/**
* File.php
*
* Description of the file
* @author Robert Schmidt <*****@*****.**>
* @version 0.1
* @package wildpack
* @subpackage
*/
include_once '../src/PhProt.php';
$pp = new PhProt();
$pp->using('ui');
$arrSpectrum = array(array('mass' => 234.062, 'intensity' => 1.9), array('mass' => 243.459, 'intensity' => 3.1), array('mass' => 249.239, 'intensity' => 26.3), array('mass' => 251.291, 'intensity' => 1.6), array('mass' => 252.147, 'intensity' => 3.8), array('mass' => 254.193, 'intensity' => 4.4), array('mass' => 259.133, 'intensity' => 1.6), array('mass' => 262.261, 'intensity' => 13.5), array('mass' => 263.038, 'intensity' => 1.9), array('mass' => 266.08, 'intensity' => 1.9), array('mass' => 267.659, 'intensity' => 7.9), array('mass' => 269.093, 'intensity' => 4.9), array('mass' => 270.453, 'intensity' => 9.6), array('mass' => 274.432, 'intensity' => 2.7), array('mass' => 277.132, 'intensity' => 78.5), array('mass' => 278.218, 'intensity' => 8.699999999999999), array('mass' => 279.391, 'intensity' => 7.8), array('mass' => 284.293, 'intensity' => 2.2), array('mass' => 289.98, 'intensity' => 8.1), array('mass' => 293.161, 'intensity' => 4.9), array('mass' => 294.286, 'intensity' => 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1619.133, 'intensity' => 20.3), array('mass' => 1620.427, 'intensity' => 4.9), array('mass' => 1663.376, 'intensity' => 1.8), array('mass' => 1666.933, 'intensity' => 4.2), array('mass' => 1692.108, 'intensity' => 15.4), array('mass' => 1699.823, 'intensity' => 5.6), array('mass' => 1700.728, 'intensity' => 9.0), array('mass' => 1702.317, 'intensity' => 9.0), array('mass' => 1714.22, 'intensity' => 1.6), array('mass' => 1714.999, 'intensity' => 5.4), array('mass' => 1715.978, 'intensity' => 6.0));
$pep = new Peptide();
$pep->Sequence = 'HGYIGEFEYVDDHR';
$pep->NTerminus = 'H';
$pep->CTerminus = 'OH';
$strIon = 'b';
$ic = new IonCalculator(array('peptide' => $pep, 'maxcharge' => 2, 'weighttype' => 'monoisotopic', 'neutralloss' => array('H2O', 'NH3'), 'customtemplate' => '{ion}{index} +{charge} {flag}'));
//print('<h3>Testing</h3>');
//print('Peptide: '.$pep->Sequence.'<br />');
$arrB = $ic->calculateIon('b');
$arrY = $ic->calculateIon('y');
$arrAll = $arrB + $arrY;
$spec = new Spectrum(array('spectrum' => $arrSpectrum, 'peptide' => $pep));
$arrAnnot = $spec->annotateSpectrum($arrAll, 'mass', 'intensity', 'custom', 300, 'ppm');
$objSpecUi = new SpectrumUi(array('drawer' => new PChartDrawer(array('width' => 900, 'height' => 400, 'is3D' => false, 'colors' => array('#888', '#00f'), 'legend' => 'none')), 'spectrum' => $arrAnnot, 'annotationproperty' => 'custom'));
$objSpecUi->draw();
/* End of file file.php */
/* Location: ./path/file.php */
$pepmcr2 = strval($pep->getTheoreticalMCR('monoisotopic', 2));
$pepmcr3 = strval($pep->getTheoreticalMCR('monoisotopic', 3));
$pepmcr4 = strval($pep->getTheoreticalMCR('monoisotopic', 4));
if (!is_numeric($iccharge)) {
$iccharge = '2';
}
//-- IonCalculator --
$ic = new IonCalculator(array('peptide' => $pep, 'maxcharge' => intval($iccharge), 'weighttype' => 'monoisotopic', 'neutralloss' => array('H2O', 'NH3'), 'customtemplate' => '{ion}{index} {charge}+ {flag}'));
$arrIcRes = array();
foreach ($arrIons as $ion) {
$arrIcRes += $ic->calculateIon($ion);
}
//-- Spectrum --
$validSpec = false;
if ($spectrum !== '') {
$spec = new Spectrum();
$validSpec = $spec->setSpectrumByString($spectrum);
if ($validSpec === true) {
$annotSpec = $spec->annotateSpectrum($arrIcRes, 'mass', 'intensity', 'custom', 300, 'ppm');
}
}
//-- Ui Spectrum --
if ($validSpec === true) {
$specUi = new SpectrumUi(array('drawer' => new PChartDrawer(array('width' => 900, 'height' => 400, 'is3D' => false, 'colors' => array('#888', '#00f'), 'legend' => 'none')), 'tofile' => dirname(__FILE__) . '/media/spectrum.png', 'spectrum' => $annotSpec, 'annotationproperty' => 'custom'));
$specUi->draw();
$specimage = '<img src="media/spectrum.png">';
}
}
}
?>
