// <substitution> ::= S_
// ::= S <seq-id> _
// ::= St, etc.
static bool ParseSubstitution(State *state) {
if (ParseTwoChar(state, "S_")) {
MaybeAppend(state, "?"); // We don't support substitutions.
return true;
}
State copy = *state;
if (ParseChar(state, 'S') && ParseSeqId(state) &&
ParseChar(state, '_')) {
MaybeAppend(state, "?"); // We don't support substitutions.
return true;
}
*state = copy;
// Expand abbreviations like "St" => "std".
if (ParseChar(state, 'S')) {
const AbbrevPair *p;
for (p = kSubstitutionList; p->abbrev != nullptr; ++p) {
if (state->mangled_cur[0] == p->abbrev[1]) {
MaybeAppend(state, "std");
if (p->real_name[0] != '\0') {
MaybeAppend(state, "::");
MaybeAppend(state, p->real_name);
}
state->mangled_cur += 1;
return true;
}
}
}
*state = copy;
return false;
}
int CSnpDb::First( const string& seqId )
{
ParseSeqId( seqId );
m_cursor.reset( new CBDB_FileCursor( *this ) );
m_cursor->SetCondition( CBDB_FileCursor::eGE, CBDB_FileCursor::eLE );
switch( m_seqIdType ) {
case eSeqId_string: m_cursor->From << m_stringId << 0; m_cursor->To << m_stringId; break;
case eSeqId_integer: m_cursor->From << m_intId << 0; m_cursor->To << m_intId; break;
}
if( m_cursor->FetchFirst() != eBDB_Ok ) { m_cursor.reset(0); return -1; }
return m_pos;
}
bool CSnpDbCreator::Insert( const string& id, int pos, double a, double c, double g, double t, EStrand strand )
{
if( strand == eStrand_reverse ) {
swap( a, t );
swap( c, g );
}
double total = a + c + g + t;
if( total == 0 )
throw logic_error( "CSnpDbCreator::Insert(): Have zero probabilities for base in "+id+" at "+NStr::IntToString( pos ) );
ParseSeqId( id );
m_pos = pos;
m_prob[0] = float( a/total );
m_prob[1] = float( c/total );
m_prob[2] = float( g/total );
m_prob[3] = float( t/total );
return CBDB_File::Insert() == eBDB_Ok;
}
