void
CCmdLineBlastXML2ReportData::x_FillScoreMatrix(const char *matrix_name)
{
if (matrix_name == NULL)
return;
int matrix[kMatrixCols][kMatrixCols];
int * tmp[kMatrixCols];
const SNCBIPackedScoreMatrix *packed_matrix = 0;
if (strcmp(matrix_name, "BLOSUM45") == 0)
packed_matrix = &NCBISM_Blosum45;
else if (strcmp(matrix_name, "BLOSUM50") == 0)
packed_matrix = &NCBISM_Blosum50;
else if (strcmp(matrix_name, "BLOSUM62") == 0)
packed_matrix = &NCBISM_Blosum62;
else if (strcmp(matrix_name, "BLOSUM80") == 0)
packed_matrix = &NCBISM_Blosum80;
else if (strcmp(matrix_name, "BLOSUM90") == 0)
packed_matrix = &NCBISM_Blosum90;
else if (strcmp(matrix_name, "PAM30") == 0)
packed_matrix = &NCBISM_Pam30;
else if (strcmp(matrix_name, "PAM70") == 0)
packed_matrix = &NCBISM_Pam70;
else if (strcmp(matrix_name, "PAM250") == 0)
packed_matrix = &NCBISM_Pam250;
else {
string prog_name = Blast_ProgramNameFromType(
m_Options->GetProgramType());
if (prog_name != "blastn" && prog_name != "megablast") {
NCBI_THROW(blast::CBlastException, eInvalidArgument,
"unsupported score matrix");
}
}
if (packed_matrix) {
SNCBIFullScoreMatrix m;
NCBISM_Unpack(packed_matrix, &m);
for (unsigned int i = 0; i < kMatrixCols; i++) {
tmp[i] = matrix[i];
for (unsigned int j = 0; j < kMatrixCols; j++) {
matrix[i][j] = m.s[i][j];
}
}
}
m_Matrix = (new CBlastFormattingMatrix(tmp, kMatrixCols, kMatrixCols));
}
void ScoreMatrix::initialize(EScoreMatrixType type) {
SNCBIPackedScoreMatrix matrix;
m_type = type;
switch (m_type) {
case eBlosum45:
matrix = NCBISM_Blosum45;
break;
case eBlosum62:
matrix = NCBISM_Blosum62;
break;
case eBlosum80:
matrix = NCBISM_Blosum80;
break;
case ePam30:
matrix = NCBISM_Pam30;
break;
case ePam70:
matrix = NCBISM_Pam70;
break;
case ePam250:
matrix = NCBISM_Pam250;
break;
case eInvalidMatrixType:
default:
m_numLetters = INVALIDSIZE;
m_alphabet = NULL;
return;
break;
}
m_name = GetScoringMatrixName(type);
if (type != eInvalidMatrixType) {
m_alphabet = matrix.symbols;
m_numLetters = strlen(m_alphabet);
NCBISM_Unpack(&matrix, &m_scoreMatrix);
}
}
int CAlnVec::CalculateScore(const string& s1, const string& s2,
bool s1_is_prot, bool s2_is_prot,
int gen_code1, int gen_code2)
{
// check the lengths
if (s1_is_prot == s2_is_prot && s1.length() != s2.length()) {
NCBI_THROW(CAlnException, eInvalidRequest,
"CAlnVec::CalculateScore(): "
"Strings should have equal lenghts.");
} else if (s1.length() * (s1_is_prot ? 1 : 3) !=
s1.length() * (s1_is_prot ? 1 : 3)) {
NCBI_THROW(CAlnException, eInvalidRequest,
"CAlnVec::CalculateScore(): "
"Strings lengths do not match.");
}
int score = 0;
const unsigned char * res1 = (unsigned char *) s1.c_str();
const unsigned char * res2 = (unsigned char *) s2.c_str();
const unsigned char * end1 = res1 + s1.length();
const unsigned char * end2 = res2 + s2.length();
static bool s_FullScoreMatrixInitialized = false;
if (s1_is_prot && s2_is_prot) {
if ( !s_FullScoreMatrixInitialized ) {
s_FullScoreMatrixInitialized = true;
NCBISM_Unpack(&NCBISM_Blosum62, &s_FullScoreMatrix);
}
// use BLOSUM62 matrix
for ( ; res1 != end1; res1++, res2++) {
_ASSERT(*res1 < NCBI_FSM_DIM);
_ASSERT(*res2 < NCBI_FSM_DIM);
score += s_FullScoreMatrix.s[*res1][*res2];
}
} else if ( !s1_is_prot && !s2_is_prot ) {
// use match score/mismatch penalty
for ( ; res1 != end1; res1++, res2++) {
if (*res1 == *res2) {
score += 1;
} else {
score -= 3;
}
}
} else {
string t;
if (s1_is_prot) {
TranslateNAToAA(s2, t, gen_code2);
for ( ; res1 != end1; res1++, res2++) {
_ASSERT(*res1 < NCBI_FSM_DIM);
_ASSERT(*res2 < NCBI_FSM_DIM);
score += s_FullScoreMatrix.s[*res1][*res2];
}
} else {
TranslateNAToAA(s1, t, gen_code1);
for ( ; res2 != end2; res1++, res2++) {
_ASSERT(*res1 < NCBI_FSM_DIM);
_ASSERT(*res2 < NCBI_FSM_DIM);
score += s_FullScoreMatrix.s[*res1][*res2];
}
}
}
return score;
}
