if ($nterminus !== '') {
$ntermmass = strval($pep->getNTerminusMass('monoisotopic'));
}
$mec = $pep->getMec();
$pepmass = strval($pep->getMass('monoisotopic'));
$pepmcr2 = strval($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">';
/**
* 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' => 152.5), array('mass' => 295.023, 'intensity' => 33.8), array('mass' => 295.863, 'intensity' => 4.8), array('mass' => 297.401, 'intensity' => 5.5), array('mass' => 298.401, 'intensity' => 2.9), array('mass' => 300.113, 'intensity' => 2.0), array('mass' => 304.182, 'intensity' => 2.7), array('mass' => 305.251, 'intensity' => 13.7), array('mass' => 306.308, 'intensity' => 17.8), array('mass' => 310.111, 'intensity' => 7.6), array('mass' => 312.218, 'intensity' => 1151.9), array('mass' => 313.3, 'intensity' => 166.3), array('mass' => 315.222, 'intensity' => 9.199999999999999), array('mass' => 320.381, 'intensity' => 5.3), array('mass' => 322.283, 'intensity' => 79.8), array('mass' => 323.202, 'intensity' => 15.9), array('mass' => 324.446, 'intensity' => 11.2), array('mass' => 327.342, 'intensity' => 13.2), array('mass' => 331.21, 'intensity' => 2.3), array('mass' => 332.192, 'intensity' => 3.2), array('mass' => 333.95, 'intensity' => 9.300000000000001), array('mass' => 336.107, 'intensity' => 8.699999999999999), array('mass' => 337.332, 'intensity' => 3.9), array('mass' => 340.173, 'intensity' => 502.5), array('mass' => 341.035, 'intensity' => 61.3), array('mass' => 342.086, 'intensity' => 2.8), array('mass' => 342.927, 'intensity' => 6.7), array('mass' => 346.16, 'intensity' => 4.9), array('mass' => 348.198, 'intensity' => 23.0), array('mass' => 348.819, 'intensity' => 1.6), array('mass' => 349.803, 'intensity' => 4.5), array('mass' => 350.411, 'intensity' => 8.1), array('mass' => 351.387, 'intensity' => 1.6), array('mass' => 353.816, 'intensity' => 6.5), array('mass' => 358.171, 'intensity' => 146.5), array('mass' => 359.166, 'intensity' => 8.5), array('mass' => 361.122, 'intensity' => 17.8), array('mass' => 362.214, 'intensity' => 3.1), array('mass' => 363.338, 'intensity' => 19.2), array('mass' => 365.312, 'intensity' => 4.0), array('mass' => 367.228, 'intensity' => 4.6), array('mass' => 369.162, 'intensity' => 5.8), array('mass' => 373.401, 'intensity' => 6.5), array('mass' => 375.162, 'intensity' => 6.5), array('mass' => 376.34, 'intensity' => 16.7), array('mass' => 377.112, 'intensity' => 5.1), array('mass' => 379.065, 'intensity' => 9.699999999999999), array('mass' => 381.129, 'intensity' => 4.1), array('mass' => 382.429, 'intensity' => 5.6), array('mass' => 383.113, 'intensity' => 5.9), array('mass' => 385.41, 'intensity' => 11.5), array('mass' => 386.297, 'intensity' => 3.9), array('mass' => 387.353, 'intensity' => 3.8), array('mass' => 389.17, 'intensity' => 2.1), array('mass' => 390.323, 'intensity' => 8.9), array('mass' => 391.181, 'intensity' => 11.1), array('mass' => 392.053, 'intensity' => 1.5), array('mass' => 393.311, 'intensity' => 14.6), array('mass' => 394.149, 'intensity' => 6.4), array('mass' => 397.196, 'intensity' => 19.8), array('mass' => 399.244, 'intensity' => 3.3), array('mass' => 405.307, 'intensity' => 3.9), array('mass' => 406.55, 'intensity' => 5.7), array('mass' => 407.352, 'intensity' => 7.4), array('mass' => 409.262, 'intensity' => 37.0), array('mass' => 410.32, 'intensity' => 6.6), array('mass' => 411.627, 'intensity' => 5.4), array('mass' => 412.309, 'intensity' => 17.4), array('mass' => 413.368, 'intensity' => 11.1), array('mass' => 414.2, 'intensity' => 2.8), array('mass' => 415.313, 'intensity' => 3.0), array('mass' => 