IPIFASTADatabaseTest.cpp File Reference

#include "IPIFASTADatabase.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include <boost/filesystem/operations.hpp>
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Functions
void	writeTestEntries (ostream &os)
void	test ()
void	testRealDatabase ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

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Function Documentation

void writeTestEntries

(

ostream &

os

)

Definition at line 38 of file IPIFASTADatabaseTest.cpp.

Referenced by test().

{
    os << ">IPI:IPI00000001.2|SWISS-PROT:O95793-1|..." << endl;
    os << "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS" << endl;
    os << "ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF" << endl;
    os << "PVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN" << endl;
    os << "LNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN" << endl;
    os << "AAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE" << endl;
    os << "KEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ" << endl;
    os << "PTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM" << endl;
    os << "VPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH" << endl;
    os << "VPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES" << endl;
    os << "CHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC" << endl;
    os << ">IPI:IPI00000005.1|SWISS-PROT:P01111|..." << endl;
    os << "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG" << endl;
    os << "QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL" << endl;
    os << "PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG" << endl;
    os << "CMGLPCVVM" << endl;
}

void test

(

)

Definition at line 59 of file IPIFASTADatabaseTest.cpp.

References os_, pwiz::proteome::IPIFASTADatabase::records(), unit_assert, and writeTestEntries().

{
    string filename = "IPIFASTADatabaseTest.test.txt";
    ofstream os(filename.c_str());
    writeTestEntries(os);
    os.close();

    IPIFASTADatabase db(filename);
    unit_assert(db.records().size() == 2);

    IPIFASTADatabase::const_iterator it = db.records().begin();
    unit_assert(it->id == 1);
    unit_assert(it->faID == "IPI:IPI00000001.2");
    unit_assert(it->sequence.size() == 577);
    unit_assert(it->sequence.find("PVPPLL") == 120);
    if (os_) *os_ << *it << endl;

    ++it;
    unit_assert(it->id == 5);
    unit_assert(it->faID == "IPI:IPI00000005.1");
    unit_assert(it->sequence.size() == 189);
    unit_assert(it->sequence.find("PTRTVD") == 120);
    if (os_) *os_ << *it << endl;

    boost::filesystem::remove(filename);
}

void testRealDatabase

(

)

Definition at line 87 of file IPIFASTADatabaseTest.cpp.

References pwiz::proteome::AminoAcid::Info::record(), and pwiz::proteome::IPIFASTADatabase::records().

{
    IPIFASTADatabase db("ipi.HUMAN.fasta");
    cout << "record count: " << db.records().size() << endl;
   
    if (!db.records().empty())
    {
        const IPIFASTADatabase::Record* record = &db.records().back();
        cout << *record << endl;
    }
}

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

Definition at line 100 of file IPIFASTADatabaseTest.cpp.

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

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        if (os_) *os_ << "IPIFASTADatabaseTest\n";
        test();
        //testRealDatabase();
    }
    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 35 of file IPIFASTADatabaseTest.cpp.