bpp-seq  2.2.0
bpp::Clustal Member List

This is the complete list of members for bpp::Clustal, including all inherited members.

AbstractIAlignment()bpp::AbstractIAlignmentinline
AbstractOAlignment()bpp::AbstractOAlignmentinline
appendAlignmentFromFile(const std::string &path, SiteContainer &sc) constbpp::AbstractIAlignmentinlineprotectedvirtual
appendAlignmentFromStream(std::istream &input, SiteContainer &sc) constbpp::Clustalvirtual
charsByLine_bpp::Clustalprivate
checkNames() constbpp::Clustalinline
checkNames(bool yn)bpp::Clustalinline
checkNames_bpp::Clustalprivate
Clustal(bool checkSequenceNames=true, unsigned int nbExtraSpacesBeforeSeq=5, unsigned int charsByLine=100)bpp::Clustalinline
getDataType() constbpp::IOSequenceinline
getFormatDescription() constbpp::Clustalinline
getFormatName() constbpp::Clustalinline
IAlignment()bpp::IAlignmentinline
IOSequence()bpp::IOSequenceinline
ISequence()bpp::ISequenceinline
nbSpacesBeforeSeq_bpp::Clustalprivate
OAlignment()bpp::OAlignmentinline
readAlignment(std::istream &input, SiteContainer &sc) constbpp::AbstractIAlignmentinlinevirtual
readAlignment(const std::string &path, SiteContainer &sc) constbpp::AbstractIAlignmentinlinevirtual
readAlignment(const std::string &path, const Alphabet *alpha) constbpp::AbstractIAlignmentinlinevirtual
readAlignment(std::istream &input, const Alphabet *alpha) constbpp::AbstractIAlignmentinlinevirtual
readAlignmentFromFile(const std::string &path, const Alphabet *alpha) constbpp::AbstractIAlignmentinlineprotectedvirtual
readAlignmentFromStream(std::istream &input, const Alphabet *alpha) constbpp::AbstractIAlignmentinlineprotectedvirtual
readSequences(std::istream &input, const Alphabet *alpha) constbpp::Clustalinlinevirtual
readSequences(const std::string &path, const Alphabet *alpha) constbpp::Clustalinlinevirtual
writeAlignment(std::ostream &output, const SiteContainer &sc) constbpp::Clustalvirtual
writeAlignment(const std::string &path, const SiteContainer &sc, bool overwrite=true) constbpp::Clustalinlinevirtual
~AbstractIAlignment()bpp::AbstractIAlignmentinlinevirtual
~AbstractOAlignment()bpp::AbstractOAlignmentinlinevirtual
~Clustal()bpp::Clustalinlinevirtual
~IAlignment()bpp::IAlignmentinlinevirtual
~IOSequence()bpp::IOSequenceinlinevirtual
~ISequence()bpp::ISequenceinlinevirtual
~OAlignment()bpp::OAlignmentinlinevirtual