418.488, 'intensity' => 6.0), array('mass' => 419.328, 'intensity' => 7.8), array('mass' => 421.614, 'intensity' => 9.800000000000001), array('mass' => 425.392, 'intensity' => 11.7), array('mass' => 426.74, 'intensity' => 19.5), array('mass' => 427.364, 'intensity' => 206.3), array('mass' => 428.485, 'intensity' => 56.1), array('mass' => 429.327, 'intensity' => 6.4), array('mass' => 430.636, 'intensity' => 6.7), array('mass' => 432.209, 'intensity' => 5.3), array('mass' => 434.078, 'intensity' => 1.5), array('mass' => 435.363, 'intensity' => 4.0), array('mass' => 436.381, 'intensity' => 3.3), array('mass' => 437.608, 'intensity' => 2.1), array('mass' => 438.417, 'intensity' => 2.7), array('mass' => 439.519, 'intensity' => 9.300000000000001), array('mass' => 441.231, 'intensity' => 4.1), array('mass' => 443.381, 'intensity' => 56.2), array('mass' => 444.746, 'intensity' => 16.5), array('mass' => 446.282, 'intensity' => 12.7), array('mass' => 447.21, 'intensity' => 3.7), array('mass' => 448.222, 'intensity' => 19.7), array('mass' => 449.193, 'intensity' => 4.0), array('mass' => 450.3, 'intensity' => 5.3), array('mass' => 451.459, 'intensity' => 3.9), array('mass' => 452.183, 'intensity' => 1.6), array('mass' => 453.253, 'intensity' => 17.9), array('mass' => 455.235, 'intensity' => 5.6), array('mass' => 456.493, 'intensity' => 5.8), array('mass' => 459.302, 'intensity' => 16.3), array('mass' => 462.12, 'intensity' => 6.8), array('mass' => 463.173, 'intensity' => 10.7), array('mass' => 464.114, 'intensity' => 8.199999999999999), array('mass' => 465.247, 'intensity' => 7.4), array('mass' => 466.432, 'intensity' => 9.800000000000001), array('mass' => 467.419, 'intensity' => 15.9), array('mass' => 469.305, 'intensity' => 11.9), array('mass' => 471.28, 'intensity' => 97.40000000000001), array('mass' => 472.343, 'intensity' => 47.7), array('mass' => 473.982, 'intensity' => 5.5), array('mass' => 475.333, 'intensity' => 10.5), array('mass' => 475.991, 'intensity' => 25.9), array('mass' => 478.212, 'intensity' => 3.5), array('mass' => 479.22, 'intensity' => 4.9), array('mass' => 480.099, 'intensity' => 25.2), array('mass' => 482.4, 'intensity' => 2.8), array('mass' => 483.515, 'intensity' => 5.2), array('mass' => 486.711, 'intensity' => 8.300000000000001), array('mass' => 487.735, 'intensity' => 3.7), array('mass' => 491.261, 'intensity' => 10.1), array('mass' => 492.284, 'intensity' => 8.800000000000001), array('mass' => 493.37, 'intensity' => 20.3), array('mass' => 496.46, 'intensity' => 15.8), array('mass' => 497.362, 'intensity' => 4.7), array('mass' => 498.86, 'intensity' => 4.2), array('mass' => 499.492, 'intensity' => 3.9), array('mass' => 500.289, 'intensity' => 8.6), array('mass' => 501.428, 'intensity' => 5.2), array('mass' => 502.328, 'intensity' => 30.3), array('mass' => 503.293, 'intensity' => 4.5), array('mass' => 506.101, 'intensity' => 18.9), array('mass' => 507.401, 'intensity' => 9.5), array('mass' => 509.35, 'intensity' => 5.4), array('mass' => 510.373, 'intensity' => 46.2), array('mass' => 511.458, 'intensity' => 3.6), array('mass' => 513.4299999999999, 'intensity' => 12.1), array('mass' => 515.086, 'intensity' => 8.199999999999999), array('mass' => 516.245, 'intensity' => 9.9), array('mass' => 517.184, 'intensity' => 19.3), array('mass' => 518.283, 'intensity' => 24.7), array('mass' => 519.314, 'intensity' => 1.6), array('mass' => 520.3869999999999, 'intensity' => 13.3), array('mass' => 523.587, 'intensity' => 15.6), array('mass' => 524.41, 'intensity' => 14.1), array('mass' => 525.329, 'intensity' => 29.4), array('mass' => 526.398, 'intensity' => 