bpp::MaseHeader Class Reference

A class to store information from the header of Mase files. More...

#include <Bpp/Seq/Io/Mase.h>

Collaboration diagram for bpp::MaseHeader:

Public Member Functions
	MaseHeader ()
virtual	~MaseHeader ()
size_t	getNumberOfTrees () const
size_t	getNumberOfSiteSelections () const
size_t	getNumberOfSequenceSelections () const
std::vector< std::string >	getTreeNames () const
std::vector< std::string >	getSiteSelectionNames () const
std::vector< std::string >	getSequenceSelectionNames () const
const std::string &	getTree (const std::string &name) const
const MultiRange< size_t > &	getSiteSelection (const std::string &name) const
const std::vector< size_t > &	getSequenceSelection (const std::string &name) const
void	setTree (const std::string &name, const std::string &tree)
void	setSiteSelection (const std::string &name, const MultiRange< size_t > &ranges)
void	setSequenceSelection (const std::string &name, const std::vector< size_t > &set)

Private Attributes
std::map< std::string, std::string >	trees_
std::map< std::string, MultiRange< size_t > >	siteSelections_
std::map< std::string, std::vector< size_t > >	sequenceSelections_

Detailed Description

A class to store information from the header of Mase files.

Author

Julien Dutheil

Definition at line 25 of file Mase.h.

Constructor & Destructor Documentation

MaseHeader()

bpp::MaseHeader::MaseHeader ( )

inline

Definition at line 33 of file Mase.h.

~MaseHeader()

virtual bpp::MaseHeader::~MaseHeader ( )

inlinevirtual

Definition at line 34 of file Mase.h.

Member Function Documentation

getNumberOfSequenceSelections()

size_t bpp::MaseHeader::getNumberOfSequenceSelections ( ) const

inline

Definition at line 39 of file Mase.h.

References sequenceSelections_.

getNumberOfSiteSelections()

size_t bpp::MaseHeader::getNumberOfSiteSelections ( ) const

inline

Definition at line 38 of file Mase.h.

References siteSelections_.

getNumberOfTrees()

size_t bpp::MaseHeader::getNumberOfTrees ( ) const

inline

Definition at line 37 of file Mase.h.

References trees_.

getSequenceSelection()

const std::vector<size_t>& bpp::MaseHeader::getSequenceSelection ( const std::string &  name ) const

inline

Definition at line 67 of file Mase.h.

References sequenceSelections_.

Referenced by bpp::Mase::writeHeader_().

getSequenceSelectionNames()

std::vector<std::string> bpp::MaseHeader::getSequenceSelectionNames ( ) const

inline

Definition at line 43 of file Mase.h.

References bpp::MapTools::getKeys(), and sequenceSelections_.

Referenced by bpp::Mase::writeHeader_().

getSiteSelection()

const MultiRange<size_t>& bpp::MaseHeader::getSiteSelection ( const std::string &  name ) const

inline

Definition at line 56 of file Mase.h.

References siteSelections_.

Referenced by bpp::Mase::writeHeader_().

getSiteSelectionNames()

std::vector<std::string> bpp::MaseHeader::getSiteSelectionNames ( ) const

inline

Definition at line 42 of file Mase.h.

References bpp::MapTools::getKeys(), and siteSelections_.

Referenced by bpp::Mase::writeHeader_().

getTree()

const std::string& bpp::MaseHeader::getTree ( const std::string &  name ) const

inline

Definition at line 45 of file Mase.h.

References trees_.

Referenced by bpp::Mase::writeHeader_().

getTreeNames()

std::vector<std::string> bpp::MaseHeader::getTreeNames ( ) const

inline

Definition at line 41 of file Mase.h.

References bpp::MapTools::getKeys(), and trees_.

Referenced by bpp::Mase::writeHeader_().

setSequenceSelection()

void bpp::MaseHeader::setSequenceSelection ( const std::string &  name, const std::vector< size_t > &  set  )

inline

Definition at line 87 of file Mase.h.

References sequenceSelections_.

Referenced by bpp::Mase::readHeader_().

setSiteSelection()

void bpp::MaseHeader::setSiteSelection ( const std::string &  name, const MultiRange< size_t > &  ranges  )

inline

Definition at line 83 of file Mase.h.

References siteSelections_.

Referenced by bpp::Mase::readHeader_().

setTree()

void bpp::MaseHeader::setTree ( const std::string &  name, const std::string &  tree  )

inline

Definition at line 79 of file Mase.h.

References trees_.

Referenced by bpp::Mase::readHeader_().

Member Data Documentation

sequenceSelections_

std::map<std::string, std::vector<size_t> > bpp::MaseHeader::sequenceSelections_

mutableprivate

Definition at line 30 of file Mase.h.

Referenced by getNumberOfSequenceSelections(), getSequenceSelection(), getSequenceSelectionNames(), and setSequenceSelection().

siteSelections_

std::map<std::string, MultiRange<size_t> > bpp::MaseHeader::siteSelections_

mutableprivate

Definition at line 29 of file Mase.h.

Referenced by getNumberOfSiteSelections(), getSiteSelection(), getSiteSelectionNames(), and setSiteSelection().

trees_

std::map<std::string, std::string> bpp::MaseHeader::trees_

mutableprivate

Definition at line 28 of file Mase.h.

Referenced by getNumberOfTrees(), getTree(), getTreeNames(), and setTree().

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The documentation for this class was generated from the following file:

• Bpp/Seq/Io/Mase.h