/**
* Write single sequence to FastA file
*
* @param VIB\Bundle\BioBundle\Entity\DNA\Abstracts\Sequence $sequence
* @return integer Position of the sequence in the file
*/
protected function writeSequence(AbstractSequence $sequence, $saveMode = false)
{
$file = $saveMode ? $this->getFile() : $this->getWorkingFile();
if ($file == null) {
throw new IOException("Cannot open file for writing.");
}
if ($sequence == null || strlen($sequence->getSequence()) == 0) {
throw new FileFormatException("Sequence is empty.");
}
if (strlen($sequence->getName()) == 0) {
throw new FileFormatException("Sequence name is empty.");
}
$position = $file->ftell();
$file->fwrite(">");
$file->fwrite(rawurlencode($sequence->getName()));
if (strlen($sequence->getDescription()) > 0) {
$file->fwrite(' ' . $sequence->getDescription());
}
$file->fwrite("\n");
$file->fwrite(wordwrap($sequence->getSequence(), 75, "\n", true));
$file->fwrite("\n");
return $position;
}
