44 #include "../Sequence.h" 45 #include "../SequenceWithQuality.h" 97 )
const throw (Exception);
115 std::vector<int>& pos
116 )
const throw (Exception);
123 const std::string
getDataType()
const {
return "SequenceWithQuality"; };
126 return "Sequences following the phd format as describe in the phred documentation.";
140 bool parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos)
const;
152 bool parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos)
const;
156 #endif // _PHREDPHD_H_ PhredPhd()
Build a new PhredPhd object.
This alphabet is used to deal NumericAlphabet.
The phd sequence file format from phred software.
bool nextSequence(std::istream &input, Sequence &seq) const
Read sequence from stream.
const std::string getFormatDescription() const
const std::string getDataType() const
bool parseFile_(std::istream &input, std::string &name, std::string &sequence, std::vector< int > &qual, std::vector< int > &pos) const
Global file parser.
The ISequenceStream interface.
bool parseDNA_(std::istream &input, std::string &sequence, std::vector< int > &qual, std::vector< int > &pos) const
Parse the DNA part of the file.
const std::string getFormatName() const