C++ (Cpp) GetDefaultWm Examples

Example #1

File: nw_aligner.cpp Project: svn2github/ncbi_tk

CNWAligner::CNWAligner(const string& seq1,
                       const string& seq2,
                       const SNCBIPackedScoreMatrix* scoremat)
    : m_Wm(GetDefaultWm()),
      m_Wms(GetDefaultWms()),
      m_Wg(GetDefaultWg()),
      m_Ws(GetDefaultWs()),
      m_esf_L1(false), m_esf_R1(false), m_esf_L2(false), m_esf_R2(false),
      m_SmithWaterman(false),
      m_GapPreference(eLater),
      m_abc(g_nwaligner_nucleotides),
      m_ScoreMatrixInvalid(true),
      m_prg_callback(0),
      m_terminate(false),
      m_Seq1Vec(seq1.begin(), seq1.end()),
      m_Seq1(&m_Seq1Vec[0]), m_SeqLen1(seq1.size()),
      m_Seq2Vec(seq2.begin(), seq2.end()),
      m_Seq2(&m_Seq2Vec[0]), m_SeqLen2(seq2.size()),
      m_score(kInfMinus),
      m_mt(false),
      m_maxthreads(1),
      m_MaxMem(GetDefaultSpaceLimit())
{
    SetScoreMatrix(scoremat);
    SetSequences(seq1, seq2);
};

Example #2

File: nw_aligner.cpp Project: svn2github/ncbi_tk

CNWAligner::CNWAligner( const char* seq1, size_t len1,
                        const char* seq2, size_t len2,
                        const SNCBIPackedScoreMatrix* scoremat )

    : m_Wm(GetDefaultWm()),
      m_Wms(GetDefaultWms()),
      m_Wg(GetDefaultWg()),
      m_Ws(GetDefaultWs()),
      m_esf_L1(false), m_esf_R1(false), m_esf_L2(false), m_esf_R2(false),
      m_SmithWaterman(false),
      m_GapPreference(eLater),
      m_abc(g_nwaligner_nucleotides),
      m_ScoreMatrixInvalid(true),
      m_prg_callback(0),
      m_terminate(false),
      m_Seq1Vec(&seq1[0], &seq1[0]+len1),
      m_Seq1(&m_Seq1Vec[0]), m_SeqLen1(len1),
      m_Seq2Vec(&seq2[0], &seq2[0]+len2),
      m_Seq2(&m_Seq2Vec[0]), m_SeqLen2(len2),
      m_PositivesAsMatches(false),
      m_score(kInfMinus),
      m_mt(false),
      m_maxthreads(1),
      m_MaxMem(GetDefaultSpaceLimit())
{
    SetScoreMatrix(scoremat);
    SetSequences(seq1, len1, seq2, len2);
}

Example #3

File: nw_aligner.cpp Project: jackgopack4/pico-blast

CNWAligner::CNWAligner()
    : m_Wm(GetDefaultWm()),
      m_Wms(GetDefaultWms()),
      m_Wg(GetDefaultWg()),
      m_Ws(GetDefaultWs()),
      m_esf_L1(false), m_esf_R1(false), m_esf_L2(false), m_esf_R2(false),
      m_abc(g_nwaligner_nucleotides),
      m_ScoreMatrixInvalid(true),
      m_prg_callback(0),
      m_terminate(false),
      m_Seq1(0), m_SeqLen1(0),
      m_Seq2(0), m_SeqLen2(0),
      m_PositivesAsMatches(false),
      m_score(kInfMinus),
      m_mt(false),
      m_maxthreads(1),
      m_MaxMem(GetDefaultSpaceLimit())
{
    SetScoreMatrix(0);
}