40 #ifndef _NEXUSIOSEQUENCE_H_ 41 #define _NEXUSIOSEQUENCE_H_ 44 #include "../Sequence.h" 45 #include "../Container/SequenceContainer.h" 46 #include "../Container/VectorSequenceContainer.h" 47 #include "../Container/AlignedSequenceContainer.h" 149 #endif //_NEXUSIOSEQUENCE_H_ The SiteContainer interface.
const std::string getFormatName() const
This alphabet is used to deal NumericAlphabet.
Partial implementation of the IAlignment interface, dedicated to alignment readers.
virtual SequenceContainer * readSequences(const std::string &path, const Alphabet *alpha) const
Create a new container from a file.
const std::string getFormatDescription() const
virtual ~NexusIOSequence()
NexusIOSequence(unsigned int charsByLine=100, bool checkSequenceNames=true)
Build a new Phylip file reader.
The Nexus format reader for sequences.
void checkNames(bool yn)
Tell whether the sequence names should be checked when reading from files.
unsigned int charsByLine_
The maximum number of chars to be written on a line.
void appendAlignmentFromStream(std::istream &input, SiteContainer &sc) const
Append sequences to a container from a stream.
const std::vector< std::string > splitNameAndSequence_(const std::string &s) const
The SequenceContainer interface.
virtual void readAlignment(std::istream &input, SiteContainer &sc) const
Add sequences to a container from a stream.
virtual SequenceContainer * readSequences(std::istream &input, const Alphabet *alpha) const
Create a new container from a stream.