test_seqport.cpp

ncbi源码

        CRef<CSeq_data> in_seq1(new CSeq_data);
        CRef<CSeq_data> in_seq2(new CSeq_data);
        CSeqportUtil::GetCopy(in_seq, in_seq1, uBeginIdx, uLength);
        CSeqportUtil::GetCopy(in_seq, in_seq2, 0, 0);
        TSeqPos uLen = CSeqportUtil::Append(out_seq,
                                      *in_seq1.GetPointer(),
                                      uBeginIdx, uLength,
                                      *in_seq2.GetPointer(), 
                                      uBeginIdx2, uLength2);
    
        cout << endl << "Append Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx1, uLength1) = (" << uBeginIdx
             << ", " << uLength << ")" << endl;
        cout << "(uBeginIdx2, uLength2) = (" << uBeginIdx2
             << ", " << uLength2 << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the Append out_seq
        cout << "Append output sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::InPlaceReverseComplementTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        CSeqportUtil::GetCopy(in_seq, out_seq, 0, 0);
        TSeqPos uLen
            = CSeqportUtil::ReverseComplement(out_seq, uBeginIdx, uLength);
        cout << endl << "In-place reverse complement results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx
             << ", " << uLength << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the In-place reverse-complement sequence
        cout << "In-place reverse-complement sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::InCopyReverseComplementTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        TSeqPos uLen = CSeqportUtil::ReverseComplement
            (in_seq, out_seq, uBeginIdx, uLength);
    
        cout << endl << "Reverse-complement Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx
             << ", " << uLength << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the reverse-complement sequence
        cout << "Reverse-complement sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::InPlaceReverseTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        CSeqportUtil::GetCopy(in_seq, out_seq, 0, 0);
        TSeqPos uLen = 
            CSeqportUtil::Reverse(out_seq, uBeginIdx, uLength);
    
        cout << endl << "In-place Reverse Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx
             << ", " << uLength << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the In-place reverse sequence
        cout << "In-place reverse sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::InCopyReverseTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        TSeqPos uLen = CSeqportUtil::Reverse
            (in_seq, out_seq, uBeginIdx, uLength);
    
        cout << endl << "Reverse Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the reverse sequence
        cout << "Reverse sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::InPlaceComplementTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        CSeqportUtil::GetCopy(in_seq, out_seq, 0, 0);
        TSeqPos uLen = CSeqportUtil::Complement
            (out_seq, uBeginIdx, uLength);
    
        cout << endl << "In-place Complement Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the In-place complement sequence
        cout << "In-place complement sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");
}
 
void CSeqportTestApp::InCopyComplementTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        TSeqPos uLen = CSeqportUtil::Complement
            (in_seq, out_seq, uBeginIdx, uLength);
    
        cout << endl << "Complement Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the complement sequence
        cout << "Complement sequence is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        //Reset out_seq to free memory
        out_seq->Reset();
    }
    STD_CATCH("");      
}

void CSeqportTestApp::FastValidateTest(const CSeq_data&     in_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        bool isValid;
    
        isValid = 
            CSeqportUtil::FastValidate(in_seq, uBeginIdx, uLength);
    
        cout << endl << "Fast Validation Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx
             << ", " << uLength << ")" <<
            endl;
        if(isValid)
            cout << "in_seq is VALID" << endl;
        else
            cout << "in_seq is NOT VALID" << endl;
    }
    STD_CATCH("");    
}

void CSeqportTestApp::ValidateTest(const CSeq_data&     in_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{
        vector<TSeqPos> badIdx;
        
        CSeqportUtil::Validate(in_seq, &badIdx, uBeginIdx, uLength);
    
    
        cout << endl << "Validation Results" << endl;
        cout << "uSeqLen = " << uSeqLen << endl;
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        if(badIdx.size() <= 50 && badIdx.size() > 0)
            {
                cout << "Bad indices are:" << endl;
                vector<TSeqPos>::iterator itor;
                for(itor = badIdx.begin(); itor != badIdx.end(); ++itor)
                    cout << *itor << " ";
                cout << endl;
            }
        else
            {
                cout << "The number of bad indices are: " << badIdx.size()
                     << endl;
            }
        badIdx.clear();
    }
    STD_CATCH("");
}

void CSeqportTestApp::GetCopyTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{
    TSeqPos uSeqLen=0;

    try{      
        TSeqPos uLen = CSeqportUtil::GetCopy
            (in_seq, out_seq, uBeginIdx, uLength);
  
        cout << endl << "Copy Results" << endl;
        cout << "uSeqLen = " << uSeqLen  << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the out sequence
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        cout << "out_seq is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::KeepTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{

    try{
        CSeqportUtil::GetCopy(in_seq, out_seq, 0, 0);
  
        TSeqPos uLen
            = CSeqportUtil::Keep(out_seq, uBeginIdx, uLength);
  
        cout << endl << "Keep Results" << endl;
        cout << "uLength = " << uLength  << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the out sequence
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        cout << "out_seq is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::PackTest(const CSeq_data&     in_seq,
              CSeq_data*           out_seq,
              TSeqPos              uBeginIdx,
              TSeqPos              uLength)
{

    try{
        CSeqportUtil::GetCopy(in_seq, out_seq, 0, 0);
  
        TSeqPos uLen = CSeqportUtil::Pack(out_seq, uLength);
  
        cout << endl << "Pack Results" << endl;
        cout << "uLength = " << uLength  << endl;
        cout << "Return length = " << uLen << endl;
  
