40 #ifndef _ABSTRACTIALIGNMENT_H_ 41 #define _ABSTRACTIALIGNMENT_H_ 43 #include "../Container/AlignedSequenceContainer.h" 44 #include "../Alphabet/Alphabet.h" 99 #if defined(NO_VIRTUAL_COV) 110 #if defined(NO_VIRTUAL_COV) 145 std::ifstream input(path.c_str(), std::ios::in);
184 #endif // _ABSTRACTIALIGNMENT_H_ virtual void readAlignment(const std::string &path, SiteContainer &sc) const
Add sequences to a container from a file.
virtual AlignedSequenceContainer * readAlignment(const std::string &path, const Alphabet *alpha) const
Create a new container from a file.
The SiteContainer interface.
Aligned sequences container.
This alphabet is used to deal NumericAlphabet.
Partial implementation of the IAlignment interface, dedicated to alignment readers.
virtual void appendAlignmentFromStream(std::istream &input, SiteContainer &sc) const =0
Append sequences to a container from a stream.
virtual AlignedSequenceContainer * readAlignmentFromStream(std::istream &input, const Alphabet *alpha) const
Read sequences from a stream.
virtual AlignedSequenceContainer * readAlignment(std::istream &input, const Alphabet *alpha) const
Create a new container from a stream.
The IAlignment interface.
virtual ~AbstractIAlignment()
virtual void appendAlignmentFromFile(const std::string &path, SiteContainer &sc) const
Append sequences to a container from a file.
virtual void readAlignment(std::istream &input, SiteContainer &sc) const
Add sequences to a container from a stream.
virtual AlignedSequenceContainer * readAlignmentFromFile(const std::string &path, const Alphabet *alpha) const
Read sequences from a file.