test_seqvector_ci.cpp

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    CScope scope(*m_OM);
    scope.AddDefaults();

    CSeq_id id;
    id.SetGi(gi);
    CBioseq_Handle handle = scope.GetBioseqHandle(id);

    // Check if the handle is valid
    if ( !handle ) {
        cout << "Can not find gi " << gi << endl;
        return 0;
    }

    // Create seq-vector
    m_Vect = handle.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
    // Prepare reference data
    m_Vect.GetSeqData(0, m_Vect.size(), m_RefBuf);

    CSeqVector_CI vit = CSeqVector_CI(m_Vect);

    string buf;

    // start > stop test
    cout << "Testing empty range (start > stop)... ";
    vit.GetSeqData(m_Vect.size(), 0, buf);
    if (buf.size() != 0) {
        cout << endl << "ERROR: Test failed -- got non-empty data" << endl;
        throw runtime_error("Empty range test failed");
    }
    cout << "OK" << endl;

    // stop > length test
    cout << "Testing past-end read (stop > size)... ";
    vit.GetSeqData(
        max<TSeqPos>(m_Vect.size(), 100) - 100, m_Vect.size() + 1, buf);
    if ( !x_CheckBuf(buf, max<TSeqPos>(m_Vect.size(), 100) - 100, 100) ) {
        cout << "ERROR: GetSeqData() failed -- invalid data" << endl;
        throw runtime_error("Past-end read test failed");
    }
    cout << "OK" << endl;

    buf = ""; // .erase();

    // Compare iterator with GetSeqData()
    // Not using x_TestIterate() to also check operator bool()
    cout << "Testing basic iterator... ";
    const char* data = m_RefBuf.data();
    const char* c = data;
    const char* data_end = data + m_RefBuf.size();
    for (vit.SetPos(0); vit; ++vit, ++c) {
        if (c == data_end ||  *vit != *c) {
            cout << "ERROR: Invalid data at " << vit.GetPos() << endl;
            throw runtime_error("Basic iterator test failed");
        }
    }
    if (c != data_end) {
        cout << "ERROR: Invalid data length" << endl;
        throw runtime_error("Basic iterator test failed");
    }
    cout << "OK" << endl;

    // Partial retrieval with GetSeqData() test, limit to 2000 bases
    cout << "Testing partial retrieval... ";
    for (unsigned i = max<int>(1, m_Vect.size() / 2 - 2000);
         i <= m_Vect.size() / 2; ++i) {
        x_TestGetData(vit, i, m_Vect.size() - i);
    }
    cout << "OK" << endl;

    // Butterfly test
    cout << "Testing butterfly reading... ";
    for (unsigned i = 1; i < m_Vect.size() / 2; ++i) {
        if (m_Vect[i] != data[i]) {
            cout << "ERROR: Butterfly test failed at position " << i << endl;
            throw runtime_error("Butterfly read test failed");
        }
    }
    cout << "OK" << endl;

    TSeqPos pos1 = 0;
    TSeqPos pos2 = 0;
    TSeqPos pos3 = 0;
    TSeqPos pos4 = 0;

    {{
        const CSeqMap& smap = handle.GetSeqMap();
        CSeqMap_CI map_it = smap.begin_resolved(&scope);
        if ( map_it ) {
            // Should happen for any non-empty sequence
            pos2 = map_it.GetEndPosition();
            ++map_it;
            if ( map_it ) {
                // Should happen for most segmented sequences
                pos3 = map_it.GetEndPosition();
                ++map_it;
                if ( map_it ) {
                    // May happen for some segmented sequences
                    pos4 = map_it.GetEndPosition();
                }
            }
        }
    }}

    // ========= Iterator tests ==========
    cout << "Testing iterator - single segment... ";
    // Single segment test, start from the middle of the first segment
    vit = CSeqVector_CI(m_Vect, (pos1 + pos2) / 2);
    // Back to the first segment start
    x_TestIterate(vit, kInvalidSeqPos, pos1);
    // Forward to the first segment end
    x_TestIterate(vit, kInvalidSeqPos, pos2);
    // Back to the first segment start again
    x_TestIterate(vit, kInvalidSeqPos, pos1);
    cout << "OK" << endl;

    // Try to run multi-segment tests
    if ( pos3 ) {
        cout << "Testing iterator - multiple segments... ";
        // Start from the middle of the second segment
        vit = CSeqVector_CI(m_Vect, (pos2 + pos3) / 2);
        // Back to the first segment start
        x_TestIterate(vit, kInvalidSeqPos, pos1);
        // Forward to the second or third segment end
        x_TestIterate(vit, kInvalidSeqPos, pos4 ? pos4 : pos3);
        // Back to the first segment start again
        x_TestIterate(vit, kInvalidSeqPos, pos1);
        cout << "OK" << endl;
    }