21.6), array('mass' => 528.417, 'intensity' => 69.5), array('mass' => 529.529, 'intensity' => 25.0), array('mass' => 531.0650000000001, 'intensity' => 8.800000000000001), array('mass' => 532.309, 'intensity' => 4.9), array('mass' => 533.865, 'intensity' => 21.6), array('mass' => 536.172, 'intensity' => 13.0), array('mass' => 537.2, 'intensity' => 8.699999999999999), array('mass' => 538.641, 'intensity' => 4.1), array('mass' => 539.4160000000001, 'intensity' => 6.0), array('mass' => 541.2, 'intensity' => 14.7), array('mass' => 542.346, 'intensity' => 123.3), array('mass' => 543.405, 'intensity' => 17.0), array('mass' => 544.35, 'intensity' => 4.7), array('mass' => 544.981, 'intensity' => 14.8), array('mass' => 545.832, 'intensity' => 19.0), array('mass' => 546.651, 'intensity' => 14.3), array('mass' => 548.96, 'intensity' => 3.7), array('mass' => 550.956, 'intensity' => 19.9), array('mass' => 552.159, 'intensity' => 14.0), array('mass' => 553.4160000000001, 'intensity' => 16.8), array('mass' => 555.569, 'intensity' => 8.4), array('mass' => 558.004, 'intensity' => 1.8), array('mass' => 559.724, 'intensity' => 2.6), array('mass' => 560.373, 'intensity' => 5.8), array('mass' => 561.925, 'intensity' => 4.3), array('mass' => 563.004, 'intensity' => 6.1), array('mass' => 564.296, 'intensity' => 8.5), array('mass' => 565.278, 'intensity' => 20.3), array('mass' => 565.896, 'intensity' => 8.699999999999999), array('mass' => 567.2, 'intensity' => 5.4), array('mass' => 568.486, 'intensity' => 9.0), array('mass' => 569.466, 'intensity' => 26.0), array('mass' => 570.332, 'intensity' => 15.9), array('mass' => 571.255, 'intensity' => 9.4), array('mass' => 572.298, 'intensity' => 7.1), array('mass' => 573.485, 'intensity' => 14.3), array('mass' => 574.4059999999999, 'intensity' => 5.7), array('mass' => 575.36, 'intensity' => 7.1), array('mass' => 576.931, 'intensity' => 4.0), array('mass' => 578.388, 'intensity' => 11.6), array('mass' => 579.309, 'intensity' => 8.300000000000001), array('mass' => 581.404, 'intensity' => 18.1), array('mass' => 582.448, 'intensity' => 22.4), array('mass' => 585.499, 'intensity' => 11.2), array('mass' => 586.271, 'intensity' => 4.0), array('mass' => 587.365, 'intensity' => 4.5), array('mass' => 589.3049999999999, 'intensity' => 30.0), array('mass' => 590.165, 'intensity' => 1.9), array('mass' => 591.125, 'intensity' => 3.0), array('mass' => 592.333, 'intensity' => 9.699999999999999), array('mass' => 593.228, 'intensity' => 24.3), array('mass' => 595.295, 'intensity' => 11.8), array('mass' => 596.472, 'intensity' => 28.0), array('mass' => 597.3869999999999, 'intensity' => 29.9), array('mass' => 598.329, 'intensity' => 6.5), array('mass' => 598.985, 'intensity' => 7.0), array('mass' => 600.448, 'intensity' => 1.5), array('mass' => 602.351, 'intensity' => 9.5), array('mass' => 604.212, 'intensity' => 21.8), array('mass' => 605.617, 'intensity' => 38.2), array('mass' => 606.561, 'intensity' => 20.4), array('mass' => 607.729, 'intensity' => 11.6), array('mass' => 609.284, 'intensity' => 13.2), array('mass' => 610.306, 'intensity' => 15.4), array('mass' => 611.423, 'intensity' => 18.4), array('mass' => 612.955, 'intensity' => 8.800000000000001), array('mass' => 614.652, 'intensity' => 2.2), array('mass' => 615.9930000000001, 'intensity' => 12.0), array('mass' => 616.98, 'intensity' => 25.0), array('mass' => 619.405, 'intensity' => 21.2), array('mass' => 620.191, 'intensity' => 12.7), array('mass' => 621.643, 'intensity' => 61.9), array('mass' => 622.401, 'intensity' => 8.699999999999999), array('mass' => 623.418, 'intensity' => 