bpp-seq  2.2.0
Public Member Functions | Private Attributes | List of all members
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 throw (Exception)
 
const MultiRange< size_t > & getSiteSelection (const std::string &name) const throw (Exception)
 
const std::vector< size_t > & getSequenceSelection (const std::string &name) const throw (Exception)
 
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 61 of file Mase.h.

Constructor & Destructor Documentation

◆ MaseHeader()

bpp::MaseHeader::MaseHeader ( )
inline

Definition at line 69 of file Mase.h.

◆ ~MaseHeader()

virtual bpp::MaseHeader::~MaseHeader ( )
inlinevirtual

Definition at line 70 of file Mase.h.

Member Function Documentation

◆ getNumberOfSequenceSelections()

size_t bpp::MaseHeader::getNumberOfSequenceSelections ( ) const
inline

Definition at line 75 of file Mase.h.

References sequenceSelections_.

◆ getNumberOfSiteSelections()

size_t bpp::MaseHeader::getNumberOfSiteSelections ( ) const
inline

Definition at line 74 of file Mase.h.

References siteSelections_.

◆ getNumberOfTrees()

size_t bpp::MaseHeader::getNumberOfTrees ( ) const
inline

Definition at line 73 of file Mase.h.

References trees_.

◆ getSequenceSelection()

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

Definition at line 95 of file Mase.h.

References sequenceSelections_.

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

◆ getSequenceSelectionNames()

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

Definition at line 79 of file Mase.h.

References sequenceSelections_.

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

◆ getSiteSelection()

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

Definition at line 88 of file Mase.h.

References siteSelections_.

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

◆ getSiteSelectionNames()

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

Definition at line 78 of file Mase.h.

References siteSelections_.

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

◆ getTree()

const std::string& bpp::MaseHeader::getTree ( const std::string &  name) const
throw (Exception
)
inline

Definition at line 81 of file Mase.h.

References trees_.

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

◆ getTreeNames()

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

Definition at line 77 of file Mase.h.

References 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 109 of file Mase.h.

References sequenceSelections_.

◆ setSiteSelection()

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

Definition at line 106 of file Mase.h.

References siteSelections_.

◆ setTree()

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

Definition at line 103 of file Mase.h.

References trees_.

Member Data Documentation

◆ sequenceSelections_

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

Definition at line 66 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 65 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 64 of file Mase.h.

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

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