ChemistryTest.cpp File Reference

#include "pwiz/utility/misc/unit.hpp"
#include "Chemistry.hpp"
#include "Ion.hpp"
#include "pwiz/utility/math/round.hpp"
#include <cstring>
#include "pwiz/utility/misc/Std.hpp"
#include "boost/thread/thread.hpp"
#include "boost/thread/barrier.hpp"

Go to the source code of this file.

Classes
struct	TestFormula

Functions
void	testMassAbundance ()
void	testFormula ()
void	testFormulaOperations ()
void	testInfo ()
void	infoExample ()
void	testPolysiloxane ()
void	testThreadSafetyWorker (boost::barrier *testBarrier)
void	testThreadSafety (const int &testThreadCount)
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0
const TestFormula	testFormulaData []
const int	testFormulaDataSize = sizeof(testFormulaData)/sizeof(TestFormula)

---

Function Documentation

void testMassAbundance

(

)

Definition at line 41 of file ChemistryTest.cpp.

References pwiz::chemistry::MassAbundance::abundance, and unit_assert.

Referenced by testThreadSafetyWorker().

{
    MassAbundance ma(1, 2);
    MassAbundance ma2(1, 4);
    unit_assert(ma != ma2);
    ma2.abundance = 2;
    unit_assert(ma == ma2);
}

void testFormula

(

)

Definition at line 71 of file ChemistryTest.cpp.

References TestFormula::avgMass, C, pwiz::chemistry::Formula::data(), TestFormula::formula, pwiz::chemistry::Formula::molecularWeight(), pwiz::chemistry::Formula::monoisotopicMass(), TestFormula::monoMass, os_, testFormulaData, testFormulaDataSize, U, unit_assert, and unit_assert_equal.

Referenced by testThreadSafetyWorker().

{
    for (int i=0; i < testFormulaDataSize; ++i)
    {
        const TestFormula& testFormula = testFormulaData[i];
        Formula formula(testFormula.formula);

        const double EPSILON = 0.001;

        unit_assert_equal(formula.monoisotopicMass(), testFormula.monoMass, EPSILON);
        unit_assert_equal(formula.molecularWeight(), testFormula.avgMass, EPSILON);
        if (os_) *os_ << formula << " " << formula.monoisotopicMass() << " " << formula.molecularWeight() << endl;

        formula[Element::C] += 2;
        unit_assert_equal(formula.monoisotopicMass(), testFormula.monoMass+24, EPSILON);
        unit_assert_equal(formula.molecularWeight(), testFormula.avgMass+12.0107*2, EPSILON);
        if (os_) *os_ << formula << " " << formula.monoisotopicMass() << " " << formula.molecularWeight() << endl;

        //const Formula& constFormula = formula;
        //constFormula[Element::C] = 1; // this won't compile, by design 

        // test copy constructor
        Formula formula2 = formula;
        formula2[Element::C] -= 2;
        unit_assert_equal(formula.monoisotopicMass(), testFormula.monoMass+24, EPSILON);
        unit_assert_equal(formula2.monoisotopicMass(), testFormula.monoMass, EPSILON);
        if (os_) *os_ << "formula: " << formula << endl;
        if (os_) *os_ << "formula2: " << formula2 << endl;

        // test operator=
        formula = formula2;
        unit_assert_equal(formula.monoisotopicMass(), formula2.monoisotopicMass(), EPSILON);
        if (os_) *os_ << "formula: " << formula << endl;
        if (os_) *os_ << "formula2: " << formula2 << endl;

        // test operator==
        unit_assert(formula == testFormula.formula); // implicit construction from string
        unit_assert(formula == formula2);
        formula2[Element::C] += 4; // test difference in CHONSP
        unit_assert(formula != formula2);
        formula2[Element::C] -= 4;
        unit_assert(formula == formula2);
        formula2[Element::U] += 2; // test difference outside CHONSP
        unit_assert(formula != formula2);
        formula2[Element::U] -= 2;
        unit_assert(formula == formula2);

        // test data()
        Formula::Map data = formula.data();
        if (os_)
        {
            *os_ << "map: "; 
            for (Formula::Map::iterator it=data.begin(), end=data.end(); it!=end; ++it)
                *os_ << it->first << it->second << " ";
            *os_ << "\n";
        }
    }
}

void testFormulaOperations

(

)

Definition at line 131 of file ChemistryTest.cpp.

References C, H, N, O, os_, S, and unit_assert.

Referenced by testThreadSafetyWorker().

{
    using namespace Element;

    Formula water("H2O1");
    Formula a("C1 H2 N3 O4 S5");

    a *= 2;
    unit_assert(a[C]==2 && a[H]==4 && a[N]==6 && a[O]==8 && a[S]==10);
    a += water;
    unit_assert(a[H]==6 && a[O]==9);
    a -= water;
    unit_assert(a[C]==2 && a[H]==4 && a[N]==6 && a[O]==8 && a[S]==10);
    a += 2*water;
    unit_assert(a[H]==8 && a[O]==10);
    a = (a - water*2);
    unit_assert(a[C]==2 && a[H]==4 && a[N]==6 && a[O]==8 && a[S]==10);
    a = water + water;
    unit_assert(a[H]==4 && a[O]==2);
    if (os_) *os_ << "water: " << a-water << endl;
}

void testInfo

(

)

Definition at line 154 of file ChemistryTest.cpp.

