Serializer_FASTA_Test.cpp File Reference

#include "Serializer_FASTA.hpp"
#include "Diff.hpp"
#include "examples.hpp"
#include "pwiz/data/common/BinaryIndexStream.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "boost/thread/thread.hpp"
#include "boost/thread/barrier.hpp"

Go to the source code of this file.

Functions
void	testWriteRead (const Serializer_FASTA::Config &config)
void	testWriteRead ()
void	testThreadSafetyWorker (pair< boost::barrier *, ProteomeData * > *args)
void	testThreadSafety (const int &testThreadCount)
void	testDuplicateId ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void testWriteRead

(

const Serializer_FASTA::Config &

config

)

Definition at line 41 of file Serializer_FASTA_Test.cpp.

References diff(), pwiz::identdata::examples::initializeTiny(), os_, pwiz::proteome::Serializer_FASTA::read(), unit_assert, and pwiz::proteome::Serializer_FASTA::write().

{
    ProteomeData pd;
    examples::initializeTiny(pd);

    Serializer_FASTA serializer(config);

    ostringstream oss;
    serializer.write(oss, pd, NULL);

    if (os_) *os_ << "oss:\n" << oss.str() << endl; 

    shared_ptr<istringstream> iss(new istringstream(oss.str()));
    ProteomeData pd2;
    serializer.read(iss, pd2);

    Diff<ProteomeData, DiffConfig> diff(pd, pd2);
    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteRead

(

)

Definition at line 63 of file Serializer_FASTA_Test.cpp.

References pwiz::proteome::Serializer_FASTA::Config::indexPtr, os_, and testWriteRead().

{
    if (os_) *os_ << "testWriteRead() MemoryIndex" << endl;
    Serializer_FASTA::Config config;
    testWriteRead(config);

    if (os_) *os_ << "testWriteRead() BinaryIndexStream" << endl;
    shared_ptr<stringstream> indexStringStream(new stringstream);
    config.indexPtr.reset(new BinaryIndexStream(indexStringStream));
    testWriteRead(config);
}

void testThreadSafetyWorker

(

pair< boost::barrier *, ProteomeData * > *

args

)

Definition at line 76 of file Serializer_FASTA_Test.cpp.

References e(), testWriteRead(), and unit_assert.

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

    try
    {
        testWriteRead();

        for (int i=0; i < 3; ++i)
        {
            for (size_t j=0; j < args->second->proteinListPtr->size(); ++j)
                unit_assert(args->second->proteinListPtr->protein(j)->index == j);   
        }
    }
    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 100 of file Serializer_FASTA_Test.cpp.

References pwiz::identdata::examples::initializeTiny(), and testThreadSafetyWorker().

{
    ProteomeData pd;
    examples::initializeTiny(pd);

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

void testDuplicateId

(

)

Definition at line 112 of file Serializer_FASTA_Test.cpp.

References pwiz::proteome::ProteomeData::id, os_, pwiz::proteome::ProteomeData::proteinListPtr, pwiz::proteome::Serializer_FASTA::read(), unit_assert_throws_what, and pwiz::proteome::Serializer_FASTA::write().

Referenced by main().

{
    ProteomeData pd;
    pd.id = "tiny";

    shared_ptr<ProteinListSimple> proteinListPtr(new ProteinListSimple);
    pd.proteinListPtr = proteinListPtr;

    proteinListPtr->proteins.push_back(ProteinPtr(new Protein("ABC123", 0, "One two three.", "ELVISLIVES")));
    proteinListPtr->proteins.push_back(ProteinPtr(new Protein("ZEBRA", 1, "Has stripes:", "BLACKANDWHITE")));
    proteinListPtr->proteins.push_back(ProteinPtr(new Protein("DEFCON42", 2, "", "DNTPANIC")));
    proteinListPtr->proteins.push_back(ProteinPtr(new Protein("ZEBRA", 1, "Black and white", "STRIPES")));

    Serializer_FASTA serializer;

    ostringstream oss;
    serializer.write(oss, pd, NULL);

    if (os_) *os_ << "oss:\n" << oss.str() << endl; 

    shared_ptr<istringstream> iss(new istringstream(oss.str()));
    ProteomeData pd2;

    unit_assert_throws_what(serializer.read(iss, pd2), runtime_error,
                            "[ProteinList_FASTA::createIndex] duplicate protein id \"ZEBRA\"");
}

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

Definition at line 140 of file Serializer_FASTA_Test.cpp.

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

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        testWriteRead();
        testThreadSafety(2);
        testThreadSafety(4);
        testThreadSafety(8);
        testDuplicateId();
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

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Variable Documentation

ostream* os_ = 0

Definition at line 38 of file Serializer_FASTA_Test.cpp.