/**
* Set sequence
*
* @param VIB\Bundle\BioBundle\Entity\DNA\Abstracts\Sequence $sequence
* @param boolean $recurse
*/
public function setSequence(Sequence $sequence, $recurse = true)
{
if ($recurse === true) {
if ($sequence != null) {
$sequence->addFeature($this, false);
} elseif ($this->sequence != null) {
$this->sequence->removeFeature($this, false);
}
}
$this->sequence = $sequence;
}
/**
* Parse the string containing FastA header
*
* @param string $line
* @param VIB\Bundle\BioBundle\Entity\DNA\Abstracts\Sequence $sequence
*/
protected function parseFastAHeader($line, AbstractSequence $sequence)
{
$match = array();
if (preg_match("/^>(\\S+)(.*)\$/", $line, $match) === 1) {
$name = rawurldecode(trim($match[1]));
if (strlen($name) > 0) {
$sequence->setName($name);
} else {
throw new FileFormatException("Sequence name is empty.");
}
$description = trim($match[2]);
if (strlen($description) > 0) {
$sequence->setDescription($description);
}
}
}
