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);
};
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);
}
CPSSMAligner::CPSSMAligner(const double** freq1, size_t len1,
const double** freq2, size_t len2,
const SNCBIPackedScoreMatrix *scoremat,
const int scale)
: CNWAligner(),
m_Pssm1(0), m_Freq1(freq1),
m_Seq2(0), m_Freq2(freq2),
m_FreqScale(scale),
m_StartWg(GetDefaultWg()),
m_StartWs(GetDefaultWs()),
m_EndWg(GetDefaultWg()),
m_EndWs(GetDefaultWs())
{
SetScoreMatrix(scoremat);
SetSequences(freq1, len1, freq2, len2, scale);
}
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);
}