/**
* Retrieves the index mass including all modifications
* @param string $weighttype The weighttype to use for masses
* @param int $index The index of the amino acid in sequence
* @return float The total mass of the amino acid including all modifications
*/
public function getIndexMass($weighttype, $index)
{
$loc = basename(__FILE__) . '/' . __METHOD__;
$arrModifications;
$dblAddMass = 0;
$dblMass = 0;
$objMod = null;
$strAa = '';
if (!isset($this->Sequence) || $this->Sequence === '') {
$this->toLog('error', $loc, 'Sequence not set', 'Failed to get modification for index. Sequence not set yet.', '');
return;
}
if ($index >= strlen($this->Sequence)) {
$this->toLog('error', $loc, 'Index out of bounds', 'Specified index is out of sequence bounds.', '');
return -1;
}
$strAa = substr($this->Sequence, $index, 1);
$dblMass = parent::getIndexMass($weighttype, $index);
$arrModifications = $this->getIndexModifications($index, $weighttype);
for ($i = 0, $j = count($arrModifications); $i < $j; $i++) {
$objMod = $arrModifications[$i];
$dblAddMass += $this->getModificationMass($objMod['accession'], $strAa, $index, $weighttype);
}
return $dblMass + $dblAddMass;
}