39.6), array('mass' => 624.653, 'intensity' => 30.7), array('mass' => 625.567, 'intensity' => 10.2), array('mass' => 626.347, 'intensity' => 19.8), array('mass' => 627.515, 'intensity' => 22.0), array('mass' => 628.136, 'intensity' => 3.6), array('mass' => 629.282, 'intensity' => 29.6), array('mass' => 629.966, 'intensity' => 18.8), array('mass' => 631.157, 'intensity' => 35.2), array('mass' => 632.1319999999999, 'intensity' => 23.9), array('mass' => 633.8099999999999, 'intensity' => 36.0), array('mass' => 634.737, 'intensity' => 60.9), array('mass' => 635.372, 'intensity' => 12.9), array('mass' => 636.582, 'intensity' => 13.6), array('mass' => 639.447, 'intensity' => 99.40000000000001), array('mass' => 640.582, 'intensity' => 32.0), array('mass' => 641.3579999999999, 'intensity' => 131.7), array('mass' => 642.746, 'intensity' => 72.90000000000001), array('mass' => 643.706, 'intensity' => 16.6), array('mass' => 646.05, 'intensity' => 6.5), array('mass' => 647.394, 'intensity' => 3.6), array('mass' => 649.373, 'intensity' => 10.3), array('mass' => 650.2910000000001, 'intensity' => 7.3), array('mass' => 651.481, 'intensity' => 3.4), array('mass' => 652.083, 'intensity' => 19.0), array('mass' => 653.328, 'intensity' => 9.0), array('mass' => 654.006, 'intensity' => 19.7), array('mass' => 654.784, 'intensity' => 9.300000000000001), array('mass' => 655.809, 'intensity' => 12.1), array('mass' => 656.629, 'intensity' 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array('mass' => 680.378, 'intensity' => 10.7), array('mass' => 681.617, 'intensity' => 65.0), array('mass' => 682.447, 'intensity' => 50.0), array('mass' => 683.628, 'intensity' => 8.9), array('mass' => 684.556, 'intensity' => 31.5), array('mass' => 686.523, 'intensity' => 15.5), array('mass' => 687.544, 'intensity' => 13.5), array('mass' => 688.49, 'intensity' => 26.5), array('mass' => 690.769, 'intensity' => 34.7), array('mass' => 691.447, 'intensity' => 10.3), array('mass' => 692.5069999999999, 'intensity' => 7.9), array('mass' => 693.237, 'intensity' => 14.8), array('mass' => 694.211, 'intensity' => 25.5), array('mass' => 695.385, 'intensity' => 7.2), array('mass' => 696.223, 'intensity' => 17.2), array('mass' => 698.546, 'intensity' => 48.0), array('mass' => 700.364, 'intensity' => 25.8), array('mass' => 702.42, 'intensity' => 32.8), array('mass' => 704.33, 'intensity' => 18.6), array('mass' => 705.1420000000001, 'intensity' => 21.1), array('mass' => 706.227, 'intensity' => 3.7), array('mass' => 707.426, 'intensity' => 17.0), array('mass' => 709.647, 'intensity' => 35.2), array('mass' => 711.5700000000001, 'intensity' => 25.9), array('mass' => 712.398, 'intensity' => 7.1), array('mass' => 713.465, 'intensity' => 7.9), array('mass' => 714.318, 'intensity' => 9.5), array('mass' => 715.643, 'intensity' => 6.9), array('mass' => 717.5119999999999, 'intensity' => 32.4), array('mass' => 718.225, 'intensity' => 2.2), array('mass' => 719.328, 'intensity' => 5.9), array('mass' => 720.345, 'intensity' => 8.699999999999999), array('mass' => 721.3630000000001, 'intensity' => 2.1), array('mass' => 722.529, 'intensity' => 32.8), array('mass' => 723.379, 'intensity' => 24.2), array('mass' => 724.349, 'intensity' => 7.1), array('mass' => 725.716, 'intensity' => 11.0), array('mass' => 726.477, 'intensity' => 3.5), array('mass' => 727.171, 'intensity' => 7.3), array('mass' => 728.668, 'intensity' => 59.8), array('mass' => 729.934, 'intensity' => 15.7), array('mass' => 730.687, 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array('mass' => 1350.912, 'intensity' => 7.2), array('mass' => 1353.366, 'intensity' => 