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

§ writeTestEntries()

void writeTestEntries ( ostream &  os)

Definition at line 38 of file IPIFASTADatabaseTest.cpp.

Referenced by test().

39 {
40  os << ">IPI:IPI00000001.2|SWISS-PROT:O95793-1|..." << endl;
41  os << "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS" << endl;
42  os << "ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF" << endl;
43  os << "PVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN" << endl;
44  os << "LNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN" << endl;
45  os << "AAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE" << endl;
46  os << "KEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ" << endl;
47  os << "PTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM" << endl;
48  os << "VPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH" << endl;
49  os << "VPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES" << endl;
50  os << "CHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC" << endl;
51  os << ">IPI:IPI00000005.1|SWISS-PROT:P01111|..." << endl;
52  os << "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG" << endl;
53  os << "QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL" << endl;
54  os << "PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG" << endl;
55  os << "CMGLPCVVM" << endl;
56 }

§ test()

void test ( )

Definition at line 59 of file IPIFASTADatabaseTest.cpp.

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

Referenced by main().

60 {
61  string filename = "IPIFASTADatabaseTest.test.txt";
62  ofstream os(filename.c_str());
63  writeTestEntries(os);
64  os.close();
65 
66  IPIFASTADatabase db(filename);
67  unit_assert(db.records().size() == 2);
68 
69  IPIFASTADatabase::const_iterator it = db.records().begin();
70  unit_assert(it->id == 1);
71  unit_assert(it->faID == "IPI:IPI00000001.2");
72  unit_assert(it->sequence.size() == 577);
73  unit_assert(it->sequence.find("PVPPLL") == 120);
74  if (os_) *os_ << *it << endl;
75 
76  ++it;
77  unit_assert(it->id == 5);
78  unit_assert(it->faID == "IPI:IPI00000005.1");
79  unit_assert(it->sequence.size() == 189);
80  unit_assert(it->sequence.find("PTRTVD") == 120);
81  if (os_) *os_ << *it << endl;
82 
83  boost::filesystem::remove(filename);
84 }
std::vector< Record >::const_iterator const_iterator
typedef to simplify declaration of Record iterator
void writeTestEntries(ostream &os)
ostream * os_
class for accessing data in ipi.*.fasta files
#define unit_assert(x)
Definition: unit.hpp:85

§ testRealDatabase()

void testRealDatabase ( )

Definition at line 87 of file IPIFASTADatabaseTest.cpp.

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

88 {
89  IPIFASTADatabase db("ipi.HUMAN.fasta");
90  cout << "record count: " << db.records().size() << endl;
91 
92  if (!db.records().empty())
93  {
94  const IPIFASTADatabase::Record* record = &db.records().back();
95  cout << *record << endl;
96  }
97 }
PWIZ_API_DECL const Record & record(Type type)
returns the amino acid&#39;s Record by type
class for accessing data in ipi.*.fasta files
structure for holding peptide info

§ main()

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

Definition at line 100 of file IPIFASTADatabaseTest.cpp.

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

101 {
102  TEST_PROLOG(argc, argv)
103 
104  try
105  {
106  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
107  if (os_) *os_ << "IPIFASTADatabaseTest\n";
108  test();
109  //testRealDatabase();
110  }
111  catch (exception& e)
112  {
113  TEST_FAILED(e.what())
114  }
115  catch (...)
116  {
117  TEST_FAILED("Caught unknown exception.")
118  }
119 
121 }
#define TEST_EPILOG
Definition: unit.hpp:182
void test()
ostream * os_
#define TEST_FAILED(x)
Definition: unit.hpp:176
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:174

Variable Documentation

§ os_

ostream* os_ = 0

Definition at line 35 of file IPIFASTADatabaseTest.cpp.

Referenced by main(), and test().