    // ========= GetSeqData() tests ==========
    cout << "Testing GetSeqData() - single segment... ";
    // Single segment test, start from the middle of the first segment
    vit = CSeqVector_CI(m_Vect, (pos1 + pos2) / 2);
    // Back to the first segment start
    x_TestGetData(vit, kInvalidSeqPos, pos1);
    // Forward to the first segment end
    x_TestGetData(vit, kInvalidSeqPos, pos2);
    // Back to the first segment start again
    x_TestGetData(vit, kInvalidSeqPos, pos1);
    cout << "OK" << endl;

    // Try to run multi-segment tests
    if ( pos3 ) {
        cout << "Testing GetSeqData() - multiple segments... ";
        // Start from the middle of the second segment
        vit = CSeqVector_CI(m_Vect, (pos2 + pos3) / 2);
        // Back to the first segment start
        x_TestGetData(vit, kInvalidSeqPos, pos1);
        // Forward to the second or third segment end
        x_TestGetData(vit, kInvalidSeqPos, pos4 ? pos4 : pos3);
        // Back to the first segment start again
        x_TestGetData(vit, kInvalidSeqPos, pos1);
        cout << "OK" << endl;
    }

    // ========= CSeqVector[] tests ==========
    cout << "Testing operator[] - single segment... ";
    // Single segment test, start from the middle of the first segment
    // Back to the first segment start
    x_TestVector((pos1 + pos2) / 2, pos1);
    // Forward to the first segment end
    x_TestVector(pos1, pos2);
    // Back to the first segment start again
    x_TestVector(pos2, pos1);
    cout << "OK" << endl;

    // Try to run multi-segment tests
    if ( pos3 ) {
        cout << "Testing operator[] - multiple segments... ";
        // Start from the middle of the second segment
        // Back to the first segment start
        x_TestVector((pos2 + pos3) / 2, pos1);
        // Forward to the second or third segment end
        x_TestVector(pos1, pos4 ? pos4 : pos3);
        // Back to the first segment start again
        x_TestVector(pos4 ? pos4 : pos3, pos1);
        cout << "OK" << endl;
    }

    // Random access tests
    cout << "Testing random access" << endl;
    unsigned int rseed = args["seed"].AsInteger();
    int cycles = args["cycles"].AsInteger();
    if (rseed == 0) {
        rseed = (unsigned)time( NULL );
    }
    cout << "Testing random reading (seed: " << rseed
         << ", cycles: " << cycles << ")... " << endl;
    CRandom random(rseed);
    vit = CSeqVector_CI(m_Vect);
    for (int i = 0; i < cycles; ++i) {
        TSeqPos start = random.GetRand(0, m_Vect.size());
        TSeqPos stop = random.GetRand(0, m_Vect.size());
        switch (i % 3) {
        case 0:
            x_TestIterate(vit, start, stop);
            break;
        case 1:
            x_TestGetData(vit, start, stop);
            break;
        case 2:
            x_TestVector(start, stop);
            break;
        }
    }
    cout << "OK" << endl;

    NcbiCout << "All tests passed" << NcbiEndl;
    return 0;
}


END_NCBI_SCOPE



/////////////////////////////////////////////////////////////////////////////
//  MAIN


USING_NCBI_SCOPE;

int main(int argc, const char* argv[])
{
    return CTestApp().AppMain(argc, argv);
}

/*
* ---------------------------------------------------------------------------
* $Log: test_seqvector_ci.cpp,v $
* Revision 1000.1  2004/06/01 19:42:39  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
*
* Revision 1.2  2004/05/21 21:42:52  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.1  2003/12/16 17:51:23  kuznets
* Code reorganization
*
* Revision 1.6  2003/11/12 20:16:15  vasilche
* Fixed error: Attempt to delete Object Manager with open scopes.
*
* Revision 1.5  2003/08/29 13:34:48  vasilche
* Rewrote CSeqVector/CSeqVector_CI code to allow better inlining.
* CSeqVector::operator[] made significantly faster.
* Added possibility to have platform dependent byte unpacking functions.
*
* Revision 1.4  2003/08/06 20:51:54  grichenk
* Use CRandom class
*
* Revision 1.3  2003/07/09 18:49:33  grichenk
* Added arguments (seed and cycles), default random cycles set to 20.
*
* Revision 1.2  2003/06/26 17:02:52  grichenk
* Simplified output, decreased number of cycles.
*
* Revision 1.1  2003/06/24 19:50:02  grichenk
* Added test for CSeqVector_CI
*
*
* ===========================================================================
*/