// Load next chromosome
ref_loc_t RefSeq::LoadNextSeq(std::ifstream &fin) {
char c;
char ch[1000];
std::string s;
fin>>c;
if (fin.eof()) return 0;
_length = 0;
// get name
fin>>_name;
fin.getline(ch, 1000);
// get seq
while (!fin.eof()) {
fin>>c;
if (fin.eof()) break;
fin.unget();
if (c == '>') break;
fin>>s;
if (_length + s.size() >= param.max_dbseq_size) {
if (s.size() > param.append_dbseq_size) {
param.max_dbseq_size += (s.size() + 10);
} else {
param.max_dbseq_size += param.append_dbseq_size;
}
_seq.resize(param.max_dbseq_size);
}
copy(s.begin(), s.end(), _seq.begin() + _length);
_length += s.size();
}
return _length;
}
void load_ref( std::ifstream &is ) {
size_t num_ref;
is >> num_ref;
m_ref_pvecs.resize( num_ref );
m_ref_aux.resize( num_ref );
for( size_t i = 0; i < m_ref_pvecs.size(); ++i ) {
size_t len;
is >> len;
while( isspace( is.get() ) && !is.eof() ) {}
is.unget();
if( is.eof() ) {
throw std::runtime_error( "unexpected end of file" );
}
m_ref_pvecs[i].resize(len);
is.read( (char*)&m_ref_pvecs[i][0], len * sizeof(int) );
m_ref_aux[i].resize(len);
is.read( (char*)&m_ref_aux[i][0], len * sizeof(unsigned int) );
// std::cout << "ref: " << i << " " << m_ref_pvecs[i].size() << "\n";
}
}
void ConfigLoader::_nextToken(std::ifstream &stream)
{
lastTok = tok;
lastTokVal = tokVal;
//EOF token
if (stream.eof())
{
tok = TOKEN_EOF;
return;
}
//(Get next character)
int ch = stream.get();
if (ch == -1)
{
tok = TOKEN_EOF;
return;
}
while ((ch == ' ' || ch == 9) && !stream.eof())
{ //Skip leading spaces / tabs
ch = stream.get();
}
if (stream.eof())
{
tok = TOKEN_EOF;
return;
}
//Newline token
if (ch == '\r' || ch == '\n')
{
do
{
ch = stream.get();
} while ((ch == '\r' || ch == '\n') && !stream.eof());
stream.unget();
tok = TOKEN_NewLine;
return;
}
//Open brace token
else if (ch == '{')
{
tok = TOKEN_OpenBrace;
return;
}
//Close brace token
else if (ch == '}')
{
tok = TOKEN_CloseBrace;
return;
}
//Text token
if (ch < 32 || ch > 122) //Verify valid char
{
throw std::runtime_error("Parse Error: Invalid character, ConfigLoader::load()");
}
tokVal = "";
tok = TOKEN_Text;
do
{
//Skip comments
if (ch == '/')
{
int ch2 = stream.peek();
//C++ style comment (//)
if (ch2 == '/')
{
stream.get();
do
{
ch = stream.get();
} while (ch != '\r' && ch != '\n' && !stream.eof());
tok = TOKEN_NewLine;
return;
}
}
//Add valid char to tokVal
tokVal += (char)ch;
//Next char
ch = stream.get();
} while (ch > 32 && ch <= 122 && !stream.eof());
stream.unget();
return;
}