROM dna WHERE sequence = '$uname'";
$result = mysql_query($query);
while($row = mysql_fetch_array($result))
{
echo $row['name'];
}

Answer 1

In order to get the similarity in percent, you might use the PHP function similar_text().
The two strings are compared and the similarity percentage is returned, if the third parameter is passed to the function.
$string_1 = 'AAA';
$string_2 = 'ABA';
similar_text($string_1, $string_2, $percent);
echo $percent;
// 66.666666666667
The database part is a bit more work. A very basic implementation could look like this.
Keep in mind, that the real problem is, that you compare a string against 1 million rows.
In general: one wouldn't do that, because instead of chars, there a bits. And to compare bits, you would use simply bit-shifts. Anyway...
Here, when working with chars/strings, a rolling row requests or limited query could help, too.
That would mean, that you ask the db for chunks of let's say 500 rows and do the calc work.
It depends on the number of rows and the memory use of the dataset.
// incomming via user input
$string_1 = $_POST['sequence'];
// temporary var to store the highest similarity percentage and it's row_id
$bestValue = array('row_id' => 0, 'similarity' => '0');
// iterate over the "total number of rows" in the database
foreach($rows as $id => $row)
{
// get a new string_2 from db
$string_2 = $row['name'];
// calculate similarity
similar_text($string_1, $string_2, $percent);
// if calculated similarity is higher, then update the "best" value
if($percent > $bestValue['similarity']) {
$bestValue = array('row_id' = $id, 'similiarity' = $percent);
}
}
var_dump($bestValue);
After all db rows are processed, bestValue will containg the highest percentage and it's row id.
You can do all kinds of things here, for instance:
switch from first match update (<) to last match update (<=)
stop iteration on first match
store row_id's, which have the same similarity (multi row match)
if you don't need multi row match, you might drop the array and use two vars for row and percent
proper error handling, escaping, mysqli usage
Be warned: this isn't the most efficient approach, especially not, when working with large datasets. If you need this on a level, which is not hobby or homework, then simply pull a tool, which is optimized for this job, like EMBOSS (http://emboss.sourceforge.net/).