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kmer_similarity.php
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kmer_similarity.php
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<?php
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
/**
* Description of kmer_similarity
*
* @author jrobertson
*/
class kmer_similarity
{
var $alphabet = "abcdefghijklmnopqrstuvwxyz123456789.() ";
var $size = 2;
var $counts = array();
var $num_combinations = 0;
function __construct()
{
$this->calcArraySize();
$this->initCounts();
}
function getWord($pos)
{
$len = strlen($this->getAlphabet());
$alphabet = $this->getAlphabet();
$size = $this->size;
$word='';
for($i=0; $i < $size; $i++)
{
$r = $pos % $len;
$word.=$alphabet[$r];
$pos = intval($pos/$len);
}
return strrev($word);
}
function calc_position($word)
{
$len = strlen($word);
$pos = array();
$alphabet = $this->getAlphabet();
$alphaSize = strlen($alphabet);
$size = $this->size-1;
for($i=0; $i < $len; $i++)
{
$char = $word[$i];
$pos[] = strpos($alphabet,$char);
}
$value = $pos[0]* pow($alphaSize,$size);
$count = count($pos);
for($i=1; $i<$count; $i++)
{
$size--;
$value = $value + $pos[$i]* pow($alphaSize,$size);
}
return $value;
}
function calcArraySize()
{
$this->num_combinations = pow(strlen($this->getAlphabet()),$this->getSize());
}
function initCounts()
{
$this->counts = array_fill(0, $this->num_combinations, 0);
}
function setAlphabet($alpha)
{
$this->alphabet = $alpha;
}
function getAlphabet()
{
return $this->alphabet;
}
function getSize()
{
return $this->size;
}
function setSize($s)
{
$this->size = $s;
}
function setKcount($word,$count)
{
$pos = $this->calc_position($word);
$this->dictionary[$pos] = $count;
}
function getKcount($word)
{
return $this->counts[$pos];
}
}