4.0), array('mass' => 1355.359, 'intensity' => 19.8), array('mass' => 1361.403, 'intensity' => 92.90000000000001), array('mass' => 1362.696, 'intensity' => 80.0), array('mass' => 1363.598, 'intensity' => 31.6), array('mass' => 1369.293, 'intensity' => 8.9), array('mass' => 1371.053, 'intensity' => 15.7), array('mass' => 1375.918, 'intensity' => 4.5), array('mass' => 1377.472, 'intensity' => 2.4), array('mass' => 1379.068, 'intensity' => 47.5), array('mass' => 1379.67, 'intensity' => 311.7), array('mass' => 1380.621, 'intensity' => 202.1), array('mass' => 1381.592, 'intensity' => 83.2), array('mass' => 1389.477, 'intensity' => 7.8), array('mass' => 1390.559, 'intensity' => 8.4), array('mass' => 1391.394, 'intensity' => 7.0), array('mass' => 1398.442, 'intensity' => 22.8), array('mass' => 1403.41, 'intensity' => 7.9), array('mass' => 1404.081, 'intensity' => 7.7), array('mass' => 1407.549, 'intensity' 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254.5), array('mass' => 1543.664, 'intensity' => 202.1), array('mass' => 1544.755, 'intensity' => 77.40000000000001), array('mass' => 1545.566, 'intensity' => 31.3), array('mass' => 1546.698, 'intensity' => 2.5), array('mass' => 1551.909, 'intensity' => 3.9), array('mass' => 1561.668, 'intensity' => 11.5), array('mass' => 1562.745, 'intensity' => 144.8), array('mass' => 1563.755, 'intensity' => 105.8), array('mass' => 1564.578, 'intensity' => 55.2), array('mass' => 1572.796, 'intensity' => 5.2), array('mass' => 1581.606, 'intensity' => 17.0), array('mass' => 1582.585, 'intensity' => 13.2), array('mass' => 1591.011, 'intensity' => 5.0), array('mass' => 1596.411, 'intensity' => 4.9), array('mass' => 1599.802, 'intensity' => 80.8), array('mass' => 1600.574, 'intensity' => 165.1), array('mass' => 1601.594, 'intensity' => 20.4), array('mass' => 1603.747, 'intensity' => 7.4), array('mass' => 1604.646, 'intensity' => 18.3), array('mass' => 1609.55, 'intensity' => 4.1), array('mass' => 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 */
include_once '../PhProt.php';
$pp = new PhProt();
$pp->using('base');
$pp->using('peptide');
$pep = new ModifiedPeptide();
$pep->Sequence = 'KDEPAEESDGDLGFGLFD';
$pep->NTerminus = 'H';
$pep->CTerminus = 'OH';
$pep->addModification(array('accession' => 21, 'position' => 7));
$strIon = 'b';
$ic = new IonCalculator(array('peptide' => $pep, 'maxcharge' => 3, 'weighttype' => 'monoisotopic', 'neutralloss' => array('H2O', 'NH3'), 'customtemplate' => '{ion}{index}{charge} {flag}'));
print '<h3>Testing</h3>';
print 'Peptide: ' . $pep->Sequence . '<br />';
print '<h3>Result for ' . $strIon . '-Ions</h3>';
print '<table style="border: null">';
$arrResult = $ic->calculateIon($strIon);
for ($i = 0; $i < count($arrResult); $i++) {
print '<tr><td>' . strval($arrResult[$i]['mass']) . '</td><td>' . $arrResult[$i]['ion'] . strval($arrResult[$i]['index']) . '</td><td>' . strval($arrResult[$i]['charge']) . '</td><td>' . $arrResult[$i]['flag'] . '</td><td>' . $arrResult[$i]['custom'] . '</td></tr>';
}
print '</table>';
print '<h3>Testing</h3>';
print 'Peptide: ' . $pep->Sequence . '<br />';
$strIon = 'y';
print '<h3>Result for ' . $strIon . '-Ions</h3>';
print '<table style="border: null">';
$arrResult = $ic->calculateIon($strIon);
for ($i = 0; $i < count($arrResult); $i++) {
print '<tr><td>' . strval($arrResult[$i]['mass']) . '</td><td>' . $arrResult[$i]['ion'] . strval($arrResult[$i]['index']) . '</td><td>' . strval($arrResult[$i]['charge']) . '</td><td>' . $arrResult[$i]['flag'] . '</td><td>' . $arrResult[$i]['custom'] . '</td></tr>';
}
print '</table>';
/* End of file CustomTestsIonCalc.php */