ProteoWizard
Functions | Variables
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

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());
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.")
}
}

Variable Documentation

ostream* os_ = 0

Definition at line 35 of file IPIFASTADatabaseTest.cpp.