        //Print the out sequence
        cout << "(uBeginIdx, uLength) = (" << uBeginIdx <<
            ", " << uLength << ")" << endl;
        switch(out_seq->Which()){
        case CSeq_data::e_Iupacna:
            cout << "out_seq is Iupacna" << endl;
            break;
        case CSeq_data::e_Ncbi4na:
            cout << "out_seq is Ncbi4na" << endl;
            break;
        case CSeq_data::e_Ncbi2na:
            cout << "out_seq is Ncbi2na" << endl;
            break;
        case CSeq_data::e_Ncbieaa:
            cout << "out_seq is Ncbieaa" << endl;
            break;
        case CSeq_data::e_Ncbistdaa:
            cout << "out_seq is Ncbistdaa" << endl;
            break;
        case CSeq_data::e_Iupacaa:
            cout << "out_seq is Iupacaa" << endl;
            break;
        default:
            cout << "out_seq type is not supported." << endl;
            break;
        }
        cout << "out_seq is: " << endl;
        DisplaySeq(*out_seq, MAX_DISPLAY);
        
        out_seq->Reset();
    }
    STD_CATCH("");
}

void CSeqportTestApp::Exit() {
    return;
}


void CSeqportTestApp::DisplaySeq(const CSeq_data& seq, TSeqPos uSize)
{
    //Print the sequence
    switch (seq.Which()) {
    case CSeq_data::e_Ncbi2na:
        {
            const vector<char>& v = seq.GetNcbi2na().Get();
            if (v.size() <= 12) {
                ITERATE (vector<char>, i, v) {
                    cout << std::hex << (unsigned short)(unsigned char) *i
                         << " " << endl;
                }
            }
            cout << "seq size = " << v.size() << endl;
            break;
        }
    case CSeq_data::e_Ncbi4na:
        {
            const vector<char>& v = seq.GetNcbi4na().Get();
            if (v.size() <= 24) {
                ITERATE (vector<char>, i, v) {
                    cout << std::hex << (unsigned short)(unsigned char) *i
                         << " " << endl;
                }
            }
            cout << "seq size = " << v.size() << endl;
            break;
        }
    case CSeq_data::e_Iupacna:
        if(seq.GetIupacna().Get().size() <= uSize)
            cout << seq.GetIupacna().Get() << endl;
        cout << "seq size = " << seq.GetIupacna().Get().size() << endl;
        break;
    case CSeq_data::e_Ncbieaa:
        if(seq.GetNcbieaa().Get().size() <= uSize)
            cout << seq.GetNcbieaa().Get() << endl;;
        cout << "seq size = " << seq.GetNcbieaa().Get().size() << endl;
        break;
    case CSeq_data::e_Ncbistdaa:
        {
            const vector<char>& v = seq.GetNcbistdaa().Get();
            if (v.size() <= uSize) {
                ITERATE (vector<char>, i, v) {
                    cout << std::hex << (unsigned short)(unsigned char) *i
                         << " " << endl;
                }
            }
            cout << "seq size = " << v.size() << endl;
            break;
        }
    case CSeq_data::e_Iupacaa:
        if(seq.GetIupacaa().Get().size() <= uSize)
            cout << seq.GetIupacaa().Get() << endl;
        cout << "seq size = " << seq.GetIupacaa().Get().size() << endl;
        break;
    default: 
        cout << "Display of requested sequence type not supported" << endl;
    }

}


int main(int argc, const char* argv[])
{
    CSeqportTestApp theApp;
    return theApp.AppMain(argc, argv, 0, eDS_Default, 0, "seqport_test");
}

 /*
 * ---------------------------------------------------------------------------
 * $Log: test_seqport.cpp,v $
 * Revision 1000.3  2004/06/01 19:33:33  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.13
 *
 * Revision 1.13  2004/05/19 17:25:27  gorelenk
 * Added include of PCH - ncbi_pch.hpp
 *
 * Revision 1.12  2004/01/30 17:21:24  shomrat
 * Removed TranslateTest due to deprecated translation code
 *
 * Revision 1.11  2003/11/06 16:13:59  shomrat
 * changed call to Pack due to change in its signature
 *
 * Revision 1.10  2003/04/15 19:48:06  vasilche
 * Fixed uninitialized variable.
 *
 * Revision 1.9  2003/03/11 15:53:25  kuznets
 * iterate -> ITERATE
 *
 * Revision 1.8  2002/07/01 16:15:08  clausen
 * Fixed defined but not used warnings
 *
 * Revision 1.7  2002/05/14 17:42:32  ucko
 * Fix type of from_to.
 *
 * Revision 1.6  2002/05/14 15:17:15  clausen
 * Reorganized code and added tests for new CSeqportUtil methods
 *
 * Revision 1.5  2002/05/03 21:28:15  ucko
 * Introduce T(Signed)SeqPos.
 *
 * Revision 1.4  2002/01/10 20:34:15  clausen
 * Added tests for GetIupacaa3, GetCode, and GetIndex
 *
 * Revision 1.3  2001/12/07 18:52:05  grichenk
 * Updated "#include"-s and forward declarations to work with the
 * new datatool version.
 *
 * Revision 1.2  2001/11/13 12:14:29  clausen
 * Changed call to CGencode::Translate to reflect new type for code breaks
 *
 * Revision 1.1  2001/08/24 00:44:05  vakatov
 * Initial revision
 *
 * ===========================================================================
 */