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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.

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}

Referenced by test().

◆ test()

void test ( )

Definition at line 59 of file IPIFASTADatabaseTest.cpp.

60{
61 string filename = "IPIFASTADatabaseTest.test.txt";
62 ofstream os(filename.c_str());
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}
ostream * os_
void writeTestEntries(ostream &os)
class for accessing data in ipi.*.fasta files
std::vector< Record >::const_iterator const_iterator
typedef to simplify declaration of Record iterator
#define unit_assert(x)
Definition unit.hpp:85

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

Referenced by main().

◆ testRealDatabase()

void testRealDatabase ( )

Definition at line 87 of file IPIFASTADatabaseTest.cpp.

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's Record by type
structure for holding peptide info

References pwiz::proteome::IPIFASTADatabase::records().

◆ main()

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

Definition at line 100 of file IPIFASTADatabaseTest.cpp.

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}
void test()
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175

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

Variable Documentation

◆ os_

ostream* os_ = 0

Definition at line 35 of file IPIFASTADatabaseTest.cpp.

Referenced by main(), and test().