test_seqvector_ci.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: test_seqvector_ci.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:47:23  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: test_seqvector_ci.cpp,v 1000.2 2004/06/01 19:47:23 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author:  Aleksey Grichenko
*
* File Description:
*   Test for CSeqVector_CI
*
* ===========================================================================
*/

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbi_limits.hpp>
#include <util/random_gen.hpp>

// Objects includes
#include <objects/seqloc/Seq_id.hpp>

// Object manager includes
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_vector_ci.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>

#include <objmgr/bioseq_handle.hpp>

BEGIN_NCBI_SCOPE
using namespace objects;


class CTestApp : public CNcbiApplication
{
public:
    virtual void Init(void);
    virtual int  Run (void);

private:
    void x_TestIterate(CSeqVector_CI& vit,
                       TSeqPos start,
                       TSeqPos stop);
    void x_TestGetData(CSeqVector_CI& vit,
                       TSeqPos start,
                       TSeqPos stop);
    void x_TestVector(TSeqPos start,
                      TSeqPos stop);
    bool x_CheckBuf(const string& buf, size_t pos, size_t len) const;

    CRef<CObjectManager> m_OM;
    CSeqVector m_Vect;
    string m_RefBuf;
};


void CTestApp::Init(void)
{
    // Prepare command line descriptions
    //

    // Create
    auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);

    // GI to fetch
    arg_desc->AddDefaultKey("gi", "SeqEntryID",
                            "GI id of the Seq-Entry to fetch",
                            CArgDescriptions::eInteger,
                            "29791621");
    arg_desc->AddDefaultKey("cycles", "RandomCycles",
                            "repeat random test 'cycles' times",
                            CArgDescriptions::eInteger, "100");
    arg_desc->AddDefaultKey("seed", "RandomSeed",
                            "Force random seed",
                            CArgDescriptions::eInteger, "0");
    arg_desc->AddFlag("no_scope", "Use seq vector with null scope");

    // Program description
    string prog_description = "Test for CSeqVector_CI\n";
    arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
                              prog_description, false);

    // Pass argument descriptions to the application
    //

    SetupArgDescriptions(arg_desc.release());
}


bool CTestApp::x_CheckBuf(const string& buf, size_t pos, size_t len) const
{
    if ( pos > m_RefBuf.size() || pos + len > m_RefBuf.size() ||
         buf.size() != len ) {
        return false;
    }
    return memcmp(buf.data(), m_RefBuf.data()+pos, len) == 0;
}


void CTestApp::x_TestIterate(CSeqVector_CI& vit,
                             TSeqPos start,
                             TSeqPos stop)
{
    if (stop > m_Vect.size()) {
        stop = m_Vect.size();
    }
    if (start != kInvalidSeqPos) {
        if (start > m_Vect.size())
            start = m_Vect.size();
        vit.SetPos(start);
    }
    else {
        start = vit.GetPos();
    }

    // cout << "Testing iterator, " << start << " - " << stop << "... ";

    if (start > stop) {
        // Moving down
        const char* data = m_RefBuf.data();
        for ( TSeqPos pos = start; pos > stop;  ) {
            --vit; --pos;
            if ( vit.GetPos() != pos ) {
                cout << endl << "ERROR: GetPos failed at position " << pos << endl;
                throw runtime_error("Test failed");
            }
            if (*vit != data[pos]) {
                cout << endl << "ERROR: Test failed at position " << pos << endl;
                throw runtime_error("Test failed");
            }
        }
    }
    else {
        // Moving up
        const char* data = m_RefBuf.data();
        for ( TSeqPos pos = start; pos < stop; ++vit, ++pos ) {
            if ( vit.GetPos() != pos ) {
                cout << endl << "ERROR: GetPos failed at position " << pos << endl;
                throw runtime_error("Test failed");
            }
            if (*vit != data[pos]) {
                cout << endl << "ERROR: Test failed at position " << pos << endl;
                throw runtime_error("Test failed");
            }
        }
    }

    // cout << "OK" << endl;
}


void CTestApp::x_TestGetData(CSeqVector_CI& vit,
                             TSeqPos start,
                             TSeqPos stop)
{
    if (start == kInvalidSeqPos) {
        start = vit.GetPos();
    }

    if (start > stop)
        swap(start, stop);

    // cout << "Testing GetSeqData(" << start << ", " << stop << ")... " << endl;

    string buf;
    vit.GetSeqData(start, stop, buf);
    if (start >= stop  &&  buf.size() > 0) {
        cout << endl << "ERROR: Test failed -- invalid data length" << endl;
        throw runtime_error("Test failed");
    }

    if (stop > m_Vect.size())
        stop = m_Vect.size();

    if ( !x_CheckBuf(buf, start, stop - start) ) {
        cout << endl << "ERROR: Test failed -- invalid data" << endl;
        throw runtime_error("Test failed");
    }
    // cout << "OK" << endl;
}


void CTestApp::x_TestVector(TSeqPos start,
                            TSeqPos stop)
{
    if (start > m_Vect.size()) {
        start = m_Vect.size();
    }
    if (stop > m_Vect.size()) {
        stop = m_Vect.size();
    }
    // cout << "Testing vector[], " << start << " - " << stop << "... ";

    if (start > stop) {
        // Moving down
        const char* data = m_RefBuf.data();
        for (TSeqPos i = start; i > stop; ) {
            --i;
            if (m_Vect[i] != data[i]) {
                cout << endl << "ERROR: Test failed at position " << i << endl;
                throw runtime_error("Test failed");
            }
        }
    }
    else {
        // Moving up
        const char* data = m_RefBuf.data();
        for (TSeqPos i = start; i < stop; ++i) {
            if (m_Vect[i] != data[i]) {
                cout << endl << "ERROR: Test failed at position " << i << endl;
                throw runtime_error("Test failed");
            }
        }
    }

    // cout << "OK" << endl;
}


int CTestApp::Run(void)
{
    // Process command line args: get GI to load
    const CArgs& args = GetArgs();

    // GI with many segments of different sizes.
    int gi = args["gi"].AsInteger(); // 29791621;

    m_OM.Reset(new CObjectManager);
    m_OM->RegisterDataLoader(*new CGBDataLoader("ID", 0, 2),
                             CObjectManager::eDefault);

    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;