45 #include "../Container/SiteContainer.h" 75 Clustal(
bool checkSequenceNames =
true,
unsigned int nbExtraSpacesBeforeSeq = 5,
unsigned int charsByLine = 100) throw (Exception) :
145 #endif // _CLUSTAL_H_ unsigned int nbSpacesBeforeSeq_
virtual SequenceContainer * readSequences(std::istream &input, const Alphabet *alpha) const
Create a new container from a stream.
The SiteContainer interface.
void checkNames(bool yn)
Tell whether the sequence names should be checked when reading from files.
This alphabet is used to deal NumericAlphabet.
Partial implementation of the IAlignment interface, dedicated to alignment readers.
const std::string getFormatName() const
Clustal(bool checkSequenceNames=true, unsigned int nbExtraSpacesBeforeSeq=5, unsigned int charsByLine=100)
Build a new Clustal object.
The clustal sequence file format.
void writeAlignment(const std::string &path, const SiteContainer &sc, bool overwrite=true) const
Write a container to a file.
void appendAlignmentFromStream(std::istream &input, SiteContainer &sc) const
Append sequences to a container from a stream.
const std::string getFormatDescription() const
unsigned int charsByLine_
virtual SequenceContainer * readSequences(const std::string &path, const Alphabet *alpha) const
Create a new container from a file.
Partial implementation of the OAlignment interface.
The SequenceContainer interface.
virtual void readAlignment(std::istream &input, SiteContainer &sc) const
Add sequences to a container from a stream.
void writeAlignment(std::ostream &output, const SiteContainer &sc) const
Write a container to a stream.
void writeAlignment(std::ostream &output, const SiteContainer &sc) const =0
Write a container to a stream.