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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2006 Louis Warschaw Prostate Cancer Center
// Cedars Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#include "IPIFASTADatabase.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include <boost/filesystem/operations.hpp>
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>
using namespace pwiz::util;
using namespace pwiz::proteome;
ostream* os_ = 0;
void writeTestEntries(ostream& os)
{
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()
{
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()
{
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[])
{
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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