References C, Ca, e(), H, os_, pwiz::proteome::AminoAcid::Info::record(), pwiz::proteome::AminoAcid::Info::Record::symbol, U, unit_assert, and unit_assert_throws_what.

Referenced by runSpecialTest(), and testThreadSafetyWorker().

{
    if (os_)
    {
        for (Element::Type e=Element::H; e<=Element::Ca; e=(Element::Type)(e+1))
            *os_ << Element::Info::record(e).symbol << " " << Element::Info::record(e).atomicNumber << endl;
        *os_ << endl;
    }

    unit_assert(Element::Info::record(Element::C).atomicNumber == 6);
    unit_assert(Element::Info::record("C").atomicNumber == 6);
    unit_assert(Element::Info::record(Element::U).atomicNumber == 92);
    unit_assert(Element::Info::record("U").atomicNumber == 92);
    unit_assert(Element::Info::record(Element::Uuh).atomicNumber == 116);
    unit_assert(Element::Info::record("Uuh").atomicNumber == 116);

    unit_assert_throws_what(Element::Info::record("foo"),
                            runtime_error,
                            "[chemistry::text2enum()] Error translating symbol foo");
}

void infoExample

(

)

Definition at line 176 of file ChemistryTest.cpp.

References os_, pwiz::proteome::AminoAcid::Info::record(), and S.

Referenced by testThreadSafetyWorker().

{
    if (os_)
    {
        *os_ << "Sulfur isotopes: " << Element::Info::record(Element::S).isotopes.size() << endl
             << Element::Info::record(Element::S).isotopes;
    }
}

void testPolysiloxane

(

)

Definition at line 186 of file ChemistryTest.cpp.

References pwiz::chemistry::Formula::molecularWeight(), pwiz::chemistry::Formula::monoisotopicMass(), pwiz::chemistry::Ion::mz(), and os_.

Referenced by testThreadSafetyWorker().

{
    Formula formula("Si6C12H36O6");

    if (os_) 
    {
        *os_ << "polysiloxane:\n"
             << formula << " " 
             << formula.monoisotopicMass() << " " 
             << formula.molecularWeight() << endl
             << "ion: " << Ion::mz(formula.monoisotopicMass(), 1) << endl;
    }
}

void testThreadSafetyWorker

(

boost::barrier *

testBarrier

)

Definition at line 201 of file ChemistryTest.cpp.

References e(), infoExample(), testFormula(), testFormulaOperations(), testInfo(), testMassAbundance(), and testPolysiloxane().

{
    testBarrier->wait(); // wait until all threads have started

    try
    {
        testMassAbundance();
        testFormula();
        testFormulaOperations();
        testInfo();
        infoExample();
        testPolysiloxane();
    }
    catch (exception& e)
    {
        cerr << "Exception in worker thread: " << e.what() << endl;
    }
    catch (...)
    {
        cerr << "Unhandled exception in worker thread." << endl;
    }
}

void testThreadSafety

(

const int &

testThreadCount

)

Definition at line 224 of file ChemistryTest.cpp.

References testThreadSafetyWorker().

{
    boost::barrier testBarrier(testThreadCount);
    boost::thread_group testThreadGroup;
    for (int i=0; i < testThreadCount; ++i)
        testThreadGroup.add_thread(new boost::thread(&testThreadSafetyWorker, &testBarrier));
    testThreadGroup.join_all();
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 234 of file ChemistryTest.cpp.

References e(), os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, and testThreadSafety().

{
    TEST_PROLOG(argc, argv)

    if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
    if (os_) *os_ << "ChemistryTest\n" << setprecision(12);

    try
    {
        //testThreadSafety(1); // does not test thread-safety of singleton initialization
        testThreadSafety(2);
        testThreadSafety(4);
        testThreadSafety(8);
        testThreadSafety(16);
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 38 of file ChemistryTest.cpp.

const TestFormula testFormulaData[]

Initial value:

{
    { "C1H2N3O4S5", 1, 2, 3, 4, 5, 279.864884, 280.36928 },
    { "C1H 2N3O4 S5", 1, 2, 3, 4, 5, 279.864884, 280.36928 },
    { "H-42", 0, -42, 0, 0, 0, -42.328651, -42.333512 },
    { "N2C-1", -1, 0, 2, 0, 0, 28.006148-12, 28.013486-12.0107 },
    { "C39H67N11O10", 39, 67, 11, 10, 0, 849.507238, 850.01698 },
    { "C3H7N1O2Se1", 3, 7, 1, 2, 0, 168.9642, 168.0532 }
}

Definition at line 59 of file ChemistryTest.cpp.

Referenced by testFormula().

const int testFormulaDataSize = sizeof(testFormulaData)/sizeof(TestFormula)

Definition at line 69 of file ChemistryTest.cpp.

Referenced by testFormula().