void addStringToContents(CharVector& contents, const std::string& str)
{
std::size_t bytesWritten = 0;
for (std::size_t i = 0; i < str.length(); ++i)
{
contents.push_back(str[i]);
++bytesWritten;
}
contents.push_back('\0');
++bytesWritten;
if (bytesWritten % 2 == 1)
{
contents.push_back('\0');
++bytesWritten;
}
}
void init_fasta_enzyme_function ( const string& enzyme )
{
static bool called = false;
if ( called ) return;
called = true;
static DigestTable& digestTable = DigestTable::instance ();
if ( enzyme == "No enzyme" ) {
ErrorHandler::genError ()->error ( "No enzyme not valid option for this program." );
return;
}
StringVector enzymeNameTable;
cnbr_digest = false;
StringSizeType start = 0;
StringSizeType end = 0;
for ( ; ; ) {
end = enzyme.find_first_of ( "/", start );
string enzymeName = enzyme.substr ( start, end-start );
if ( enzymeName == "CNBr" ) cnbr_digest = true;
enzymeNameTable.push_back ( enzymeName );
if ( end == string::npos ) break;
start = end + 1;
}
numDigests = enzymeNameTable.size ();
for ( int i = 0 ; i < numDigests ; i++ ) {
string br_aas = digestTable.getBreakMask (enzymeNameTable[i]);
break_aas_array.push_back ( br_aas );
break_mask_array.push_back ( string_to_mask ( br_aas ) );
string exclude_aas = digestTable.getExcludeMask (enzymeNameTable[i]);
exclude_aas_array.push_back ( exclude_aas );
if ( exclude_aas != "-" ) exclude_mask_array.push_back ( string_to_mask ( exclude_aas ) );
else exclude_mask_array.push_back ( 0 );
digestSpecificityArray.push_back ( digestTable.getSpecificity (enzymeNameTable[i]) );
}
if ( numDigests == 1 ) {
break_mask = break_mask_array [0];
break_aas = break_aas_array [0];
exclude_mask = exclude_mask_array [0];
digestSpecificity = digestSpecificityArray [0];
if ( digestSpecificity == 'C' ) enzyme_fragmenter = calc_fasta_c_term_fragments;
else enzyme_fragmenter = calc_fasta_n_term_fragments;
}
else {
int i;
for ( i = 1 ; i < numDigests ; i++ ) {
if ( digestSpecificityArray [i] != digestSpecificityArray [0] ) break;
}
if ( i == numDigests ) digestSpecificity = digestSpecificityArray [0]; /* All digest specificities must be the same for digestSpecificity to be set */
enzyme_fragmenter = calc_fasta_multi_digest_fragments;
}
}
virtual void put (midibyte b)
{
m_char_vector.push_back(b);
}